Journal name: Tree genetics & genomes / Publication Year: 2016 / Text Availability: Citation in PubAg

1. ADH and PDC genes involved in tannins coagulation leading to natural de-astringency in Chinese pollination constant and non-astringency persimmon (Diospyros kaki Thunb.)

Author:: Rongli Mo; Sichao Yang; Yanmei Huang; Wenxing Chen; Qinglin Zhang; Zhengrong Luo
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 17
ISSN:: 1614-2942
Subject:: Diospyros kaki; acetaldehyde; astringency; coagulation; cultivars; fruiting; genes; leaves; persimmons; pollination; tannins
Abstract:: ... Pollination constant non-astringency (PCNA)-type persimmons are the most desirable cultivar because the fruit loses astringency naturally and does not require any treatments for edibility. The mechanism of natural astringency loss in Chinese PCNA (C-PCNA)-type persimmon is probably related to the coagulation of soluble tannins into insoluble tannins, which is quite different from that in the Japan ...
DOI:: 10.1007/s11295-016-0976-0
: https://doi.org/10.1007/s11295-016-0976-0

2. Additive and non-additive genetic parameters for multipurpose traits in a clonally replicated incomplete factorial test of Castanea spp.

Author:: B. Míguez-Soto; A. López-Villamor; J. Fernández-López
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 47
ISSN:: 1614-2942
Subject:: Castanea crenata; Castanea sativa; Phytophthora; breeding value; clones; crossing; disease resistance; epistasis; genetic correlation; genetic variance; growth traits; heirloom varieties; heritability; hybrids; multiple trait selection; parents; phenotype; stem form; variance; wood quality
Abstract:: ... Second-year traits of growth, stem form, terminal flushing, and survival were assessed in 1770 ramets from 295 clones of 16 full-sib families of Castanea spp. Additive, dominance, and epistatic genetic variances were estimated in a clonally replicated incomplete 5 × 4 factorial test. Parents of the mating design were selected mainly on their phenotypes for wood quality (Castanea sativa traditional ...
DOI:: 10.1007/s11295-016-1004-0
: https://doi.org/10.1007/s11295-016-1004-0

3. Ancient split of major genetic lineages of European Black Pine: evidence from chloroplast DNA

Author:: Krassimir D. Naydenov; Michel K. Naydenov; Alexander Alexandrov; Kole Vasilevski; Veselka Gyuleva; Vlado Matevski; Biljana Nikolic; Venceslas Goudiaby; Faruk Bogunic; Despina Paitaridou; Andreas Christou; Irina Goia; Christopher Carcaillet; Adrian Escudero Alcantara; Cengiz Ture; Suleyman Gulcu; Lorenzo Peruzzi; Salim Kamary; Srdjan Bojovic; Georgi Hinkov; Anatoly Tsarev
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 68
ISSN:: 1614-2942
Subject:: Pinus nigra; ancestry; chloroplast DNA; electrophoresis; forests; genetic distance; geographical distribution; microsatellite repeats; phylogeography; polymerase chain reaction; population size; refuge habitats; sequence analysis; single nucleotide polymorphism; Mediterranean region; Turkey (country)
Abstract:: ... The European Black Pine (Pinus nigra Arn.) has a long and complex history. Genetic distance and frequency analyses identified three differentiated genetic groups, which corresponded to three wide geographical areas: Westerns Mediterranean, Balkan Peninsula and Asia Minor. These groups shared common ancestors (14.75 and 10.72 Ma). The most recent splits occurred after the Messinian Salinity Crisis ...
DOI:: 10.1007/s11295-016-1022-y
: https://doi.org/10.1007/s11295-016-1022-y

4. Apple NPR1 homologs and their alternative splicing forms may contribute to SA and disease responses

Author:: Junke Zhang; Peng Jiao; Chong Zhang; Xiaolei Tong; Qinping Wei; Lingfei Xu
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 92
ISSN:: 1614-2942
Subject:: Arabidopsis; Diplocarpon mali; Malus baccata; Malus domestica; alternative splicing; amino acid sequences; apples; disease resistance; genes; immune response; leaves; phylogeny; reverse transcriptase polymerase chain reaction; salicylic acid; sequence alignment; signal transduction; systemic acquired resistance; transcription (genetics)
Abstract:: ... The non-expressor of pathogenesis-related genes 1 (NPR1) plays essential roles in the salicylic acid (SA) signal pathway and in systemic acquired resistance (SAR) responses. Although a genome-wide analysis of NPR1 gene family has been conducted in some plant species, little is known about these genes in apple (Malus spp.). In this study, eight NPR1 homologs were identified within the apple genome ...
DOI:: 10.1007/s11295-016-1050-7
: https://doi.org/10.1007/s11295-016-1050-7

5. Association of single nucleotide polymorphisms with form traits in three New Zealand populations of radiata pine in the presence of genotype by environment interactions

Author:: Yongjun Li; Phillip Wilcox; Emily Telfer; Natalie Graham; Lisa Stanbra
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 63
ISSN:: 1614-2942
Subject:: Pinus radiata; breeding; genetic variance; genotype-environment interaction; models; single nucleotide polymorphism; New Zealand
Abstract:: ... Associations of single nucleotide polymorphisms (SNP) with the form traits, branch cluster frequency and stem straightness, were studied in three radiata pine (Pinus radiata D. Don) breeding populations. For branch cluster frequency, high genotype by environment (G×E) interactions were found between two sites of the POP1 trial series (Tarawera and Glenledi) and between two sites of the POP2 trial ...
DOI:: 10.1007/s11295-016-1019-6
: https://doi.org/10.1007/s11295-016-1019-6

6. Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata)

Author:: Paul F. Gugger; Shawn J. Cokus; Victoria L. Sork
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 15
ISSN:: 1614-2942
Subject:: Quercus lobata; climate; demography; gene flow; genes; genetic variation; landscapes; loci; natural selection; ordination techniques; single nucleotide polymorphism; spring; summer; temperature; transcriptome; transcriptomics; variance; California
Abstract:: ... A fundamental goal of evolutionary biology is to understand how environment shapes genetic variation through its effect on demographic processes and through natural selection. In non-model species, transcriptome sequencing generates large single nucleotide polymorphism (SNP) panels to disentangle these influences. Quercus lobata (valley oak) offers an excellent system for such analyses because it ...
DOI:: 10.1007/s11295-016-0975-1
: https://doi.org/10.1007/s11295-016-0975-1

7. Association studies reveal the effect of genetic variation in lncRNA UGTRL and its putative target PtoUGT88A1 on wood formation in Populus tomentosa

Author:: Mingyang Quan; Jiaxing Tian; Xiaohui Yang; Qingzhang Du; Yuepeng Song; Qingshi Wang; Jinhui Chen; Deqiang Zhang
Source:: Tree genetics & genomes 2016 v.12 no.1 pp. 8
ISSN:: 1614-2942
Subject:: Populus tomentosa; cambium; chromosome mapping; epistasis; gene frequency; genes; genetic variation; growth and development; herbaceous plants; messenger RNA; models; non-coding RNA; phenotypic variation; photosynthesis; single nucleotide polymorphism; tree growth; trees; wood; wood properties; xylem
Abstract:: ... Long noncoding RNAs (lncRNAs) play significant roles in the growth and development of herbaceous plants by regulating target genes; however, the significance of lncRNA-messenger RNA (mRNA) interactions needs to be investigated in perennial trees. Here, we combined transcript profiling and multi-single-nucleotide polymorphism (SNP) association mapping to analyze the genetic variation and putative i ...
DOI:: 10.1007/s11295-015-0967-6
: https://doi.org/10.1007/s11295-015-0967-6

8. Auxin- and cytokinin-induced berries set in grapevine partly rely on enhanced gibberellin biosynthesis

Author:: Long Lu; Jinjun Liang; Xiang Zhu; Kun Xiao; Tianzhong Li; Jianfang Hu
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 41
ISSN:: 1614-2942
Subject:: 4-CPA; Vitis labrusca; Vitis vinifera; benzyladenine; biosynthesis; cytokinins; flowering; fruits; gene expression regulation; genes; gibberellins; grapes; indole acetic acid; paclobutrazol; parthenocarpy; plant ovary; small fruits
Abstract:: ... Gibberellins (GAs) have been widely used for many years to induce seedless grapevine and increase fruit set in production. However, the role of GAs and how they crosstalk with auxin and cytokinin during fruit set in grapevine remains unclarified. To investigate their role, GA₃, 4-chlorophenoxyacetic acid (4-CPA), 6-benzylaminopurine (6-BA), and different hormone combinations were applied to unpoll ...
DOI:: 10.1007/s11295-016-0980-4
: https://doi.org/10.1007/s11295-016-0980-4

9. Broad-scale genetic homogeneity in natural populations of common hazel (Corylus avellana) in Ireland

Author:: James A. Brown; Gemma E. Beatty; W. Ian Montgomery; Jim Provan
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 122
ISSN:: 1614-2942
Subject:: Corylus avellana; broadleaved trees; climate change; gene flow; genetic markers; genetic similarity; genetic variation; habitat destruction; invasive species; nuts; pathogens; woodlands; Ireland
Abstract:: ... Hazel (Corylus avellana) has been a key species in European woodlands throughout the Holocene (10 KYA–present). Like many tree species, it is increasingly under threat from climate change, habitat loss and fragmentation, invasive species and emergent pathogens. As knowledge of the genetic structure of natural populations of trees is vital for managing these threats, as well as an essential basis f ...
DOI:: 10.1007/s11295-016-1079-7
: https://doi.org/10.1007/s11295-016-1079-7

10. Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee

Author:: Collins Ogutu; Ting Fang; Lin Yan; Lu Wang; Lifang Huang; Xiaoyang Wang; Baiquan Ma; Xianbao Deng; Albert Owiti; Aggrey Nyende; Yuepeng Han
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 54
ISSN:: 1614-2942
Subject:: Coffea canephora; alleles; beverages; domestication; genetic similarity; genetic variation; germplasm; loci; microsatellite repeats; wild relatives; Kenya
Abstract:: ... Coffee is an important beverage crop in the world and has a significant contribution to Kenya’s economy. Here, we analyzed the genome-wide distribution of microsatellites in the Coffea canephora genome. A total of 159,041 SSRs were identified, with an overall density of 308 SSRs per Mb. Tetra-nucleotide repeats are the most abundant, accounting for 32 % of the total SSRs. AT-rich motifs are domina ...
DOI:: 10.1007/s11295-016-1014-y
: https://doi.org/10.1007/s11295-016-1014-y

11. Characterization of genome-wide simple sequence repeats and application in interspecific genetic map integration in kiwifruit

Author:: Chunyan Liu; Qiong Zhang; Xiaohong Yao; Caihong Zhong; Chunlin Yan; Hongwen Huang
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 21
ISSN:: 1614-2942
Subject:: Actinidia chinensis; chromosome mapping; dioecy; genetic markers; genome; kiwifruit; marker-assisted selection; microsatellite repeats; plant breeding; quantitative trait loci; sex determination
Abstract:: ... Simple sequence repeats (SSRs) have been widely used in the construction of linkage maps, quantitative trait loci (QTLs) mapping, and marker-assisted selection (MAS). The availability of the sequenced Actinidia chinensis (kiwifruit) genome allows for the inexpensive and efficient development of microsatellite markers. In this study, a total of 49,067 SSRs were identified and characterized in the g ...
DOI:: 10.1007/s11295-016-0982-2
: https://doi.org/10.1007/s11295-016-0982-2

12. Climate change risk management in tree improvement programs: selection and movement of genotypes

Author:: Laura K. Gray; Andreas Hamann; Sally John; Deogratias Rweyongeza; Leonard Barnhardt; Barb R. Thomas
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 23
ISSN:: 1614-2942
Subject:: Picea glauca; breeding; case studies; climate; climate change; cold; ecoregions; genotype; government agencies; planting; reforestation; risk; risk management; temperature; trees; Alberta
Abstract:: ... Tree improvement programs usually consist of multiple breeding populations that target different climatic or ecological regions. Parent breeding material normally originates from and is deployed within the same breeding region, assuming optimal local adaptation of populations. Given the climate trends observed over the last several decades in western Canada, this assumption is unlikely to still be ...
DOI:: 10.1007/s11295-016-0983-1
: https://doi.org/10.1007/s11295-016-0983-1

13. Climate-related adaptive genetic variation and population structure in natural stands of Norway spruce in the South-Eastern Alps

Author:: Erica A. Di Pierro; Elena Mosca; Duccio Rocchini; Giorgio Binelli; David B. Neale; Nicola La Porta
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 16
ISSN:: 1614-2942
Subject:: Picea abies; climate change; climatic factors; conifers; forest trees; genes; genetic variation; genotype; genotyping; landscapes; loci; population structure; single nucleotide polymorphism; soil water; temperature; Alps region; Italy
Abstract:: ... Forest trees dominate many Alpine landscapes that are currently exposed to changing climate. Norway spruce is one of the most important conifer species of the Italian Alps, and natural populations are found across steep environmental gradients with large differences in temperature and moisture availability. This study seeks to determine and quantify patterns of genetic diversity in natural populat ...
DOI:: 10.1007/s11295-016-0972-4
: https://doi.org/10.1007/s11295-016-0972-4

