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1. Comprehensive mechanistic insights into the citrus genetics, breeding challenges, biotechnological implications, and omics-based interventions

Author:
Komaljeet Gill; Pankaj Kumar; Anshul Kumar; Bhuvnesh Kapoor; Rajnish Sharma; Ajay Kumar Joshi
Source:
Tree genetics & genomes 2022 v.18 no.2 pp. 9
ISSN:
1614-2942
Subject:
Citrus; biotechnology; cultivars; cytogenetics; fruits; genetic variation; genome; genomics; metabolomics; molecular biology; mutation; phylogeny; plant genetics; proteomics; scions; transcriptomics
Abstract:
... Citrus is an economically important fruit crop growing worldwide, with enormous health benefits. However, conventional citrus breeding has been hindered by a variety of genetic factors, thereby becoming obsolete and insufficient. Citrus research mostly focused on botanical, taxonomic, and cytogenetics issues. Nowadays the knowledge base has strengthened with the plausible outcomes of commercially ...
DOI:
10.1007/s11295-022-01544-z

2. Date palm (Phoenix dactylifera L.) genetic improvement via biotechnological approaches

Author:
Mojtaba Kordrostami; Mohammad Mafakheri; Jameel M. Al-Khayri
Source:
Tree genetics & genomes 2022 v.18 no.3 pp. 26
ISSN:
1614-2942
Subject:
Phoenix dactylifera; backcrossing; biotechnology; dioecy; environmental factors; genetic drift; genetic engineering; genetic improvement; genetic variation; genomics; germplasm conservation; heterozygosity; plant genetics; plant tissues; tissue culture; vegetative propagation; Middle East; Northern Africa
Abstract:
... Date palm (Phoenix dactylifera L.), a monocotyledonous species of the Arecaceae family, is widely cultivated in the arid regions of the Middle East and North Africa. Considering the prolonged generation cycle, the dioecious nature of date palm trees, and high heterozygosity, the traditional breeding approaches in date palm are lengthy and laborious, and numerous crosses and back-crosses all have l ...
DOI:
10.1007/s11295-022-01559-6

3. Differential gene expression in Eucalyptus clones in response to nutrient deficiency

Author:
Bruno Cesar Rossini; Jean-Marc Bouvet; Julien Frouin; Iraê Amaral Guerrini; Talitha Casella Moreira de Freitas; Magali Ribeiro da Silva; Jean-Pierre Bouillet; Jean-Paul Laclau; Celso Luis Marino
Source:
Tree genetics & genomes 2022 v.18 no.2 pp. 14
ISSN:
1614-2942
Subject:
Eucalyptus; fertilizers; gene expression; gene expression regulation; gene ontology; genes; leaves; nitrogen; nutrient deficiencies; phosphorus; plant genetics; potassium; tree growth; tree height; xylem
Abstract:
... We evaluated differential expression of genes in leaf and xylem tissues for three Eucalyptus clones in the field using Illumina sequencing, under four contrasting fertilization regimes: a control combining nitrogen (N), phosphorus (P), and potassium (K) and three regimes with N, K, and P deficiency. The field results showed significantly better performance with a control fertilizing regime for hei ...
DOI:
10.1007/s11295-022-01546-x

4. Filling gaps of reference DNA barcodes in Syzygium from rainforest fragments in Sumatra

Author:
Ridha Wati; Fitri Yola Amandita; Fabian Brambach; Iskandar Z. Siregar; Oliver Gailing; Carina Carneiro de Melo Moura
Source:
Tree genetics & genomes 2022 v.18 no.1 pp. 6
ISSN:
1614-2942
Subject:
DNA barcoding; Syzygium; algorithms; biodiversity; genome; monophyly; plant genetics; rain forests; Indonesia
Abstract:
... Given the difficulties for rapid biodiversity assessments in understudied regions, DNA barcoding appears as a suitable alternative. Still, this approach relies heavily on accurate reference sequence databases for correct taxonomic assignments. In this study, we evaluated the effectiveness of matK, rbcL, and ITS regions for the identification of Myrtaceae species with emphasis on the megadiverse ge ...
DOI:
10.1007/s11295-022-01536-z