14. Comparative analyses of squalene synthase (SQS) proteins in poplar and pine by using bioinformatics tools

Author:: Ertugrul Filiz; Ibrahim Ilker Ozyigit; Recep Vatansever
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 32
ISSN:: 1614-2942
Subject:: phytosterols; Pinus massoniana; proteins; plant stress; biosynthesis; aspartic acid; bioinformatics; phylogeny; isoelectric point; amino acid sequences; Populus trichocarpa; trees; binding sites; genes; Liliopsida; phytoene synthase; stress tolerance
Abstract:: ... Squalene synthase (SQS, EC 2.5.1.21) is a major enzyme in biosynthesis of isoprenoid (farnesyl pyrophosphate (FPP) squalene). In the present study, we have analyzed SQS enzymes of black cottonwood (Populus trichocarpa, hereafter Pt) and Masson’s pine (Pinus massoniana, hereafter Pm) using bioinformatics tools. PtSQS and PmSQS sequences were found to have very similar physicochemical properties wit ...
DOI:: 10.1007/s11295-016-0992-0
: https://doi.org/10.1007/s11295-016-0992-0

15. Complete chloroplast genome sequences of Eucommia ulmoides: genome structure and evolution

Author:: Lin Wang; Ta-na Wuyun; Hongyan Du; Depeng Wang; Deming Cao
Source:: Tree genetics & genomes 2016 v.12 no.1 pp. 12
ISSN:: 1614-2942
Subject:: Aucuba; Eucommia ulmoides; Nicotiana; Sesamum; chloroplast genome; chloroplasts; genes; medicinal plants; microsatellite repeats; phylogeny; ribosomal RNA; sequence analysis; transfer RNA
Abstract:: ... Eucommia ulmoides is an important traditional medicinal plant that is used for the production of locative Eucommia rubber. In this study, the complete chloroplast (cp) genome sequence of E. ulmoides was obtained by total DNA sequencing; this is the first cp genome sequence of the order Garryales. The cp genome of E. ulmoides was 163,341 bp long and included a pair of inverted repeat (IR) regions ( ...
DOI:: 10.1007/s11295-016-0970-6
: https://doi.org/10.1007/s11295-016-0970-6

16. Conservation genetics of rare trees restricted to subtropical montane cloud forests in southern China: a case study from Quercus arbutifolia (Fagaceae)

Author:: Jin Xu; Xiao-Long Jiang; Min Deng; Murphy Westwood; Yi-Gang Song; Si-Si Zheng
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 90
ISSN:: 1614-2942
Subject:: Quercus; case studies; chloroplast DNA; chloroplasts; climate change; drainage systems; genetic variation; habitat destruction; habitat fragmentation; haplotypes; internal transcribed spacers; long term effects; niches; population growth; population size; trees; tropical montane cloud forests; vulnerable species; China; Vietnam
Abstract:: ... Montane cloud forests (MCFs), with their isolated nature, offer excellent opportunities to study the long-term effects of habitat fragmentation and the impacts of climate change. Quercus arbutifolia is a rare oak in MCFs of southern China and Vietnam. Its isolated populations, small population size and unique ecological niche make this species vulnerable to climate change and habitat loss. In this ...
DOI:: 10.1007/s11295-016-1048-1
: https://doi.org/10.1007/s11295-016-1048-1

17. Construction of a high density linkage map and its application in the identification of QTLs for soluble sugar and organic acid components in apple

Author:: Baiquan Ma; Shuang Zhao; Benhong Wu; Dongmei Wang; Qian Peng; Albert Owiti; Ting Fang; Liao Liao; Collins Ogutu; Schuyler S. Korban; Shaohua Li; Yuepeng Han
Source:: Tree genetics & genomes 2016 v.12 no.1 pp. 1
ISSN:: 1614-2942
Subject:: Malus domestica; apples; chromosome mapping; citric acid; fructose; fruit quality; genetic markers; genotyping; glucose; linkage groups; malic acid; marker-assisted selection; microsatellite repeats; quantitative trait loci; sensory properties; single nucleotide polymorphism; sorbitol; sucrose
Abstract:: ... Soluble sugars and organic acids have a strong impact on the overall organoleptic quality of fruits. In this study, we report the identification of quantitative trait loci (QTLs) for individual sugars and organic acids in apple. A high density linkage map of apple was constructed using the 1536 EST-derived SNP GoldenGate genotyping platform. The linkage map consists of 601 molecular markers, inclu ...
DOI:: 10.1007/s11295-015-0959-6
: https://doi.org/10.1007/s11295-015-0959-6

18. Construction of a high-density genetic map of Ziziphus jujuba Mill. using genotyping by sequencing technology

Author:: Zhong Zhang; Tianjun Wei; Ying Zhong; Xingang Li; Jian Huang
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 76
ISSN:: 1614-2942
Subject:: Ziziphus jujuba; breeding; chromosome mapping; chromosome number; cost effectiveness; fruit trees; genome; genome assembly; genomics; genotyping; haploidy; linkage groups; parents; single nucleotide polymorphism; China
Abstract:: ... The Chinese jujube (Ziziphus jujuba Mill., 2n = 2 × = 24), one of the most popular fruit trees in China, is widely cultivated and utilized in Asia. High-density genetic linkage maps are valuable resources for molecular breeding and functional genomics; however, they are still under-developed for the jujube. The genotyping by sequencing (GBS) strategy could be an efficient and cost-effective tool f ...
DOI:: 10.1007/s11295-016-1032-9
: https://doi.org/10.1007/s11295-016-1032-9

19. DNA fingerprinting of oil camellia cultivars with SSR markers

Author:: Yingnan Chen; Xiaogang Dai; Jing Hou; Hongwei Guan; Yuxiao Wang; Yi Li; Tongming Yin
Source:: Tree genetics & genomes 2016 v.12 no.1 pp. 7
ISSN:: 1614-2942
Subject:: Camellia oleifera; DNA fingerprinting; cultivars; databases; genetic markers; microsatellite repeats; mutants; new variety; oils; plantations; seedlings; China
Abstract:: ... Oil camellia (Camellia oleifera Abel.) is a widely cultivated economically important plant. In China, more than 100 elite cultivars have been authorized for commercial plantations, representing the developmental base for the oil camellia industry. Since oil camellia seedlings are frequently traded and introduced to new places, there is an active demand to develop a rapid and reliable identificatio ...
DOI:: 10.1007/s11295-015-0966-7
: https://doi.org/10.1007/s11295-015-0966-7

20. Development of SNP-based assays for disease resistance and fruit quality traits in apple (Malus × domestica Borkh.) and validation in breeding pilot studies

Author:: Isabelle O. Baumgartner; Markus Kellerhals; Fabrizio Costa; Luca Dondini; Giulia Pagliarani; Roberto Gregori; Stefano Tartarini; Lucie Leumann; François Laurens; Andrea Patocchi
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 35
ISSN:: 1614-2942
Subject:: DNA; Dysaphis plantaginea; Malus domestica; Venturia inaequalis; apples; disease resistance; firmness; fruit quality; genes; genetic markers; genomics; genotyping; marker-assisted selection; pest resistance; planting seed; polymerase chain reaction; powdery mildew; seedlings; single nucleotide polymorphism; sowing; storage quality; texture
Abstract:: ... The development of molecular markers linked to specific traits is now routine practice, but the gap between genomics and breeding often delays their application. In the frame of the FP7 European project FruitBreedomics, apple pilot studies were designed to exploit the project’s outcomes towards the practical application of marker-assisted breeding (MAB) programs. The aim of this pilot study was to ...
DOI:: 10.1007/s11295-016-0994-y
: https://doi.org/10.1007/s11295-016-0994-y

21. Development of microsatellite markers and their use in genetic diversity and population structure analysis in Casuarina

Author:: A. R. K. Kullan; A. V. Kulkarni; R. Suresh Kumar; R. Rajkumar
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 49
ISSN:: 1614-2942
Subject:: Casuarina equisetifolia; alleles; breeding; expressed sequence tags; genetic markers; genetic variation; genomics; germplasm; heterozygosity; loci; microsatellite repeats; plantations; population structure; trees; India
Abstract:: ... Casuarina is a widely cultivated plantation tree species in coastal India, primarily due to its fast growth, high productivity and suitable for pulp and paper production. However, genetic studies of Casuarina have been hindered by lack of genomic resources and genetic markers. Knowledge of the genetic diversity and population structure of Casuarina germplasms will provide the basis for utilizing a ...
DOI:: 10.1007/s11295-016-1009-8
: https://doi.org/10.1007/s11295-016-1009-8

22. Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)

Author:: R. Mariotti; N. G. M. Cultrera; S. Mousavi; F. Baglivo; M. Rossi; E. Albertini; F. Alagna; F. Carbone; G. Perrotta; Luciana Baldoni
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 120
ISSN:: 1614-2942
Subject:: Olea europaea; alleles; cultivars; genotyping; microsatellite repeats; olives; prediction; screening; tissues; transcription (genetics); transcriptome; wild plants
Abstract:: ... Rapid and effective genotyping is an important goal to discriminate among the numerous olive cultivars and their wild related forms. The largely used di-nucleotide simple sequence repeat (SSR) markers show a high level of polymorphism and have strongly contributed to solve many inconsistencies in varietal identity, but many problems related to difficult discrimination of neighboring alleles and lo ...
DOI:: 10.1007/s11295-016-1077-9
: https://doi.org/10.1007/s11295-016-1077-9

23. Disentangling the effects of isolation-by-distance and isolation-by-environment on genetic differentiation among Rhododendron lineages in the subgenus Tsutsusi

Author:: Chun-Lin Huang; Jui-Hung Chen; Chung-Te Chang; Jeng-Der Chung; Pei-Chun Liao; Jenn-Che Wang; Shih-Ying Hwang
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 53
ISSN:: 1614-2942
Subject:: Rhododendron simsii; environmental factors; expressed sequence tags; genetic variation; geography; introgression; microsatellite repeats; reproductive isolation; soil pH; temperature; Taiwan
Abstract:: ... Ecological speciation has long been noted as a central topic in the field of evolutionary biology, and investigation into the relative importance of ecological and geographical factors is becoming increasingly emphasized. We surveyed genetic variation of 277 samples from 25 populations of nine Rhododendron species within Tsutsusi subgenus in Taiwan using simple sequence repeats of expressed sequen ...
DOI:: 10.1007/s11295-016-1010-2
: https://doi.org/10.1007/s11295-016-1010-2

24. Dissection of additive, dominant, epistatic roles of allelic variation within heat shock factor genes in Chinese indigenous poplar (Populus simonii)

Author:: Qingzhang Du; Zunzheng Wei; Xing Zhao; Xiaohui Yang; Dong Ci; Deqiang Zhang
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 91
ISSN:: 1614-2942
Subject:: Populus simonii; bioinformatics; drought; epistasis; genes; genetic variation; growth and development; heat shock proteins; heat stress; leaves; linkage disequilibrium; molecular cloning; perennials; plant response; roots; single nucleotide polymorphism; sugars; temperature; transcription factors; tree growth; xylem; China
Abstract:: ... Heat shock transcription factors (Hsfs) play a crucial role in plant growth and development, but the significance of Hsfs is not clearly understood in long-lived perennial plants. Here, two class A Hsf members (PsHsfA1c1 and PsHsfA7a1) were identified in Populus simonii, an important and pioneering species in northern China, using bioinformatics analysis and molecular cloning. Tissue-specific expr ...
DOI:: 10.1007/s11295-016-1049-0
: https://doi.org/10.1007/s11295-016-1049-0

25. Effective gene flow in a historically fragmented area at the southern edge of silver fir (Abies alba Mill.) distribution

Author:: Cristina Leonarduzzi; Andrea Piotti; Ilaria Spanu; Giovanni Giuseppe Vendramin
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 95
ISSN:: 1614-2942
Subject:: Abies alba; adults; chloroplasts; gene flow; genes; genetic markers; genetic variation; germ cells; inbreeding; microsatellite repeats; natural regeneration; parentage
Abstract:: ... Fragmented populations at the edges of a species’ distribution can be highly exposed to the loss of genetic variation, unless sufficient gene flow maintains their genetic connectivity. Gene movements leading to successful establishment of external gametes (i.e. effective gene flow) into fragmented populations can solely be assessed by investigating the origin of natural regeneration. This study is ...
DOI:: 10.1007/s11295-016-1053-4
: https://doi.org/10.1007/s11295-016-1053-4

26. Effects of different silvicultural systems on the genetic diversity of Shorea parvifolia populations in the tropical rainforest of Southeast Asia

Author:: Widiyatno; S. Indrioko; M. Na’iem; K. Uchiyama; S. Numata; M. Ohtani; A. Matsumoto; Y. Tsumura
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 73
ISSN:: 1614-2942
Subject:: Shorea; alleles; cutting; forest decline; forest resources; genetic variation; harvesting; logging; planting; silvicultural systems; tree and stand measurements; trees; tropical rain forests; South East Asia
Abstract:: ... Selective logging systems have been used to prevent the rapid decline of forest resources in Southeast Asia, but little is known about the impacts of selective logging on the genetic diversity of Southeast Asian rainforests. We evaluated the effects of silvicultural systems with differing cutting rotations and enrichment planting regimes on the genetic diversity of Shorea parvifolia, an abundant a ...
DOI:: 10.1007/s11295-016-1030-y
: https://doi.org/10.1007/s11295-016-1030-y

27. Estimation of number and size of QTL effects in forest tree traits

Author:: David Hall; Henrik R. Hallingbäck; Harry X. Wu
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 110
ISSN:: 1614-2942
Subject:: breeding; chromosome mapping; disease resistance; forest trees; genetic variation; growth traits; loci; phenotypic variation; population size; quantitative trait loci
Abstract:: ... Mapping the genetic architecture of forest tree traits is important in order to understand the evolutionary forces that have shaped these traits and to facilitate the development of genomic-based breeding strategies. We examined the number, size, and distribution of allelic effects influencing eight types of traits using 30 published mapping studies (linkage and association mapping) in forest tree ...
DOI:: 10.1007/s11295-016-1073-0
: https://doi.org/10.1007/s11295-016-1073-0

28. Evaluation of genetic homogeneity of in vitro-raised plants of Tecomella undulata (Sm.) Seem. using molecular markers

Author:: Sidhika Chhajer; Rajwant K. Kalia
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 100
ISSN:: 1614-2942
Subject:: DNA; DNA fragmentation; Tecomella undulata; arid zones; endangered species; forest trees; genetic markers; genetic similarity; micropropagation; microsatellite repeats; plantlets; random amplified polymorphic DNA technique; reforestation; seeds; shoots; start codon; vegetative propagation; India
Abstract:: ... Tecomella undulata (Sm.) Seem (family Bignoniaceae) is an economically and pharmaceutically important timber tree of arid regions of India. Overexploitation of natural stands coupled with minimal conservation and reforestation efforts has led to its incorporation in list of endangered species. This monotypic genus can be propagated only through seeds as no methods are available for its vegetative ...
DOI:: 10.1007/s11295-016-1057-0
: https://doi.org/10.1007/s11295-016-1057-0

29. Evaluation of the best linear unbiased prediction method for breeding values of fruit-quality traits in citrus

Author:: A. Imai; T. Kuniga; T. Yoshioka; K. Nonaka; N. Mitani; H. Fukamachi; N. Hiehata; M. Yamamoto; T. Hayashi
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 119
ISSN:: 1614-2942
Subject:: crossing; heritability; fruit trees; texture; phenotype; breeding programs; fruit quality; genotype; natural selection; Citrus; cultivars; firmness; progeny; sugar content; prediction; pedigree; genetic correlation; color; pulp; breeding value; Japan
Abstract:: ... Fruit-quality trait improvement is an important objective in citrus breeding; however, fruit breeding programs often accumulate highly unbalanced phenotypic records, which are a serious obstacle in comparing and selecting genotypes. The best linear unbiased prediction (BLUP) method can be used to overcome these difficulties, but few fruit breeding programs have adopted the method, and to our knowl ...
DOI:: 10.1007/s11295-016-1078-8
: https://doi.org/10.1007/s11295-016-1078-8

30. Evidence for different QTL underlying the immune and hypersensitive responses of Eucalyptus globulus to the rust pathogen Puccinia psidii

Author:: J. B. Butler; J. S. Freeman; R. E. Vaillancourt; B. M. Potts; M. Glen; D. J. Lee; G. S. Pegg
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 39
ISSN:: 1614-2942
Subject:: Eucalyptus globulus; Eucalyptus grandis; Puccinia psidii; disease resistance; flora; genes; genotype; hypersensitive response; linkage groups; loci; open pollination; pathogens; progeny; quantitative trait loci; rust diseases; trees; Australia; South America
Abstract:: ... The rust Puccinia psidii infects many species in the family Myrtaceae. Native to South America, the pathogen has recently entered Australia which has a rich Myrtaceous flora, including trees of the ecologically and economically important genus Eucalyptus. We studied the genetic basis of variation in rust resistance in Eucalyptus globulus, the main plantation eucalypt in Australia. Quantitative tra ...
DOI:: 10.1007/s11295-016-0987-x
: https://doi.org/10.1007/s11295-016-0987-x

31. Evolutionary history of subtropical evergreen broad-leaved forest in Yunnan Plateau and adjacent areas: an insight from Quercus schottkyana (Fagaceae)

Author:: Xiao-Long Jiang; Min Deng; Ying Li
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 104
ISSN:: 1614-2942
Subject:: Quercus; broadleaved evergreen forests; broadleaved evergreens; climate; deciduous forests; ecosystems; genetic variation; geographical distribution; habitats; haplotypes; indigenous species; latitude; models; paleoecology; palynology; phylogeography; plateaus; regression analysis; vascular plants; China
Abstract:: ... Yunnan Plateau and its adjacent areas (YPA) with typical subtropical evergreen broad-leaved forests (SEBF) have a rich number of vascular plants and high endemism. However, how ancient geological and climatic events in YPA have shaped the SEBF remains poorly understood. In this study, we integrated multilocus phylogeography, species distribution models (SDMs), and regression analysis to investigat ...
DOI:: 10.1007/s11295-016-1063-2
: https://doi.org/10.1007/s11295-016-1063-2

32. Fine mapping of the rosy apple aphid resistance locus Dp-fl on linkage group 8 of the apple cultivar ‘Florina’

Author:: G. Pagliarani; E. Dapena; M. Miñarro; C. Denancé; Y. Lespinasse; E. Rat-Morris; M. Troggio; C. E. Durel; S. Tartarini
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 56
ISSN:: 1614-2942
Subject:: Dysaphis plantaginea; apples; chromosome mapping; cultivars; fruit growing; genes; genetic markers; insect pests; linkage groups; loci; marker-assisted selection; microsatellite repeats; pest resistance; plant damage; polymerase chain reaction; single nucleotide polymorphism
Abstract:: ... Rosy apple aphid (Dysaphis plantaginea), is one of the major insect pests of apple, causing serious physical and economic damage to fruit production. A dominant resistance gene Dp-fl was previously mapped at the bottom of linkage group LG8 from the cultivar ‘Florina’, linked to the SSR CH01h10. The development of additional genetic markers mapping closer to Dp-fl was needed to position the gene ac ...
DOI:: 10.1007/s11295-016-1015-x
: https://doi.org/10.1007/s11295-016-1015-x

33. Fine-scale spatial genetic structure in the frankincense tree Boswellia papyrifera (Del.) Hochst. and implications for conservation

Author:: A. B. Addisalem; J. Duminil; D. Wouters; F. Bongers; M. J. M. Smulders
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 86
ISSN:: 1614-2942
Subject:: Boswellia; adults; ex situ conservation; genes; genetic correlation; genetic markers; genetic variation; germplasm conservation; heterozygosity; kinship; mating systems; outcrossing; reforestation; seed collecting; seedlings; seeds; species dispersal; trees; tropical forests; Ethiopia
Abstract:: ... The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species’ biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented such as Boswellia papyrifera. This species occurs in ...
DOI:: 10.1007/s11295-016-1039-2
: https://doi.org/10.1007/s11295-016-1039-2

34. Gene expression profiles in different stem internodes reveal the genetic regulation of primary and secondary stem development in Betula platyphylla

Author:: Huiyan Guo; Yucheng Wang; Ping Hu; Yanmin Wang; Ying Jiang; Chuanping Yang; Chao Wang
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 113
ISSN:: 1614-2942
Subject:: Betula pendula subsp. mandshurica; biosynthesis; breeding; cambium; cell walls; cellulose; gene expression regulation; genes; internodes; lignin; phloem; seedlings; somatotropin; stem elongation; trees; xylem
Abstract:: ... Secondary growth of stems is an important process for the radial increase of trees. To gain an insight into the molecular mechanisms underlying stem development from primary to secondary growth and to provide information for molecular research and breeding in Betula platyphylla (birch), the gene expression profiles of material from the first, third, and fifth internodes (IN) of 3-month-old seedlin ...
DOI:: 10.1007/s11295-016-1068-x
: https://doi.org/10.1007/s11295-016-1068-x

35. Gene flow among Hancornia speciosa (Apocynaceae) varieties and hybrid fitness

Author:: Rosane G. Collevatti; Ana Maria Olivatti; Mariana P. C. Telles; Lázaro J. Chaves
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 74
ISSN:: 1614-2942
Subject:: Apocynaceae; adults; cross pollination; gene flow; genetic variation; germplasm; heterosis; hybrids; leaves; microsatellite repeats; outcrossing; parentage; pollen; progeny; seeds; self-pollination; Brazil
Abstract:: ... The fate of hybrids and the temporal and spatial dynamics of hybrid zones depend on hybrid fitness in comparison to non-hybrids. We studied cross-pollination among Hancornia speciosa varieties and compared progeny fitness in a nursery to address whether hybrid fitness differed from non-hybrids and whether maternal and paternal taxa contribute differentially to offspring fitness. This species has e ...
DOI:: 10.1007/s11295-016-1031-x
: https://doi.org/10.1007/s11295-016-1031-x

36. Genetic analyses reveal high levels of seed and pollen flow in hawthorn (Crataegus monogyna Jacq.), a key component of hedgerows

Author:: James A. Brown; Gemma E. Beatty; Caroline M. V. Finlay; W. Ian Montgomery; David G. Tosh; Jim Provan
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 58
ISSN:: 1614-2942
Subject:: Crataegus monogyna; chloroplasts; climate change; emerging diseases; gene flow; genetic markers; genetic variation; invasive species; land use change; landscapes; pollen; pollen flow; trees; woodlands
Abstract:: ... Hedgerows represent important components of agri-environment landscapes that are increasingly coming under threat from climate change, emergent diseases, invasive species and land use change. Given that population genetic data can be used to inform best-practice management strategies for woodland and hedgerow tree species, we carried out a study on hawthorn (Crataegus monogyna Jacq.), a key compon ...
DOI:: 10.1007/s11295-016-1020-0
: https://doi.org/10.1007/s11295-016-1020-0

37. Genetic analysis of fiber dimensions and their correlation with stem diameter and solid-wood properties in Norway spruce

Author:: Zhi-Qiang Chen; Bo Karlsson; Tommy Mörling; Lars Olsson; Ewa J. Mellerowicz; Harry X. Wu; Sven-Olof Lundqvist; María Rosario García Gil
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 123
ISSN:: 1614-2942
Subject:: Picea abies; bark; breeding programs; conifers; early selection; genetic analysis; genetic correlation; growth traits; heritability; modulus of elasticity; open pollination; pith; profitability; progeny; trees; wood density; Sweden
Abstract:: ... Adverse genetic correlations between growth traits and solid-wood, as well as fiber traits are a concern in conifer breeding programs. To evaluate the impact of selection for growth and solid-wood properties on fiber dimensions, we investigated the inheritance and efficiency of early selection for different wood-fiber traits and their correlations with stem diameter, wood density, modulus of elast ...
DOI:: 10.1007/s11295-016-1065-0
: https://doi.org/10.1007/s11295-016-1065-0

38. Genetic analysis of salt tolerance in a progeny derived from the citrus rootstocks Cleopatra mandarin and trifoliate orange

Author:: V. Raga; D. S. Intrigliolo; G. P. Bernet; E. A. Carbonell; M. J. Asins
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 34
ISSN:: 1614-2942
Subject:: Citrus; Poncirus trifoliata; boron; chromosome mapping; defoliation; genotype; heritability; hybrids; iron; leaf area; leaf water potential; leaves; linkage groups; mandarins; potassium; progeny; quantitative trait loci; rootstocks; salinity; salt tolerance; sodium; sodium chloride; vegetative growth; vigor
Abstract:: ... A total of 60 traits that could be related to salt tolerance were genetically analyzed using nucellar plants as repetitions of apomictic hybrids in a reference population derived from two common citrus rootstocks, Cleopatra mandarin (salt tolerant) and trifoliate orange (salt sensitive), in two experiments differing in duration (1 versus 3 years) [NaCl] (30 versus 25 mM) and environmental control ...
DOI:: 10.1007/s11295-016-0991-1
: https://doi.org/10.1007/s11295-016-0991-1

39. Genetic architecture of apple fruit quality traits following storage and implications for genetic improvement

Author:: Craig M. Hardner; Kate Evans; Chris Brien; Fred Bliss; Cameron Peace
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 20
ISSN:: 1614-2942
Subject:: Malus domestica; apples; breeding; color; crop production; cultivars; firmness; fruit quality; genetic correlation; genetic improvement; genetic variation; hardness; juiciness; models; prediction; selection response; storage time; sweetness; titratable acidity; Washington (state)
Abstract:: ... Accurate prediction of genetic potential and response to selection in breeding requires knowledge of genetic parameters for important selection traits. Data from breeding trials can be used to obtain estimates of these parameters so that predictions are directly relevant to the improvement program. Here, a factor allocation diagram was developed to describe the sampling design used to assess the q ...
DOI:: 10.1007/s11295-016-0977-z
: https://doi.org/10.1007/s11295-016-0977-z

40. Genetic determination of tannins and herbivore resistance in Quercus ilex

Author:: Alejandro Solla; Slobodan Milanović; Alejandro Gallardo; Ana Bueno; Tamara Corcobado; Yonatan Cáceres; David Morcuende; Alberto Quesada; Gerardo Moreno; Fernando Pulido
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 117
ISSN:: 1614-2942
Subject:: Lymantria dispar; Quercus ilex; chemical analysis; chemical composition; defoliation; genetic variation; genotype; herbivores; heritability; insect larvae; leaves; open pollination; population dynamics; provenance; seedlings; tannins; tissues; trees; trichomes; weight gain; Spain
Abstract:: ... Genetic variability of trees influences the chemical composition of tissues. This determines herbivore impact and, consequently, herbivore performance. We evaluated the independent effects of plant genotype and provenance on the tannin content of holm oak (Quercus ilex) and their consequences for herbivory and performance of gypsy moth (Lymantria dispar) larvae. Oak seedlings of 48 open-pollinated ...
DOI:: 10.1007/s11295-016-1069-9
: https://doi.org/10.1007/s11295-016-1069-9

41. Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers

Author:: Aziz Ebrahimi; Abdolkarim Zarei; Shaneka Lawson; Keith E. Woeste; M. J. M. Smulders
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 114
ISSN:: 1614-2942
Subject:: Juglans regia; alleles; center of diversity; cluster analysis; computer software; genetic relationships; genetic variation; geography; heterozygosity; loci; microsatellite repeats; walnuts; Algeria; Greece; Hungary; Iran; Middle East; Slovakia; Tunisia; Turkey (country)
Abstract:: ... Persian walnut (Juglans regia L.) is the world’s most widely grown nut crop, but large-scale assessments and comparisons of the genetic diversity of the crop are notably lacking. To guide the conservation and utilization of Persian walnut genetic resources, genotypes (n = 189) from 25 different regions in 14 countries on three continents were sampled to investigate their genetic relationships and ...
DOI:: 10.1007/s11295-016-1075-y
: https://doi.org/10.1007/s11295-016-1075-y

42. Genetic diversity and genetic structure of black alder (Alnus glutinosa [L.] Gaertn) in the Belgium-Luxembourg-France cross-border area

Author:: Dominique Mingeot; Claude Husson; Patrick Mertens; Bernard Watillon; Pierre Bertin; Philippe Druart
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 24
ISSN:: 1614-2942
Subject:: Alnus glutinosa; alleles; chloroplast DNA; ecosystems; genetic markers; genetic variation; germplasm; haplotypes; loci; microsatellite repeats; pathogens; planting; provenance; statistical analysis; trees; watersheds; Belgium; France; Luxembourg
Abstract:: ... Due to its beneficial effects on river ecosystems, black alder (Alnus glutinosa) is one of the tree species selected for planting on riverbanks in the cross-border area encompassing Wallonia in Belgium, Lorraine in France, and Luxembourg. The preservation of this species, however, is threatened by an invasive pathogen that particularly targets and kills young alder individuals. The objectives of t ...
DOI:: 10.1007/s11295-016-0981-3
: https://doi.org/10.1007/s11295-016-0981-3

43. Genetic diversity and population structure of common walnut (Juglans regia) in China based on EST-SSRs and the nuclear gene phenylalanine ammonia-lyase (PAL)

Author:: Huan Han; Keith E. Woeste; Yiheng Hu; Meng Dang; Tian Zhang; Xiao-Xiao Gao; Huijuan Zhou; Xiaojia Feng; Guifang Zhao; Peng Zhao
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 111
ISSN:: 1614-2942
Subject:: Juglans regia; genes; genetic variation; germplasm; haplotypes; hybridization; mountains; phenylalanine ammonia-lyase; population structure; reproductive isolation; trees; walnuts; wood; China
Abstract:: ... Common walnut (Juglans regia L.) is an economically important temperate tree species valued for both its nut and wood. We investigated the genetic diversity and population structure of J. regia germplasm from 13 locations in China using 10 markers derived from expressed sequences (EST-SSR) and sequence polymorphisms within the phenylalanine ammonia-lyase (PAL) gene. Analysis of the population gene ...
DOI:: 10.1007/s11295-016-1064-1
: https://doi.org/10.1007/s11295-016-1064-1

44. Genetic diversity and structure of the globally invasive tree, Paraserianthes lophantha subspecies lophantha, suggest an introduction history characterised by varying propagule pressure

Author:: G. D. Thompson; D. M. Richardson; J. R. U. Wilson; D. U. Bellstedt; J. J. Le Roux
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 27
ISSN:: 1614-2942
Subject:: Acacia; Paraserianthes; genetic variation; genotype; indigenous species; introduced species; invasive species; microsatellite repeats; phylogeny; provenance; selfing; sequence analysis; trees; Maui; New South Wales; Portugal; South Africa; South Australia; Western Australia
Abstract:: ... An emerging insight in invasion biology is that intra-specific genetic variation, human usage, and introduction histories interact to shape genetic diversity and its distribution in populations of invasive species. We explore these aspects for the tree species Paraserianthes lophantha subsp. lophantha, a close relative of Australian wattles (genus Acacia). This species is native to Western Austral ...
DOI:: 10.1007/s11295-016-0984-0
: https://doi.org/10.1007/s11295-016-0984-0

45. Genetic diversity of naturalized cacao (Theobroma cacao L.) in Puerto Rico

Author:: S . Cosme; H. E. Cuevas; D. Zhang; T. K. Oleksyk; B. M. Irish
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 88
ISSN:: 1614-2942
Subject:: Theobroma cacao; agronomic traits; ancestry; crops; disease resistance; genetic background; genetic variation; genotyping; germplasm exchange; pests; population structure; property rights; sensory properties; single nucleotide polymorphism; surveys; trees; Central America; Puerto Rico; Venezuela
Abstract:: ... Identification of genetically diverse cacao with disease resistance, high productivity, and desirable organoleptic traits is vitally important to the agricultural crop’s long-term sustainability. Environmental changes, pests, and diseases as well as nation’s sovereign property rights have led to a decrease in accessibility and exchange of germplasm of interest. Having been introduced during coloni ...
DOI:: 10.1007/s11295-016-1045-4
: https://doi.org/10.1007/s11295-016-1045-4

46. Genetic diversity of the African poplar (Populus ilicifolia) populations in Kenya

Author:: Sammy Muraguri Mutegi; Alice Muchugi; Sammy Carsan; Robert Kariba; Ramni Jamnadass; Phanuel Oballa; Amy M. Brunner; Steven Runo
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 66
ISSN:: 1614-2942
Subject:: Populus deltoides; amplified fragment length polymorphism; domestication; ex situ conservation; gene flow; genetic variation; heterozygosity; introduced species; loci; planting; India; Kenya; North America
Abstract:: ... We evaluated the genetic diversity of the African poplar (Populus ilicifolia) populations found in Kenya compared with reference samples of five poplar species from North America and one species introduced in Kenya from India (KEFRI-Kenya). Amplified fragment length polymorphism (AFLP) was used with the objective of providing important information for breeding and in situ/ex situ conservation of t ...
DOI:: 10.1007/s11295-016-1013-z
: https://doi.org/10.1007/s11295-016-1013-z

47. Genetic pool structure of local apple cultivars from Portugal assessed by microsatellites

Author:: V. Ferreira; A. M. Ramos-Cabrer; V. Carnide; O. Pinto-Carnide; A. Assunção; A. Marreiros; R. Rodrigues; S. Pereira-Lorenzo; I. Castro
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 36
ISSN:: 1614-2942
Subject:: Malus domestica; analysis of variance; apples; correspondence analysis; cultivars; diploidy; gene pool; genetic techniques and protocols; genetic variation; genotype; germplasm; germplasm conservation; homonym; hybridization; landraces; microsatellite repeats; triploidy; Portugal
Abstract:: ... A set of 87 apple accessions, located in three Portuguese apple germplasm collections, plus eight reference cultivars, were analyzed using 16 SSRs with the aim of assessing their genetic diversity and structure and evaluating relationships among them. Among the accessions studied, 64 unique genotypes were identified, 51 diploids and 13 putative triploids, revealing 19 groups of synonyms and 4 of h ...
DOI:: 10.1007/s11295-016-0997-8
: https://doi.org/10.1007/s11295-016-0997-8

48. Genetic structure and diversity of populations of polyploid Tibouchina pulchra Cogn. (Melastomataceae) under different environmental conditions in extremes of an elevational gradient

Author:: Vinícius L. G. Brito; Gustavo M. Mori; Bianca B. Z. Vigna; Marianne Azevedo-Silva; Anete P. Souza; Marlies Sazima
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 101
ISSN:: 1614-2942
Subject:: Tibouchina; adults; environmental factors; fathers; gene flow; genetic drift; genetic variation; genotype; microsatellite repeats; mutation; paternity; pollen; pollination; polyploidy; probability; progeny; selfing; trees
Abstract:: ... The genetic structure and diversity of plants may change significantly in an elevational gradient because different elevations regulate different ecological conditions. Several factors may influence genetic variation, such as mutations, selection, genetic drift, and gene flow. The aim of the present study was to evaluate the genetic structure and diversity of populations of Tibouchina pulchra Cogn ...
DOI:: 10.1007/s11295-016-1059-y
: https://doi.org/10.1007/s11295-016-1059-y

49. Genetic variation for needle traits in Scots pine (Pinus sylvestris L.)

Author:: Kevin Donnelly; Stephen Cavers; Joan E. Cottrell; Richard A. Ennos
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 40
ISSN:: 1614-2942
Subject:: Pinus sylvestris; altitude; frost resistance; genetic variation; heritability; highlands; leaves; longitude; phenology; phenotypic variation; rain; saplings; temperature; Scotland
Abstract:: ... The remnants of the Caledonian Native Pinewood are distributed across a relatively narrow geographic area in the Scottish Highlands yet inhabit a steep environmental gradient in terms of rainfall, temperature and altitude. Previous work based on common garden trials has demonstrated that native pine populations (Pinus sylvestris (L.)) exhibit differentiation in terms of growth, phenology and frost ...
DOI:: 10.1007/s11295-016-1000-4
: https://doi.org/10.1007/s11295-016-1000-4

50. Genetics of frost hardiness in Juglans regia L. and relationship with growth and phenology

Author:: Mercè Guàrdia; Guillaume Charrier; Antoni Vilanova; Robert Savé; Thierry Ameglio; Neus Aletà
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 83
ISSN:: 1614-2942
Subject:: Juglans regia; autumn; breeding; climate change; electrolytes; freezing; frost; growers; growing season; heritability; phenology; plantations; temperature; winter; Mediterranean region
Abstract:: ... The growing interest in broadleaf timber plantations in the Mediterranean area has promoted several studies focusing on the identification and characterization of variability sources in main timber-producing species. J. regia is one of these species, well-adapted to this area, but with freezing, damages registrations. Breeding focused on productive traits should include knowledge of adaptation, re ...
DOI:: 10.1007/s11295-016-1038-3
: https://doi.org/10.1007/s11295-016-1038-3

51. Genome-wide analysis of LTR-retrotransposon expression in leaves of Populus × canadensis water-deprived plants

Author:: Tommaso Giordani; Rosa Maria Cossu; Flavia Mascagni; Fabio Marroni; Michele Morgante; Andrea Cavallini; Lucia Natali
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 75
ISSN:: 1614-2942
Subject:: Populus canadensis; RNA; chromatin; drought; gene expression regulation; genes; high-throughput nucleotide sequencing; hybrids; leaves; methylation; retrotransposons; transcription (genetics); water deprivation
Abstract:: ... Retrotransposons represent a major component of plant genomes; however, large-scale studies on their expression are rare. Massively parallel sequencing offers new analytical possibilities enabling a comprehensive study of retrotransposon RNA transcription. We evaluated the expression of long terminal repeat-retrotransposons in leaves of two sister hybrids Populus × canadensis (P. deltoides × P. ni ...
DOI:: 10.1007/s11295-016-1036-5
: https://doi.org/10.1007/s11295-016-1036-5

52. Genome-wide analysis of poplar VQ gene family and expression profiling under PEG, NaCl, and SA treatments

Author:: Wenyuan Chu; Bin Liu; Yujiao Wang; Feng Pan; Zhu Chen; Hanwei Yan; Yan Xiang
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 124
ISSN:: 1614-2942
Subject:: Arabidopsis thaliana; quantitative polymerase chain reaction; chromosomes; Oryza sativa; stress response; breeding; glycerol; reverse transcriptase polymerase chain reaction; Populus trichocarpa; polyethylene; salicylic acid; sodium chloride; Vitis vinifera; introns
Abstract:: ... The past research has demonstrated that the VQ genes in Arabidopsis thaliana, Oryza sativa, and Vitis vinifera L play vital roles in their growth, development, and stress responses. So far, no information available describes the functions of the VQ genes in Populus trichocarpa. In our study, comprehensive analysis of poplar VQ genes were performed including genome-wide identification, characteriza ...
DOI:: 10.1007/s11295-016-1082-z
: https://doi.org/10.1007/s11295-016-1082-z

53. Genome-wide analysis of the terpene synthase gene family in physic nut (Jatropha curcas L.) and functional identification of six terpene synthases

Author:: Wangdan Xiong; Pingzhi Wu; Yongxia Jia; Xiaoyi Wei; Liangxiong Xu; Yanfang Yang; Deyou Qiu; Yaping Chen; Meiru Li; Huawu Jiang; Guojiang Wu
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 97
ISSN:: 1614-2942
Subject:: Escherichia coli; Jatropha curcas; diterpenoids; genes; heterologous gene expression; proteins; secondary metabolites; seeds; sesquiterpenoids; trees
Abstract:: ... Plant terpenes constitute a large class of compounds and have numerous biological roles as either primary or secondary metabolites. Terpene synthases (TPSs) play key roles on catalyzing the formation of different terpenes; they are divided into seven subfamilies based on sequence relatedness (TPSa–h). TPS-a proteins catalyze the formation of sesquiterpenes and diterpenes in plants. Physic nut (Jat ...
DOI:: 10.1007/s11295-016-1054-3
: https://doi.org/10.1007/s11295-016-1054-3