5. Genetic diversity and population structure analysis reveals the unique genetic composition of South African selected macadamia accessions

Author:
Mary Ranketse; Charles A. Hefer; Rian Pierneef; Gerda Fourie; Alexander A. Myburg
Source:
Tree genetics & genomes 2022 v.18 no.2 pp. 15
ISSN:
1614-2942
Subject:
Macadamia integrifolia; Macadamia tetraphylla; economic valuation; gene pool; genetic variation; genome; genomics; geographical distribution; germplasm; hybrids; industry; microsatellite repeats; phylogeny; plant genetics; population structure; seeds; Australia; California; Israel; South Africa
Abstract:
... Macadamia nuts are known globally for their high quality and economic value. Global macadamia commercial nut production amounts to 60,000 metric tonnes and is increasing steadily. South Africa is the leading producer with 29% of worldwide kernel production. Commercial macadamia germplasm was originally selected from a small genepool (mainly Macadamia integrifolia species) from a limited geographic ...
DOI:
10.1007/s11295-022-01543-0

6. Genomic breeding values’ prediction including populational selfing rate in an open-pollinated Eucalyptus globulus breeding population

Author:
Marianella Quezada; Ignacio Aguilar; Gustavo Balmelli
Source:
Tree genetics & genomes 2022 v.18 no.2 pp. 10
ISSN:
1614-2942
Subject:
Eucalyptus globulus; disease resistance; forest trees; genetic merit; genome; genomics; heritability; models; open pollination; pedigree; plant genetics; prediction; selfing
Abstract:
... In forest tree breeding programs, open-pollinated families are frequently used to estimate genetic parameters and evaluate genetic merit of individuals. However, the presence of selfing events not documented in the pedigree affects the estimation of these parameters. In this study, 194 open-pollinated families of Eucalyptus globulus Labill. trees were used to compare the precision of estimated gen ...
DOI:
10.1007/s11295-021-01534-7

7. Patterns of genomic diversity and linkage disequilibrium across the disjunct range of the Australian forest tree Eucalyptus globulus

Author:
Jakob B. Butler; Jules S. Freeman; Brad M. Potts; René E. Vaillancourt; Hossein V. Kahrood; Peter K. Ades; Philippe Rigault; Josquin F. G. Tibbits
Source:
Tree genetics & genomes 2022 v.18 no.3 pp. 28
ISSN:
1614-2942
Subject:
Eucalyptus globulus; allelic variation; forest trees; genomics; hybridization; linkage disequilibrium; models; plant genetics; Tasmania
Abstract:
... The evolutionary trajectory of a population both influences and is influenced by characteristics of its genome. A disjunct population, for example is likely to exhibit genomic features distinct from those of continuous populations, reflecting its specific evolutionary history and influencing future recombination outcomes. We examined genetic diversity, population differentiation and linkage disequ ...
DOI:
10.1007/s11295-022-01558-7

8. QTL mapping of polymethoxyflavone (PMF) accumulation in citrus

Author:
Yomi Matsumoto; Takehiro Kubo; Yuri Itami; Md. Zaherul Islam; Satoshi Watanabe; Nobuhiro Kotoda
Source:
Tree genetics & genomes 2022 v.18 no.1 pp. 7
ISSN:
1614-2942
Subject:
Citrus; biochemical pathways; biosynthesis; chromosome mapping; flavanone 3-dioxygenase; genetic distance; genotyping; health promotion; major genes; methyltransferases; plant genetics; polymethoxyflavones; quantitative trait loci; single nucleotide polymorphism
Abstract:
... Polymethoxyflavones (PMFs) are bioactive flavonoids exclusively found in the genus citrus, and they show various health-promoting activities. Researchers have studied the biosynthesis of PMFs and focused on isolation and characterization of the responsible genes. However, our knowledge about the biosynthesis of PMFs is still limited. In this study, we aimed to reveal the loci for causative factors ...
DOI:
10.1007/s11295-022-01539-w

9. Screening clonally replicated Acacia mangium breeding populations for tolerance to Ceratocystis canker and wilt disease