54. Genome-wide association mapping of sexual incompatibility genes in cacao (Theobroma cacao L.)

Author:: Marcos Ramos da Silva; Didier Clément; Karina Peres Gramacho; Wilson Reis Monteiro; Xavier Argout; Claire Lanaud; Uilson Lopes
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 62
ISSN:: 1614-2942
Subject:: DNA; Theobroma cacao; chromosome mapping; chromosomes; cleaning; clones; early selection; flowers; genetic markers; genotyping; leaves; linkage disequilibrium; major genes; plantations; pollination; single nucleotide polymorphism; trees
Abstract:: ... Sexual compatibility limits the production of cacao plantations, being an important selection criterion in breeding programs. However, the current method for characterizing compatibility, based on the frequency of flower setting after controlled pollination, is time consuming, requiring a long time to identify self-compatible individuals. The identification of molecular markers in genomic regions ...
DOI:: 10.1007/s11295-016-1012-0
: https://doi.org/10.1007/s11295-016-1012-0

55. Genome-wide identification and expression analysis of the bZIP gene family in apple (Malus domestica)

Author:: Yuan-Yuan Li; Dong Meng; Mingjun Li; Lailiang Cheng
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 82
ISSN:: 1614-2942
Subject:: Malus domestica; apples; basic-leucine zipper transcription factors; drought; fruiting; gene expression regulation; genes; growth and development; leaves; leucine zipper; models; plant growth; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; roots; salt stress; stress response; stress tolerance; transcription (genetics)
Abstract:: ... The basic leucine zipper (bZIP) family is one of the largest transcription factor (TF) families in plants, which play crucial roles in plant growth and development. bZIP proteins are involved in multiple biological processes, as well as responses to various biotic/abiotic stresses. Although genome-wide analysis of the bZIP gene family has been conducted in several plant species, only few comprehen ...
DOI:: 10.1007/s11295-016-1043-6
: https://doi.org/10.1007/s11295-016-1043-6

56. Genome-wide mining for microRNAs and their targets in Betula luminifera using high-throughput sequencing and degradome analyses

Author:: Junhong Zhang; Menghui Huang; Junsheng Liang; Ying Pan; Longjun Cheng; Jun Wu; Zaikang Tong
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 99
ISSN:: 1614-2942
Subject:: Betula; complementary DNA; enzymes; genes; genome mining; high-throughput nucleotide sequencing; leaves; microRNA; nitrogen; nucleotides; rapid amplification of cDNA ends; roots; starvation; stems; stress response; transcription (genetics); transcription factors
Abstract:: ... microRNAs (miRNAs) play vital roles in plants regulating a panoply of biological processes, such as development, hormone signaling, and stress response, by inhibiting target genes at the post-transcriptional level. However, the roles of miRNAs in Betula luminifera remain elusive. To mine for B. luminifera miRNAs and targets, we used a deep sequencing approach to analyze the sRNAs and degradome seq ...
DOI:: 10.1007/s11295-016-1047-2
: https://doi.org/10.1007/s11295-016-1047-2

57. Genome-wide survey and expression analysis of the stress-associated protein gene family in desert poplar, Populus euphratica

Author:: Huixia Jia; Jianbo Li; Jin Zhang; Yiqiu Ren; Jianjun Hu; Mengzhu Lu
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 78
ISSN:: 1614-2942
Subject:: Populus euphratica; abscisic acid; algorithms; cold; drought; genes; heat; heat stress; phylogeny; promoter regions; proteins; quantitative polymerase chain reaction; resistance mechanisms; single nucleotide polymorphism; stress response; stress tolerance; surveys; woody plants; zinc finger motif
Abstract:: ... Stress-associated proteins (SAPs) are a novel class of zinc finger proteins that extensively participate in abiotic stress responses. To date, no overall analysis and expression profiling of SAP genes in woody plants have been reported. Populus euphratica is distributed in desert regions and is extraordinarily adaptable to abiotic stresses. Thus, it is regarded as a promising candidate for studyin ...
DOI:: 10.1007/s11295-016-1033-8
: https://doi.org/10.1007/s11295-016-1033-8

58. Global comparative analysis of expressed genes in ovules and leaves of Ginkgo biloba L.

Author:: Li Wang; Zhaogeng Lu; Weixing Li; Jing Xu; Kaige Luo; Weichao Lu; Li Zhang; Biao Jin
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 29
ISSN:: 1614-2942
Subject:: flowering; cell growth; flavonoids; regulator genes; starch; cell division; gene expression; Angiospermae; gene expression regulation; databases; Ginkgo biloba; ovules; complementary DNA; sucrose; transcription (genetics); microscopy; biosynthesis; unigenes; flowers; genomics; stomata; chloroplasts
Abstract:: ... Ovules are an essential reproductive structure in all seed plants. However, limited information is available on the genetics and genomics of ovules in gymnosperms. Here, we used Illumina sequencing to derive comprehensive gene expression profiles for ovules and leaves in the extant basal gymnosperm Ginkgo biloba. A total of 100,124 transcripts, including 77,898 unigenes, were obtained by de novo a ...
DOI:: 10.1007/s11295-016-0989-8
: https://doi.org/10.1007/s11295-016-0989-8

59. High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

Author:: Francesco Mercati; Gabriella De Lorenzis; Lucio Brancadoro; Antonio Lupini; Maria Rosa Abenavoli; Maria Gabriella Barbagallo; Rosario Di Lorenzo; Attilio Scienza; Francesco Sunseri
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 59
ISSN:: 1614-2942
Subject:: Vitis vinifera; biotypes; cultivar identification; cultivars; genetic markers; genetic variation; genome; genotyping; germplasm; grapes; microsatellite repeats; multivariate analysis; parentage; single nucleotide polymorphism; viticulture; Italy; Sicily
Abstract:: ... The viticulture of Sicily, for its vocation, is one of the most important and ancient forms in Italy. Autochthonous grapevine cultivars, many of which known throughout the world, have always been cultivated in the island from many centuries. With the aim to preserve this large grapevine diversity, previous studies have already started to assess the genetic variability among the Sicilian cultivars ...
DOI:: 10.1007/s11295-016-1021-z
: https://doi.org/10.1007/s11295-016-1021-z

60. Homologs of the FB_MR5 fire blight resistance gene of Malus ×robusta 5 are present in other Malus wild species accessions

Author:: Thomas Wöhner; Erik Szentgyörgyi; Andreas Peil; Klaus Richter; Magda-Viola Hanke; Henryk Flachowsky
Source:: Tree genetics & genomes 2016 v.12 no.1 pp. 2
ISSN:: 1614-2942
Subject:: Erwinia amylovora; Malus baccata; Malus domestica; Malus prunifolia; alleles; apples; breeding; genotype; germplasm conservation; loci; microsatellite repeats; pathogens; sequence analysis; Korean Peninsula
Abstract:: ... Breeding for fire blight resistance is a major goal of nearly all apple breeding programs worldwide. Resources for resistance can be found in Malus wild species accession such as Malus ×robusta 5 (Mr5) which carries the FB_MR5 CC-NBS-LRR fire blight resistance gene. To study the occurrence of FB_MR5 in other genetic resources of Malus, a total of 394 wild species accessions of three international ...
DOI:: 10.1007/s11295-015-0962-y
: https://doi.org/10.1007/s11295-015-0962-y

61. Hybridization in contact zone between temperate European pine species

Author:: Witold Wachowiak; Weronika B. Żukowska; Błażej Wójkiewicz; Stephen Cavers; Monika Litkowiec
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 48
ISSN:: 1614-2942
Subject:: Pinus mugo; Pinus sylvestris; Pinus uncinata; chloroplast DNA; environmental factors; evolution; gene flow; genes; genetic markers; hybridization; hybrids; nucleotide sequences; phenotype; population structure; trees; Poland
Abstract:: ... Hybridization studies are important to advance our understanding of the interspecific gene flow and its evolutionary consequences in closely related species. Hybridization and admixture patterns were assessed in a contact zone and reference populations of European pine species using sequence data from 26 nuclear genes and a species-diagnostic cpDNA marker. Reference populations formed three distin ...
DOI:: 10.1007/s11295-016-1007-x
: https://doi.org/10.1007/s11295-016-1007-x

62. Identification and joint modeling of competition effects and environmental heterogeneity in three Douglas-fir (Pseudotsuga menziesii var. menziesii) trials

Author:: Eduardo P. Cappa; Michael U. Stoehr; Chang-Yi Xie; Alvin D. Yanchuk
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 102
ISSN:: 1614-2942
Subject:: Pseudotsuga menziesii var. menziesii; breeding value; covariance; environmental factors; genetic improvement; progeny; statistical models; tree and stand measurements; trees; variance; British Columbia
Abstract:: ... (Co)variance matrices for the assumed model, and thus the specification of the dispersion parameters, should take into account both the negative competition and the positive spatial correlations. In this context, we applied several approaches to identify and quantify the genetic and environmental competition effects and/or environmental heterogeneity in three Douglas-fir genetic trials from the Br ...
DOI:: 10.1007/s11295-016-1061-4
: https://doi.org/10.1007/s11295-016-1061-4

63. Identification of russet-associated microRNAs in the exocarp of a Dangshansuli pear mutant (Pyrus bretschneideri Rehd.) by high-throughput sequencing

Author:: Wei Heng; Bing Jia; Hai-na Huang; Jin-yu Yang; Zi-teng Wang; Pu Liu; Li Liu; Zhen-feng Ye; Li-wu Zhu
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 107
ISSN:: 1614-2942
Subject:: Pyrus bretschneideri; abiotic stress; biosynthesis; exocarp; gene expression regulation; high-throughput nucleotide sequencing; microRNA; mutants; pears; quantitative polymerase chain reaction; suberin
Abstract:: ... Russet skin is a very important trait that allows pear fruits to defend themselves against biotic and abiotic stresses. Small RNAs from a russet skin mutant ‘Xiusu’ derived from a ‘Dangshansuli’ pear were sequenced by high-throughput sequencing to reveal the role of miRNAs in the regulation of pear russet skin formation. A total of 12,158,547 and 12,053,678 high-quality reads were obtained for ‘Da ...
DOI:: 10.1007/s11295-016-1058-z
: https://doi.org/10.1007/s11295-016-1058-z

64. Identifying SNP markers tightly associated with six major genes in peach [Prunus persica (L.) Batsch] using a high-density SNP array with an objective of marker-assisted selection (MAS)

Author:: Patrick Lambert; Jose Antonio Campoy; Igor Pacheco; Jehan-Baptiste Mauroux; Cassia Da Silva Linge; Diego Micheletti; Daniele Bassi; Laura Rossini; Elisabeth Dirlewanger; Thierry Pascal; Michela Troggio; Maria Jose Aranzana; Andrea Patocchi; Pere Arús
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 121
ISSN:: 1614-2942
Subject:: Mendelian inheritance; Myzus persicae; Prunus persica; alleles; breeding programs; color; genetic markers; genomics; linkage groups; loci; major genes; marker-assisted selection; peaches; phenotype; seedlings; single nucleotide polymorphism; texture
Abstract:: ... One of the applications of genomics is to identify genetic markers linked to loci responsible for variation in phenotypic traits, which could be used in breeding programs to select individuals with favorable alleles, particularly at the seedling stage. With this aim, in the framework of the European project FruitBreedomics, we selected five main peach fruit characters and a resistance trait, contr ...
DOI:: 10.1007/s11295-016-1080-1
: https://doi.org/10.1007/s11295-016-1080-1

65. Identifying candidate genes for wood formation in poplar based on microarray network analysis and graph theory

Author:: Huanping Zhang; Tongming Yin
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 61
ISSN:: 1614-2942
Subject:: Populus; data collection; gene expression; genes; leaves; mathematical theory; microarray technology; trees; wood; wood properties; wood quality
Abstract:: ... In poplar, genetic research on wood properties is very important for the improvement of wood quality. Studies of wood formation genes at each developmental stage using modern biotechnology have often been limited to several genes or gene families. Because of the complex regulatory network involved in the co-expression and interactions of thousands of genes, however, the genetic mechanisms of wood ...
DOI:: 10.1007/s11295-016-1016-9
: https://doi.org/10.1007/s11295-016-1016-9

66. Inheritance of reproductive phenology traits and related QTL identification in apricot

Author:: Juan Alfonso Salazar; David Ruiz; José Antonio Campoy; Stefano Tartarini; Luca Dondini; Pedro Martínez-Gómez
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 71
ISSN:: 1614-2942
Subject:: Prunus armeniaca; apricots; chromosome mapping; crossing; flowering; fruiting; genetic markers; linkage groups; microsatellite repeats; phenology; quantitative trait loci; ripening; single nucleotide polymorphism
Abstract:: ... Reproductive phenological traits of great agronomical interest in apricot species, including flowering date, ripening date and fruit development period, were studied during 3 years in two F₁ progenies derived from the crosses ‘Bergeron’ × ‘Currot’ (B × C) and ‘Goldrich’ × ‘Currot’ (G × C). Results showed great variability and segregation in each population, confirming the polygenic nature and quan ...
DOI:: 10.1007/s11295-016-1027-6
: https://doi.org/10.1007/s11295-016-1027-6

67. Local habitat condition rather than geographic distance determines the genetic structure of Tamarix chinensis populations in Yellow River Delta, China