Author:
Jeremy Todd Brawner; Sri Sunarti; Arif Nirsatmanto; Heru Indrayadi; Marthin Tarigan; Muhammad Yuliarto; Sri Rahayu; Eko Bhakti Hardiyanto; Morag Glen; Caroline Mohammed; Anto Rimbawanto
Source:
Tree genetics & genomes 2022 v.18 no.2 pp. 17
ISSN:
1614-2942
Subject:
Acacia mangium; Ceratocystis; clones; disease resistance; genome; heritability; plant genetics; progeny; selection intensity; vascular wilt; Indonesia; Papua New Guinea; Queensland
Abstract:
... Three screening trials of clonally replicated Acacia mangium seedlings were evaluated for survival and lesion length following inoculation with locally collected strains of Ceratocystis in Indonesia. Tolerance in the population was low with 6.7% of the 1033 clones represented by more than 4 ramets surviving repeated inoculations. Differences in tolerance among populations were slight; however, pop ...
DOI:
10.1007/s11295-022-01548-9

10. Spatial genetic structure and mating system in forest tree populations from seasonally dry tropical forests: a review

Author:
Alejandra Lorena Goncalves; María Victoria García; María Eugenia Barrandeguy; Santiago César González-Martínez; Myriam Heuertz
Source:
Tree genetics & genomes 2022 v.18 no.3 pp. 18
ISSN:
1614-2942
Subject:
anemochory; autochory; forest trees; genes; kinship; landscapes; outcrossing; plant genetics; population density; wind; zoochory
Abstract:
... Gene dispersal processes shape demographic and microevolutionary dynamics of tree species. Gene dispersal patterns can be studied by spatially explicit methods. Spatial genetic structure (SGS), summarized in the Sp statistic, provides indirect estimates of gene dispersal across generations for a known or assumed population effective density. Sp is modulated by exogenous and endogenous factors incl ...
DOI:
10.1007/s11295-022-01550-1

11. Strong spatial structuring of clonal genetic diversity within blackthorn (Prunus spinosa) hedgerows and woodlands

Author:
James A. Brown; W. Ian Montgomery; Jim Provan
Source:
Tree genetics & genomes 2022 v.18 no.1 pp. 5
ISSN:
1614-2942
Subject:
Prunus spinosa; asexual reproduction; chloroplasts; climate change; genetic variation; genome; genotype; genotyping; habitat destruction; invasive species; land use change; microsatellite repeats; peatlands; plant genetics
Abstract:
... Hedgerows are an important component of agricultural landscapes, but in recent years have increasingly faced threats such as habitat loss, land use change, climate change, invasive species, pests and plant pathogens. Given the potential importance of genetic diversity in countering these threats, and the spatial distribution of such diversity within and across natural populations, we analyzed leve ...
DOI:
10.1007/s11295-022-01538-x

12. A genetic platform for predicting and reducing non-tenera contamination in oil palm (Elaeis guineensis) seed supply

Author:
Rajinder Singh; Leslie Cheng-Li Ooi; Ngoot-Chin Ting; Eng-Ti Leslie Low; Meilina Ong-Abdullah; Rajanaidu Nookiah; Marhalil Marjuni; Suzana Mustaffa; Mohamad Arif Abdul Manaf; Peggy Garner; Jerry Reed; Corey Wischmeyer; Melissa Beil; Blaire Bacher; Nathan D. Lakey; Jared M. Ordway; Ravigadevi Sambanthamurthi
Source:
Tree genetics & genomes 2021 v.17 no.6 pp. 45
ISSN:
1614-2942
Subject:
Elaeis guineensis; aneuploidy; cost effectiveness; fruits; genes; genotyping; heterozygosity; hybrids; industry; plant genetics; prediction; supply chain
Abstract:
... Optimal oil palm (Elaeis guineensis) crop yields rely on the purity of the tenera fruit form. The high yielding hybrid tenera fruit form is the consequence of heterozygosity for one of nine genetic variants within the SHELL gene. High-throughput genotyping allows cost-efficient screening prior to planting to decrease unintentional non-tenera palm cultivation. We present a paradigm for dramatically ...
DOI:
10.1007/s11295-021-01527-6