Author:: Zhu Zhu; Luoyan Zhang; Lexuan Gao; Shaoqing Tang; Yao Zhao; Ji Yang
Source:: Tree genetics & genomes 2016 v.12 no.1 pp. 14
ISSN:: 1614-2942
Subject:: Tamarix chinensis; adaptive radiation; alleles; genetic variation; habitats; loci; microsatellite repeats; population structure; river deltas; soil salinity; China; Yellow River
Abstract:: ... Understanding the extent of genetic diversity in natural populations and the correlations between population structure and environmental heterogeneity is of great importance to estimation of the potential for species to undergo rapid adaptive changes in response to environmental variation. In this study, we systematically sampled 800 individuals from 26 Tamarix chinensis populations distributed th ...
DOI:: 10.1007/s11295-016-0971-5
: https://doi.org/10.1007/s11295-016-0971-5

68. Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps

Author:: José Luis Zeballos; Walid Abidi; Rosa Giménez; Antonio J. Monforte; María Ángeles Moreno; Yolanda Gogorcena
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 37
ISSN:: 1614-2942
Subject:: anthocyanins; quantitative trait loci; cultivars; microsatellite repeats; marker-assisted selection; new variety; chromosomes; peaches; linkage groups; models; fruit quality; Prunus persica; genotyping; progeny; antioxidants; nectarines; single nucleotide polymorphism
Abstract:: ... Fruit quality is an essential criterion used to select new cultivars in peach breeding programs and is determined based on a combination of organoleptic and nutritional traits. The aim of this study was to identify quantitative trait loci (QTLs) for fruit quality traits in an F₁ nectarine population derived from ‘Venus’ and ‘Big Top’ cultivars. The progeny were evaluated over 4 years for agronomic ...
DOI:: 10.1007/s11295-016-0996-9
: https://doi.org/10.1007/s11295-016-0996-9

69. Marker-assisted introgression (MAI) of almond genes into the peach background: a fast method to mine and integrate novel variation from exotic sources in long intergeneration species

Author:: Octávio Serra; José Manuel Donoso; Roger Picañol; Ignasi Batlle; Werner Howad; Iban Eduardo; Pere Arús
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 96
ISSN:: 1614-2942
Subject:: Prunus dulcis; Prunus persica; almonds; backcrossing; crops; genotype; germplasm; hybrids; inheritance (genetics); introgression; major genes; peaches; phenotype; quantitative trait loci; selfing
Abstract:: ... This paper proposes a new breeding strategy, marker-assisted introgression (MAI), to obtain lines of perennial species with a single introgressed fragment from a compatible species two generations after the interspecific hybrid. MAI allows enrichment of the genome of a species with genes from a wild or exotic relative in a short timeframe and with an intermediate step that allows a first explorati ...
DOI:: 10.1007/s11295-016-1056-1
: https://doi.org/10.1007/s11295-016-1056-1

70. Mating dynamics of Scots pine in isolation tents

Author:: Tomas Funda; Ulfstand Wennström; Curt Almqvist; Bengt Andersson Gull; Xiao-Ru Wang
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 112
ISSN:: 1614-2942
Subject:: Pinus sylvestris; crops; females; flowering; forest industries; forest trees; genotyping; microsatellite repeats; parents; paternity; phenology; pollen; pollen flow; progeny; seed orchards; selfing; Sweden
Abstract:: ... Seed orchards are forest tree production populations for supplying the forest industry with consistent and abundant seed crops of superior genetic quality. However, genetic quality can be severely affected by non-random mating among parents and the occurrence of background pollination. This study analyzed mating structure and background pollination in six large isolation tents established in a clo ...
DOI:: 10.1007/s11295-016-1074-z
: https://doi.org/10.1007/s11295-016-1074-z

71. Maximization of minority classes in core collections designed for association studies

Author:: Alba María Vargas; María Teresa de Andrés; Javier Ibáñez
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 28
ISSN:: 1614-2942
Subject:: alleles; breeding; genetic improvement; germplasm conservation; plant genetics
Abstract:: ... Core collections are nowadays widely employed in diverse studies on plant genetics. The more extensively used method to build core collections (maximization strategy) is based on the selection, from a global collection, of those accessions which maximize the number of different alleles and phenotypic classes (classes’ richness). However, different core collections should be created for different t ...
DOI:: 10.1007/s11295-016-0988-9
: https://doi.org/10.1007/s11295-016-0988-9

72. Molecular characterization, critical amino acid identification, and promoter analysis of a lycopene β-cyclase gene from citrus

Author:: Suwen Lu; Yin Zhang; Xiongjie Zheng; Kaijie Zhu; Qiang Xu; Xiuxin Deng
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 106
ISSN:: 1614-2942
Subject:: Citrus sinensis; alleles; amino acids; bioinformatics; biosynthesis; enzyme activity; fruits; gene expression; lycopene; lycopene beta-cyclase; mutation; oranges; promoter regions; tomatoes
Abstract:: ... Lycopene β-cyclases (LCYBs) are key enzymes functioning at the branch point of the carotenoid biosynthesis pathway and determining the lycopene content in citrus fruit. There are two types of LCYBs, each of which possesses two different alleles (LCYb1a, LCYb1b, LCYb2a, and LCYb2b) in most citrus species. In this study, we performed detailed analyses of enzyme activities and transcript levels of al ...
DOI:: 10.1007/s11295-016-1066-z
: https://doi.org/10.1007/s11295-016-1066-z

73. Nuclear genetic variation of Rosa odorata var. gigantea (Rosaceae): population structure and conservation implications

Author:: Jing Meng; Shui-Lian He; De-Zhu Li; Ting-Shuang Yi
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 65
ISSN:: 1614-2942
Subject:: Rosa; ancestry; decision making; endangered species; flowering; flowers; gene flow; genes; genetic distance; genetic markers; genetic variation; habitat destruction; microsatellite repeats; models; niches; odors; planning; population structure; China
Abstract:: ... Rosa odorata var. gigantea is one of the most important ancestors of modern roses, which owns many merit traits including large flower, early flowering, and tea scent. Due to habitat loss and fragmentation, it has been listed as a rare and endangered species in China. In this study, a total of 424 accessions from 27 locations across its major distribution range were sampled. Its genetic diversity ...
DOI:: 10.1007/s11295-016-1024-9
: https://doi.org/10.1007/s11295-016-1024-9

74. Nuclear microsatellites reveal the genetic architecture and breeding history of tea germplasm of East Africa

Author:: M. C. Wambulwa; M. K. Meegahakumbura; R. Chalo; S. Kamunya; A. Muchugi; J. C. Xu; J. Liu; D. Z. Li; L. M. Gao
Source:: Tree genetics & genomes 2016 v.12 no.1 pp. 11
ISSN:: 1614-2942
Subject:: Camellia sinensis var. assamica; alleles; backcrossing; beverages; cultivars; gene banks; genetic variation; germplasm; hybridization; hybrids; leaves; loci; microsatellite repeats; pedigree; pigmentation; provenance; tea; trees; Kenya
Abstract:: ... Tea is the most popular non-alcoholic beverage worldwide and is one of the most important tree cash crops in East Africa. However, no comprehensive study has been carried out on the genetic structure and diversity of tea germplasm for this region to date. In the present study, 193 tea accessions held at the ex situ Germplasm Bank of the Tea Research Institute (TRI), Kenya, were analysed using gene ...
DOI:: 10.1007/s11295-015-0963-x
: https://doi.org/10.1007/s11295-015-0963-x

75. Optimum neighborhood seed orchard design

Author:: Kateřina Chaloupková; Jan Stejskal; Yousry A. El-Kassaby; Milan Lstibůrek
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 105
ISSN:: 1614-2942
Subject:: algorithms; assortative mating; forestry; germplasm conservation; seed orchards; threatened species
Abstract:: ... Original seed orchard algorithm “Optimum Neighborhood Seed Orchard Design” was developed as local heuristics to facilitate the establishment of advanced-generation seed orchards with complex configurations. The scheme leads to uniform spatial distribution among adjacent genetic entries, promoting panmixia. The resulting scheme is thus suitable to establishing both productive seed orchards as well ...
DOI:: 10.1007/s11295-016-1067-y
: https://doi.org/10.1007/s11295-016-1067-y

76. Overexpression of PaHAP3A stimulates differentiation of ectopic embryos from maturing somatic embryos of Norway spruce

Author:: Daniel Uddenberg; Malin Abrahamsson; Sara von Arnold
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 18
ISSN:: 1614-2942
Subject:: Arabidopsis thaliana; Picea abies; adults; conifers; gene overexpression; genes; germination; plant propagation; promoter regions; seedlings; somatic embryogenesis; somatic embryos; totipotency; trees
Abstract:: ... Somatic embryogenesis can be used for large-scale propagation of plants. In most conifers, it is only possible to establish embryogenic cultures from zygotic embryos or young seedlings. There is, however, a great interest to propagate selected trees with valuable traits via somatic embryos. To be able to establish embryogenic cultures from adult tissues, more knowledge about the molecular regulati ...
DOI:: 10.1007/s11295-016-0974-2
: https://doi.org/10.1007/s11295-016-0974-2

77. Patterns of neutral and adaptive genetic diversity across the natural range of sugar pine (Pinus lambertiana Dougl.)

Author:: Carl Vangestel; Alejandra Vázquez-Lobo; Pedro J. Martínez-García; Irina Calic; Jill L. Wegrzyn; David B. Neale
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 51
ISSN:: 1614-2942
Subject:: Pinus lambertiana; climate change; coniferous forests; drought; drought tolerance; environmental factors; genes; genetic similarity; genetic variation; mitochondria; physiological transport; population structure; single nucleotide polymorphism; trees; California
Abstract:: ... Demographic and environmental forces shape geographical patterns of genetic diversity. Knowledge thereof is not only important for evolutionary ecologists but, in light of future climate change, will be of interest to conservation biologists as well. Sugar pine (Pinus lambertiana Dougl.) is an ecologically important species found in mixed conifer forests across western North America. We applied a ...
DOI:: 10.1007/s11295-016-0998-7
: https://doi.org/10.1007/s11295-016-0998-7

78. Phylogenetic relationships among cultivated Zanthoxylum species in China based on cpDNA markers

Author:: Shijing Feng; Zhenshan Liu; Lv Chen; Na Hou; Tuxi Yang; Anzhi Wei
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 45
ISSN:: 1614-2942
Subject:: Zanthoxylum armatum; Zanthoxylum bungeanum; Zanthoxylum schinifolium; ancestry; breeding; chloroplast DNA; cultivars; genetic variation; haplotypes; phylogeny; provenance; China
Abstract:: ... We here present a molecular phylogenetic analysis of cultivated Zanthoxylum species which have a long history of cultivation both for economic and for chemical values in China. Three cpDNA markers, including matK, rbcL, and trnL-F, were sequenced, with the goals of untangling phylogenetic relationships and inferring biogeographic origin and patterns of distribution among Zanthoxylum species. Based ...
DOI:: 10.1007/s11295-016-1005-z
: https://doi.org/10.1007/s11295-016-1005-z

79. Phylogenetic relationships, molecular taxonomy, biogeography of Betula, with emphasis on phylogenetic position of Iranian populations

Author:: Hamid Bina; Hamed Yousefzadeh; Syed Shujait Ali; Mohammad Esmailpour
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 84
ISSN:: 1614-2942
Subject:: Betula; ancestry; biogeography; intergenic DNA; internal transcribed spacers; molecular systematics; phylogeny; tetraploidy; trees; Iran; South East Asia
Abstract:: ... Birch trees inhabiting the high-altitude Hyrcanian forest (the southern shores of the Caspian Sea of Iran and Azerbaijan) are classified in the EN (endangered) category of the International Union for Conservation of Nature (IUCN). Taxonomic status and phylogenetic relationship of Iranian populations, molecular taxonomy, and biogeography of the genus Betula in the world have been considered. Four r ...
DOI:: 10.1007/s11295-016-1037-4
: https://doi.org/10.1007/s11295-016-1037-4

80. Phylogeography and evolution of two closely related oak species (Quercus) from north and northeast China

Author:: Jia Yang; Xiaoyao Di; Xu Meng; Li Feng; Zhanlin Liu; Guifang Zhao
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 89
ISSN:: 1614-2942
Subject:: Quercus mongolica; chloroplast DNA; chloroplasts; demography; evolution; gene flow; genes; genetic techniques and protocols; models; phylogeography; China
Abstract:: ... Orographic and climatic influences during the Pleistocene have had a crucial role on interspecific divergence and population demography during speciation. However, associations between demographic histories of closely related species and related climatic events, especially in north and northeast China, are still underexplored. Genetic analyses with four chloroplast DNA and two nuclear genes and sp ...
DOI:: 10.1007/s11295-016-1044-5
: https://doi.org/10.1007/s11295-016-1044-5

81. Pollen and seed flow under different predominant winds in wind-pollinated and wind-dispersed species Engelhardia roxburghiana

Author:: Zheng-Feng Wang; Ju-Yu Lian; Wan-Hui Ye; Hong-Lin Cao; Qian-Mei Zhang; Zhang-Ming Wang
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 19
ISSN:: 1614-2942
Subject:: forest canopy; forests; gene flow; models; pollen; pollen flow; seed dispersal; wind direction; China
Abstract:: ... In most plants, the contributions of pollen and seed flow to their genetic structures are generally difficult to disentangle. For typical wind-pollinated and wind-dispersed species Engelhardia roxburghiana in a 20-ha natural forest plot in lower subtropic China, because the prevailing wind directions change during its pollen release and seed dispersal seasons, we could compare its genetic structur ...
DOI:: 10.1007/s11295-016-0973-3
: https://doi.org/10.1007/s11295-016-0973-3

82. Pollen dispersal patterns and population persistence in a small isolated population of Fagus crenata

Author:: Michiko Inanaga; Yasuhiro Koyama; Hideyuki Ida; Mitsuhiro Okada; Atsushi Nakanishi; Makoto Takahashi; Nobuhiro Tomaru
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 69
ISSN:: 1614-2942
Subject:: Fagus crenata; alleles; gene flow; genetic drift; genetic variation; heterozygosity; inbreeding; linkage disequilibrium; mature plants; microsatellite repeats; outbreeding; parentage; pollen; pollen flow; population dynamics; population size; progeny; seedlings; seeds
Abstract:: ... The potential of long-distance pollen dispersal and the effects of small population size and population isolation on persistence of Fagus crenata populations were investigated in a small, severely isolated population (the Gofuku-ji population) and two other populations located within 7 km of this population (including 87 adult trees in total). Parentage analysis using 13 microsatellite loci showed ...
DOI:: 10.1007/s11295-016-1026-7
: https://doi.org/10.1007/s11295-016-1026-7

83. Pollen-mediated gene flow promotes low nuclear genetic differentiation among populations of Cycas debaoensis (Cycadaceae)

Author:: Yi-Qing Gong; Xun Gong
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 93
ISSN:: 1614-2942
Subject:: Cycas; alleles; anthropogenic activities; chloroplast DNA; gene flow; genetic variation; habitats; haplotypes; indigenous species; inheritance (genetics); karsts; microsatellite repeats; population structure; sand; China
Abstract:: ... Cycas debaoensis is a critically endangered cycad species endemic to China. This species is found on two kinds of habitats according to the edaphic differences, sand and karst. A previous chloroplast DNA (cpDNA) study indicated that C. debaoensis had low genetic variation within populations and high genetic differentiation among populations. Because maternally inherited cpDNA does not fully charac ...
DOI:: 10.1007/s11295-016-1051-6
: https://doi.org/10.1007/s11295-016-1051-6

84. Polygenic inheritance of resistance to Cacopsylla pyri in a Pyrus communis × P. ussuriensis progeny is explained by three QTLs involving an epistatic interaction

Author:: Perchepied L.; Guérif P.; Ravon E.; Denancé C.; Laurens F.; Robert P.; Bouvier L.; Lespinasse Y.; Durel C.E.
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 108
ISSN:: 1614-2942
Subject:: Cacopsylla pyri; Pyrus communis; Pyrus ussuriensis; breeding; cultivars; epistasis; genotype; linkage groups; loci; nymphs; pears; pest control; pesticides; polygenic inheritance; progeny; quantitative trait loci
Abstract:: ... Pear psylla (Cacopsylla pyri) causes severe damage on European pear cultivars, resulting in high yield losses. Its control has become difficult since it developed resistance to a wide range of pesticides, while the number of authorized molecules for pest control has decreased. Identifying pear psylla resistance factors should help breeding new resistant pear cultivars. We analyzed the quantitative ...
DOI:: 10.1007/s11295-016-1072-1
: https://doi.org/10.1007/s11295-016-1072-1

85. Population genetic diversity of the rare hardwood butternut (Juglans cinerea) in the northeastern USA

Author:: A. Boraks; K. D. Broders
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 43
ISSN:: 1614-2942
Subject:: Bayesian theory; Juglans cinerea; Ophiognomonia clavigignenti-juglandacearum; alleles; fungi; gene flow; genetic markers; genetic variation; habitats; hardwood; highlands; mortality; pathogens; Northeastern United States
Abstract:: ... Populations of butternut tree (Juglans cinerea) have undergone range-wide extirpation. A fungal pathogen, Ophiognomonia clavigignenti-juglandacearum, of unknown origin has been recognized as the causal factor. This population collapse has allowed for observations of a broadleaf hardwood in rapid decline. This study made use of six neutral microsatellite markers to describe the present genetic dive ...
DOI:: 10.1007/s11295-016-1002-2
: https://doi.org/10.1007/s11295-016-1002-2

86. Postmating barriers to hybridization between an island’s native eucalypts and an introduced congener

Author:: Matthew J. Larcombe; Robert C. Barbour; Rebecca C. Jones; René E. Vaillancourt; Brad M. Potts
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 26
ISSN:: 1614-2942
Subject:: Eucalyptus nitens; evolution; females; flowers; gene flow; genetic distance; hybrids; interspecific hybridization; males; plantations; pollen; reproductive isolation; risk management; Tasmania
Abstract:: ... We evaluate postmating barriers to hybridization between an exotic eucalypt and a group of native congeners on the island of Tasmania. We aimed to better understand the basis of reproductive isolation between the species, glean insights into the evolution of isolating mechanisms, and inform genetic risk management. Compatibility between the exotic plantation species Eucalyptus nitens (pollen paren ...
DOI:: 10.1007/s11295-016-0979-x
: https://doi.org/10.1007/s11295-016-0979-x

87. Provenance and progeny performances and genotype × environment interactions of Eucalyptus robusta grown in Madagascar

Author:: Andriambelo Radonirina Razafimahatratra; Tahiana Ramananantoandro; Vololoniriana Razafimaharo; Gilles Chaix
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 38
ISSN:: 1614-2942
Subject:: Eucalyptus robusta; climate change; forestry; genetic improvement; genetic variation; genotype; growth traits; heritability; progeny; provenance; rain; seed orchards; soil types; summer; temperature; trees; wood; Australia; Madagascar
Abstract:: ... In Madagascar, plantations of Eucalyptus robusta are grown on more than 150,000 ha. Coppice-managed plantations of this species supply most of the charcoal to the capital, Antananarivo. A study of genetic variability and genotype × environment interactions for growth and wood volume production was undertaken. It involved five E. robusta trials (two provenance trials and three progeny trials) in tw ...
DOI:: 10.1007/s11295-016-0999-6
: https://doi.org/10.1007/s11295-016-0999-6

88. PtFCA from precocious trifoliate orange is regulated by alternative splicing and affects flowering time and root development in transgenic Arabidopsis

Author:: Xiao-Yan Ai; Jin-Zhi Zhang; Tian-Jia Liu; Chun -Gen Hu
Source:: Tree genetics & genomes 2016 v.12 no.5 pp. 85
ISSN:: 1614-2942
Subject:: Arabidopsis; Citrus; Poncirus trifoliata; RNA-binding proteins; abscisic acid; alternative splicing; ambient temperature; early development; flowering; mutants; phase transition; phenotype; protein-protein interactions; transgenic plants
Abstract:: ... The transition to flowering is a major developmental switch in flowering plants. The nuclear RNA-binding protein FCA responds to seasonal signals and abscisic acid (ABA), which can control the flowering time via ambient temperature and autonomous pathways. Citrus FCA ortholog (PtFCA) has been isolated and characterized from precocious trifoliate orange (Poncirus trifoliata L. Raf). Three alternati ...
DOI:: 10.1007/s11295-016-1035-6
: https://doi.org/10.1007/s11295-016-1035-6

89. QTL mapping and breeding value estimation through pedigree-based analysis of fruit size and weight in four diverse peach breeding programs

Author:: Jonathan Fresnedo-Ramírez; Terrence J. Frett; Paul J. Sandefur; Alejandra Salgado-Rojas; John R. Clark; Ksenija Gasic; Cameron P. Peace; Natalie Anderson; Timothy P. Hartmann; David H. Byrne; Marco C. A. M. Bink; Eric van de Weg; Carlos H. Crisosto; Thomas M. Gradziel
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 25
ISSN:: 1614-2942
Subject:: Markov chain; Prunus persica; analytical methods; breeding value; crops; genetic background; genetic markers; germplasm; marker-assisted selection; models; peaches; pedigree; phenotypic variation; quantitative trait loci; quantitative traits; yield components
Abstract:: ... The narrow genetic base of peach (Prunus persica L. Batsch) challenges efforts to accurately dissect the genetic architecture of complex traits. Standardized phenotypic assessment of pedigree-linked breeding germplasm and new molecular strategies and analytical approaches developed and conducted during the RosBREED project for enabling marker-assisted breeding (MAB) in Rosaceae crops has overcome ...
DOI:: 10.1007/s11295-016-0985-z
: https://doi.org/10.1007/s11295-016-0985-z

90. QTL mapping for resistance to Ceratocystis wilt in Eucalyptus

Author:: Carla Cristina Gonçalves Rosado; Lúcio Mauro da Silva Guimarães; Danielle Assis Faria; Marcos Deon Vilela de Resende; Cosme Damião Cruz; Dario Grattapaglia; Acelino Couto Alfenas
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 72
ISSN:: 1614-2942
Subject:: Ceratocystis fimbriata; Eucalyptus globulus; Eucalyptus grandis; Eucalyptus urophylla; chromosomes; disease control; disease resistance; fungal wilt; fungi; genes; genetic markers; genotype; genotyping; heritability; hybrids; linkage groups; microsatellite repeats; phenotype; plantations; progeny; quantitative trait loci; quantitative traits; trees; Brazil
Abstract:: ... Ceratocystis wilt caused by the fungus Ceratocystis fimbriata, is currently one of the major diseases in commercial plantations of Eucalyptus trees in Brazil. Deployment of resistant genotypes has been the main strategy for effective disease management. The present study aimed at identifying genomic regions underlying the genetic control of resistance to Ceratocystis wilt in Eucalyptus by quantita ...
DOI:: 10.1007/s11295-016-1029-4
: https://doi.org/10.1007/s11295-016-1029-4

91. QTL mapping of mandarin (Citrus reticulata) fruit characters using high-throughput SNP markers

Author:: Yuan Yu; Chunxian Chen; Frederick G. Gmitter Jr.
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 77
ISSN:: 1614-2942
Subject:: Citrus clementina; Citrus reticulata; biochemical pathways; carotenoids; chromosome mapping; clementines; color; cultivars; flavor; fruit quality; genes; genetic markers; juices; juvenility; linkage groups; mandarins; marker-assisted selection; quantitative trait loci; seedless varieties; single nucleotide polymorphism; trees
Abstract:: ... Seedlessness, flavor, and color are top priorities for mandarin (Citrus reticulata Blanco) cultivar improvement. Given long juvenility, large tree size, and high breeding cost, marker-assisted selection (MAS) may be an expeditious and economical approach to these challenges. The objectives of this study were to construct high-density mandarin genetic maps and to identify single nucleotide polymorp ...
DOI:: 10.1007/s11295-016-1034-7
: https://doi.org/10.1007/s11295-016-1034-7

92. RNA-seq analysis in forest tree species: bioinformatic problems and solutions

Author:: Unai López de Heredia; José Luis Vázquez-Poletti
Source:: Tree genetics & genomes 2016 v.12 no.2 pp. 30
ISSN:: 1614-2942
Subject:: Pinus taeda; RNA; bioinformatics; computer software; forest trees; gene expression; genome; high-throughput nucleotide sequencing
Abstract:: ... Direct sequencing of RNA (RNA-seq) using next-generation sequencing platforms has allowed a growing number of gene expression studies focused on forest trees in the last 5 years. Bioinformatic analyses derived from RNA-seq of forest trees are particularly challenging, because the massive genome length (~20.1 Gbp for loblolly pine) and the absence of annotated reference genomes require specific bio ...
DOI:: 10.1007/s11295-016-0995-x
: https://doi.org/10.1007/s11295-016-0995-x

93. Recent landscape genomics studies in forest trees—what can we believe?

Author:: Irina Ćalić; Filippo Bussotti; Pedro J. Martínez-García; David B. Neale
Source:: Tree genetics & genomes 2016 v.12 no.1 pp. 3
ISSN:: 1614-2942
Subject:: Picea abies; climate change; databases; environmental factors; experimental design; forest ecosystems; forest trees; forests; genes; genetic variation; genomics; geographic information systems; habitats; landscapes; single nucleotide polymorphism
Abstract:: ... Landscape genomics is potentially a powerful research field for discovery of genes underlying complex patterns of adaptation in forest ecosystems. The general approach is to search for associations between genetic variation in tree populations and environmental variation in the habitats these trees occupy. For example, environmental data from GIS databases can be associated with single nucleotide ...
DOI:: 10.1007/s11295-015-0960-0
: https://doi.org/10.1007/s11295-015-0960-0

94. Root transcriptome sequencing and differentially expressed drought-responsive genes in the Platycladus orientalis (L.)