13. A high-density genetic map from a cacao F2 progeny and QTL detection for resistance to witches’ broom disease

Author:
Julio Alfonso Chia Wong; Didier Pierre Louis Clement; Pierre Mournet; Analine dos Santos Nascimento; José Luis Solís Bonilla; Uilson Vanderlei Lopes; Jose Luis Pires; Karina Peres Gramacho
Source:
Tree genetics & genomes 2022 v.18 no.4 pp. 31
ISSN:
1614-2942
Subject:
autocorrelation; brooms; chromosome mapping; genomics; glutathione peroxidase; linkage groups; plant genetics; pleiotropy; polygenic inheritance; progeny; tree growth
Abstract:
... The genetic architecture of resistance for witches’ broom disease of cacao (WBD) was reexamined in an F2 population (Sca-6 × ICS-1), addressing symptom-specificity and possible genetic basis for the differences in disease scores from terminal and cushion brooms. A high-density genetic linkage map was constructed with 494 individuals and 2968 SNPs, obtaining 10 linkage groups comprising 1595 centiM ...
DOI:
10.1007/s11295-022-01562-x

14. Advanced genebank management of genetic resources of European wild apple, Malus sylvestris, using genome-wide SNP array data

Author:
Joukje Buiteveld; Herma JJ Koehorst-van Putten; Linda Kodde; Ivo Laros; Giorgio Tumino; Nicholas P. Howard; Eric van de Weg; Marinus J.M. Smulders
Source:
Tree genetics & genomes 2021 v.17 no.4 pp. 32
ISSN:
1614-2942
Subject:
Malus sylvestris; alleles; apples; effective population size; gene banks; genetic relationships; genotyping; haplotypes; introgression; plant genetics; pollination; seed orchards; single nucleotide polymorphism; single nucleotide polymorphism arrays; Netherlands
Abstract:
... The Netherlands’ field genebank collection of European wild apple (Malus sylvestris), consisting of 115 accessions, was studied in order to determine whether duplicates and mistakes had been introduced, and to develop a strategy to optimize the planting design of the collection as a seed orchard. We used the apple 20K Infinium single nucleotide polymorphism (SNP) array, developed in M. domestica, ...
DOI:
10.1007/s11295-021-01513-y

15. Comparison of selection methods for the establishment of a core collection using SSR markers for hazelnut (Corylus avellana L.) accessions from European germplasm repositories

Author:
Paolo Boccacci; Maria Aramini; Matthew Ordidge; Theo J. L. van Hintum; Daniela Torello Marinoni; Nadia Valentini; Jean-Paul Sarraquigne; Anita Solar; Mercè Rovira; Loretta Bacchetta; Roberto Botta
Source:
Tree genetics & genomes 2021 v.17 no.6 pp. 48
ISSN:
1614-2942
Subject:
Corylus avellana; alleles; genetic variation; germplasm; germplasm conservation; hazelnuts; landraces; microsatellite repeats; plant genetics; population structure; Europe
Abstract:
... Hazelnut (Corylus avellana L.) is one of the most important tree nut crops in Europe. Germplasm accessions are conserved in ex situ repositories, located in countries where hazelnut production occurs. In this work, we used ten simple sequence repeat (SSR) markers as the basis to establish a core collection representative of the hazelnut genetic diversity conserved in different European collections ...
DOI:
10.1007/s11295-021-01526-7

16. Correction of database SNP accession numbers misassigned to SNPs of the 8K IRSC apple SNP array

Author:
Daniel A. Edge-Garza; Miguel Villamil-Castro; Dorrie Main; Craig Hardner
Source:
Tree genetics & genomes 2021 v.17 no.2 pp. 17
ISSN:
1614-2942
Subject:
National Center for Biotechnology Information; Rosaceae; apples; data collection; databases; genome; loci; plant genetics; single nucleotide polymorphism arrays
Abstract:
... Accurate SNP locus identifiers are essential for the correct matching and aggregation of multiple historical datasets. The National Center for Biotechnology Information (NCBI) issued unique “submitted SNP identification” numbers (ssIDs) for every published SNP submitted to its database. Discrepant ssID information was discovered for 78 SNPs for the 8K IRSC apple SNP array while attempting to colla ...
DOI:
10.1007/s11295-021-01500-3