Author:: Sheng Zhang; Lingling Zhang; Zhong Zhao; Yiming Li; Kaikai Zhou; Li Su; Qianyi Zhou
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 79
ISSN:: 1614-2942
Subject:: Platycladus orientalis; afforestation; arginine; biosynthesis; cDNA libraries; complementary DNA; drought; drought tolerance; gene expression; gene expression regulation; genetic databases; ingredients; phenylalanine; proline; roots; secondary metabolites; seedlings; semiarid zones; starch; sucrose; transcription (genetics); transcription factors; transcriptome; transcriptomics; trees; unigenes; water stress
Abstract:: ... Platycladus orientalis (L.) is used extensively for afforestation and is a common medicinal ingredient. Because of its drought tolerance, P. orientalis is widely used for afforestation in arid and semi-arid areas. To better understand the mechanisms involved in drought-stress tolerance in this important tree, the transcriptome profiles of drought-treated P. orientalis seedlings were analyzed using ...
DOI:: 10.1007/s11295-016-1042-7
: https://doi.org/10.1007/s11295-016-1042-7

95. SSR markers reveal the population structure of Sri Lankan yellow dwarf coconuts (Cocos nucifera L.)

Author:: L. C. J. Kamaral; P. N. Dassanayaka; K. L. N. S. Perera; S. A. C. N. Perera
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 116
ISSN:: 1614-2942
Subject:: Cocos nucifera; alleles; coconuts; color; computer software; crops; cross pollination; domestication; evolution; genetic variation; germplasm; germplasm conservation; heterozygosity; hybridization; loci; microsatellite repeats; models; parents; phenotype; population structure; self-pollination; trees
Abstract:: ... World coconut germplasm has been classified broadly as tall and dwarf coconuts based on palm stature. Dwarf coconuts are predominantly self-breeding purelines hypothesised to have derived from tall coconuts. Dwarfs are categorized as yellow, green, red and brown on the colour of epicarp and are important as parents in hybridization of coconuts for desirable traits. Sri Lankan yellow dwarfs (SLYD) ...
DOI:: 10.1007/s11295-016-1076-x
: https://doi.org/10.1007/s11295-016-1076-x

96. SSR-based genetic mapping and QTL analysis for timing of spring bud flush, young shoot color, and mature leaf size in tea plant (Camellia sinensis)

Author:: Li-Qiang Tan; Li-Yuan Wang; Li-Yi Xu; Li-Yun Wu; Min Peng; Cheng-Cai Zhang; Kang Wei; Pei-Xian Bai; Hai-Lin Li; Hao Cheng; Gui-Nian Qi
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 52
ISSN:: 1614-2942
Subject:: Camellia sinensis; agronomic traits; chromosome mapping; color; crossing; data collection; genes; genetic markers; leaf development; leaves; linkage groups; loci; marker-assisted selection; microsatellite repeats; phenotype; quantitative trait loci; spring; tea
Abstract:: ... Tea plant (Camellia sinensis) is a major beverage crop across the world. To uncover the genetic controls of agronomic traits and facilitate marker-assisted breeding (MAB) in tea plant, we constructed a saturated SSR-based linkage map using an F₁ population derived from the crossing of ‘Longjin43’ × ‘Baihaozao’. A total of 483 SSR markers, consisting of 117 novel loci, 129 transferred from other te ...
DOI:: 10.1007/s11295-016-1008-9
: https://doi.org/10.1007/s11295-016-1008-9

97. Selection and testing of reference genes for accurate RT-qPCR in adult needles and seedlings of maritime pine

Author:: José M. Granados; Concepción Ávila; Francisco M. Cánovas; Rafael A. Cañas
Source:: Tree genetics & genomes 2016 v.12 no.3 pp. 60
ISSN:: 1614-2942
Subject:: Pinus pinaster; adults; conifer needles; gene expression; genes; mature plants; microarray technology; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; seedlings
Abstract:: ... Quantitative real-time PCR (RT-qPCR) techniques have revolutionized gene expression analyses. To obtain accurate results, raw RT-qPCR results need to be normalized by using endogenous reference genes whose expression is assumed invariable in all studied samples. However, there are no universal reference genes, and candidate genes need to be evaluated for each experimental condition. In this work, ...
DOI:: 10.1007/s11295-016-1018-7
: https://doi.org/10.1007/s11295-016-1018-7

98. Sex-specific pattern of spatial genetic structure in dioecious and clonal tree species, Populus alba L.

Author:: Monika Dering; Grzegorz Rączka; Janusz Szmyt
Source:: Tree genetics & genomes 2016 v.12 no.4 pp. 70
ISSN:: 1614-2942
Subject:: Populus alba; asexual reproduction; clones; females; foraging; genetic markers; life history; males; pedigree; sexual dimorphism; siblings; trees
Abstract:: ... Fine-scale spatial genetic structure (SGS) has profound ecological and genetic consequences for plant populations, and some studies indicate that clonal reproduction may significantly enhance SGS. Clonality is widespread among dioecious species, but little is known about the relationship between clonal reproduction and SGS in the frame of sexual dimorphism. We asked the following questions: (1) Is ...
DOI:: 10.1007/s11295-016-1028-5
: https://doi.org/10.1007/s11295-016-1028-5

99. Signatures of natural selection on Pinus cembra and P. mugo along elevational gradients in the Alps

Author:: Elena Mosca; Felix Gugerli; Andrew J. Eckert; David B. Neale
Source:: Tree genetics & genomes 2016 v.12 no.1 pp. 9
ISSN:: 1614-2942
Subject:: Pinus cembra; Pinus mugo; abiotic stress; altitude; ecosystems; forest trees; gene flow; genes; genetic variation; genotyping; natural selection; plant response; single nucleotide polymorphism; statistical models; temperature; Alps region
Abstract:: ... Alpine regions represent an interesting biome for studying local adaptation in forest trees. Strong genetic differentiation is expected along elevational gradients in spite of extensive gene flow. We sampled 18 and 20 natural populations of Pinus cembra and Pinus mugo, in two subregions and four elevational gradients. To investigate the effects of elevation on genetic diversity and adaptation, 768 ...
DOI:: 10.1007/s11295-015-0964-9
: https://doi.org/10.1007/s11295-015-0964-9

100. Single nucleotide polymorphisms in two GID1 orthologs associate with growth and wood property traits in Populus tomentosa

Author:: Haijiao Yang; Xiaohui Yang; Longxin Wang; Chenrui Gong; Beibei Chen; Qingzhang Du; Deqiang Zhang
Source:: Tree genetics & genomes 2016 v.12 no.6 pp. 109
ISSN:: 1614-2942
Subject:: Populus tomentosa; amino acids; complementary DNA; genes; genetic variation; gibberellins; haplotypes; leaves; linkage disequilibrium; open reading frames; phenotypic variation; reverse transcriptase polymerase chain reaction; single nucleotide polymorphism; transcription (genetics); trees; wood; wood properties
Abstract:: ... Gibberellic acids (GAs) have multiple functions in various stages of plant growth and wood development, and GA receptor GIBBERELLIN INSENSITIVE DWARF 1 (GID1) is a key player in GA signaling. Here, we used association studies to examine the allelic variation within PtoGID1a and PtoGID1b associated with growth and wood properties in a natural population of Populus tomentosa. We isolated two full-le ...
DOI:: 10.1007/s11295-016-1070-3
: https://doi.org/10.1007/s11295-016-1070-3

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1. ADH and PDC genes involved in tannins coagulation leading to natural de-astringency in Chinese pollination constant and non-astringency persimmon (Diospyros kaki Thunb.)

2. Additive and non-additive genetic parameters for multipurpose traits in a clonally replicated incomplete factorial test of Castanea spp.

3. Ancient split of major genetic lineages of European Black Pine: evidence from chloroplast DNA

4. Apple NPR1 homologs and their alternative splicing forms may contribute to SA and disease responses

5. Association of single nucleotide polymorphisms with form traits in three New Zealand populations of radiata pine in the presence of genotype by environment interactions

6. Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata)

7. Association studies reveal the effect of genetic variation in lncRNA UGTRL and its putative target PtoUGT88A1 on wood formation in Populus tomentosa

8. Auxin- and cytokinin-induced berries set in grapevine partly rely on enhanced gibberellin biosynthesis

9. Broad-scale genetic homogeneity in natural populations of common hazel (Corylus avellana) in Ireland

10. Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee

11. Characterization of genome-wide simple sequence repeats and application in interspecific genetic map integration in kiwifruit

12. Climate change risk management in tree improvement programs: selection and movement of genotypes

13. Climate-related adaptive genetic variation and population structure in natural stands of Norway spruce in the South-Eastern Alps

14. Comparative analyses of squalene synthase (SQS) proteins in poplar and pine by using bioinformatics tools

15. Complete chloroplast genome sequences of Eucommia ulmoides: genome structure and evolution

16. Conservation genetics of rare trees restricted to subtropical montane cloud forests in southern China: a case study from Quercus arbutifolia (Fagaceae)

17. Construction of a high density linkage map and its application in the identification of QTLs for soluble sugar and organic acid components in apple

18. Construction of a high-density genetic map of Ziziphus jujuba Mill. using genotyping by sequencing technology

19. DNA fingerprinting of oil camellia cultivars with SSR markers

20. Development of SNP-based assays for disease resistance and fruit quality traits in apple (Malus × domestica Borkh.) and validation in breeding pilot studies

21. Development of microsatellite markers and their use in genetic diversity and population structure analysis in Casuarina

22. Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)

23. Disentangling the effects of isolation-by-distance and isolation-by-environment on genetic differentiation among Rhododendron lineages in the subgenus Tsutsusi

24. Dissection of additive, dominant, epistatic roles of allelic variation within heat shock factor genes in Chinese indigenous poplar (Populus simonii)

25. Effective gene flow in a historically fragmented area at the southern edge of silver fir (Abies alba Mill.) distribution

26. Effects of different silvicultural systems on the genetic diversity of Shorea parvifolia populations in the tropical rainforest of Southeast Asia

27. Estimation of number and size of QTL effects in forest tree traits

28. Evaluation of genetic homogeneity of in vitro-raised plants of Tecomella undulata (Sm.) Seem. using molecular markers

29. Evaluation of the best linear unbiased prediction method for breeding values of fruit-quality traits in citrus

30. Evidence for different QTL underlying the immune and hypersensitive responses of Eucalyptus globulus to the rust pathogen Puccinia psidii

31. Evolutionary history of subtropical evergreen broad-leaved forest in Yunnan Plateau and adjacent areas: an insight from Quercus schottkyana (Fagaceae)

32. Fine mapping of the rosy apple aphid resistance locus Dp-fl on linkage group 8 of the apple cultivar ‘Florina’

33. Fine-scale spatial genetic structure in the frankincense tree Boswellia papyrifera (Del.) Hochst. and implications for conservation

34. Gene expression profiles in different stem internodes reveal the genetic regulation of primary and secondary stem development in Betula platyphylla

35. Gene flow among Hancornia speciosa (Apocynaceae) varieties and hybrid fitness

36. Genetic analyses reveal high levels of seed and pollen flow in hawthorn (Crataegus monogyna Jacq.), a key component of hedgerows

37. Genetic analysis of fiber dimensions and their correlation with stem diameter and solid-wood properties in Norway spruce

38. Genetic analysis of salt tolerance in a progeny derived from the citrus rootstocks Cleopatra mandarin and trifoliate orange

39. Genetic architecture of apple fruit quality traits following storage and implications for genetic improvement

40. Genetic determination of tannins and herbivore resistance in Quercus ilex

41. Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers

42. Genetic diversity and genetic structure of black alder (Alnus glutinosa [L.] Gaertn) in the Belgium-Luxembourg-France cross-border area

43. Genetic diversity and population structure of common walnut (Juglans regia) in China based on EST-SSRs and the nuclear gene phenylalanine ammonia-lyase (PAL)

44. Genetic diversity and structure of the globally invasive tree, Paraserianthes lophantha subspecies lophantha, suggest an introduction history characterised by varying propagule pressure

45. Genetic diversity of naturalized cacao (Theobroma cacao L.) in Puerto Rico

46. Genetic diversity of the African poplar (Populus ilicifolia) populations in Kenya

47. Genetic pool structure of local apple cultivars from Portugal assessed by microsatellites

48. Genetic structure and diversity of populations of polyploid Tibouchina pulchra Cogn. (Melastomataceae) under different environmental conditions in extremes of an elevational gradient

49. Genetic variation for needle traits in Scots pine (Pinus sylvestris L.)

50. Genetics of frost hardiness in Juglans regia L. and relationship with growth and phenology

51. Genome-wide analysis of LTR-retrotransposon expression in leaves of Populus × canadensis water-deprived plants

52. Genome-wide analysis of poplar VQ gene family and expression profiling under PEG, NaCl, and SA treatments

53. Genome-wide analysis of the terpene synthase gene family in physic nut (Jatropha curcas L.) and functional identification of six terpene synthases

54. Genome-wide association mapping of sexual incompatibility genes in cacao (Theobroma cacao L.)

55. Genome-wide identification and expression analysis of the bZIP gene family in apple (Malus domestica)

56. Genome-wide mining for microRNAs and their targets in Betula luminifera using high-throughput sequencing and degradome analyses

57. Genome-wide survey and expression analysis of the stress-associated protein gene family in desert poplar, Populus euphratica

58. Global comparative analysis of expressed genes in ovules and leaves of Ginkgo biloba L.

59. High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

60. Homologs of the FB_MR5 fire blight resistance gene of Malus ×robusta 5 are present in other Malus wild species accessions

61. Hybridization in contact zone between temperate European pine species

62. Identification and joint modeling of competition effects and environmental heterogeneity in three Douglas-fir (Pseudotsuga menziesii var. menziesii) trials

63. Identification of russet-associated microRNAs in the exocarp of a Dangshansuli pear mutant (Pyrus bretschneideri Rehd.) by high-throughput sequencing

64. Identifying SNP markers tightly associated with six major genes in peach [Prunus persica (L.) Batsch] using a high-density SNP array with an objective of marker-assisted selection (MAS)

65. Identifying candidate genes for wood formation in poplar based on microarray network analysis and graph theory

66. Inheritance of reproductive phenology traits and related QTL identification in apricot

67. Local habitat condition rather than geographic distance determines the genetic structure of Tamarix chinensis populations in Yellow River Delta, China

68. Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps

69. Marker-assisted introgression (MAI) of almond genes into the peach background: a fast method to mine and integrate novel variation from exotic sources in long intergeneration species

70. Mating dynamics of Scots pine in isolation tents