17. Early-growth results within a Eucalyptus globulus breeding population suggest limited scope for selection focused on CO2 responsiveness

Author:
Matthew Theodore Brookhouse; David Bush; Milos Ivkovich; Florian Busch; Graham Douglas Farquhar; Elizabeth Pinkard
Source:
Tree genetics & genomes 2022 v.18 no.2 pp. 16
ISSN:
1614-2942
Subject:
carbon; carbon dioxide; genome; germination; greenhouses; open pollination; plant genetics; statistical models; trees
Abstract:
... Increasing [CO₂] may influence commercial crop and timber yield. While selection of genotypes sensitive to elevated [CO₂] (e[CO₂]) appears possible in agricultural crops, there is limited evidence for genotype-by-CO₂ (G × CO₂) interactions in commercial tree species. We examined [CO₂] responsiveness in 124 open-pollinated Eucalyptus globulus ssp. globulus (E. globulus) families with the aim of ass ...
DOI:
10.1007/s11295-022-01547-w

18. Efficient low-cost marker-assisted selection of trees with MALE STERILITY 1 (MS1) in Japanese cedar (Cryptomeria japonica D. Don) using bulk DNA samples

Author:
Masahiro Watanabe; Saneyoshi Ueno; Yoichi Hasegawa; Yoshinari Moriguchi
Source:
Tree genetics & genomes 2022 v.18 no.4 pp. 29
ISSN:
1614-2942
Subject:
Cryptomeria japonica; DNA; alleles; genotyping; heterozygosity; labor; male sterility; marker-assisted selection; mutants; plant genetics; sample size
Abstract:
... Recently, a candidate gene (CJt020762) for MALE STERILITY 1 (MS1) in Cryptomeria japonica has been identified, which made it possible to perform accurate selection of trees with mutant alleles (ms1–1 or ms1–2). Marker-assisted selection (MAS) is an effective method for drastically reducing the time required for a breeding cycle; however, a larger sample size for selection increases the labor and c ...
DOI:
10.1007/s11295-022-01561-y

19. Estimation of genetic parameters associated with frosty pod rot (Moniliophthora roreri) and cacao production in Mexico

Author:
José Luis Solís Bonilla; Uilson Vanderlei Lopes; Alfredo Zamarripa Colmenero; Biaani Beeu Martínez Valencia; Carlos Hugo Avendaño Arrazate; Karina Peres Gramacho
Source:
Tree genetics & genomes 2021 v.17 no.3 pp. 24
ISSN:
1614-2942
Subject:
Moniliophthora roreri; beans; frosty pod rot; genome; heritability; plant genetics; prediction; progeny; statistical analysis; statistical models; trees; Mexico
Abstract:
... Genetic parameters were estimated for frosty pod rot resistance and yield components in cacao using a linear mixed model approach (restricted maximum likelihood and best linear unbiased prediction). Two progeny trials established in the Rosario Izapa Experimental Field of the INIFAP in Chiapas, Mexico, were evaluated for frosty pod rot incidence and yield components, including the number of pods p ...
DOI:
10.1007/s11295-021-01498-8

20. Gene-ecological zonation and population genetic structure of Tectona grandis L.f. in India revealed by genome-wide SSR markers

Author:
Swathi Balakrishnan; Suma Arun Dev; Ambothi Rathnasamy Sakthi; Balasubramanian Vikashini; Reshma Bhasker T; Nochyil Sivan Magesh; Yasodha Ramasamy
Source:
Tree genetics & genomes 2021 v.17 no.4 pp. 33
ISSN:
1614-2942
Subject:
Tectona grandis; climate change; decline; forest trees; gene flow; genetic drift; genetic improvement; genetic structure; genetic variation; habitat destruction; metagenomics; plant genetics; population structure; refuge habitats; tropical wood; India
Abstract:
... Population genomics determines the evolutionary potential of a species by decoding the genetic structure and diversity of populations from diverse eco-geographical gradients. Tectona grandis L.f., being a tropical timber tree species distributed in diverse environmental and geographical conditions, is more responsive to local adaptation. This study investigates the extent of genetic variation of t ...
DOI:
10.1007/s11295-021-01514-x