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1. Karnal bunt of wheat: Etiology, breeding and integrated management

Author:
Kumar, Satish; Singroha, Garima; Singh, Gyanendra Pratap; Sharma, Pradeep
Source:
Crop protection 2021 v.139 pp. 105376
ISSN:
0261-2194
Subject:
quantitative trait loci,   etc   ; Tilletia indica; Triticum; chromosome mapping; climate change; exports; genes; genotype; globalization; host-pathogen relationships; humidity; imports; karnal bunt; pathogenesis; plant breeding; plant pathogenic fungi; quarantine; temperature; trade liberalization; transportation; wheat; winter; India;     Show all 23 Subjects
Abstract:
... Karnal bunt (KB) of wheat caused by Tilletia indica Mitra (Nevossia indica Mundkur), was first reported in Karnal, India, in 1931 hence named as ‘Karnal bunt’. The disease mainly occurs in wheat growing regions with low winter temperatures and high humidity. The disease is a major concern for wheat import and export countries as the fungus is listed as causing a quarantine disease by many countrie ...
DOI:
10.1016/j.cropro.2020.105376

2. A taxonomic conundrum: Characterizing a cryptic radiation of Asian gracile skinks (Squamata: Scincidae: Riopa) in Myanmar

Author:
Freitas, Elyse S.; Miller, Aryeh H.; Reynolds, R. Graham; Siler, Cameron D.
Source:
Molecular phylogenetics and evolution 2020 v.146 pp. 106754
ISSN:
1055-7903
Subject:
quantitative traits,   etc   ; Scincidae; genetic variation; phylogeny; species diversity; Myanmar;     Show all 6 Subjects
Abstract:
... Recognizing species-level diversity is important for studying evolutionary patterns across biological disciplines and is critical for conservation efforts. However, challenges remain in delimiting species-level diversity, especially in cryptic radiations where species are genetically divergent but show little morphological differentiation. Using multilocus molecular data, phylogenetic analyses, sp ...
DOI:
10.1016/j.ympev.2020.106754

3. Complete Genome Sequence Resource for the Necrotrophic Plant-Pathogenic Bacterium Pectobacterium carotovorum WPP14

Author:
Liu, Yingyu; Helmann, Tyler C.; Stodghill, Paul; Filiatrault, Melanie J.
Source:
Plant disease 2021 v.105 no.1 pp. 196-198
ISSN:
0191-2917
Subject:
quantitative trait loci,   etc   ; Pectobacterium carotovorum; Puccinia striiformis f. tritici; Triticum; breeding lines; breeding programs; cultivars; disease resistance; durability; fungi; genetic markers; genome-wide association study; genotyping; loci; mature plants; nucleotide sequences; plant breeding; plant pathogenic bacteria; races; resistance genes; seedlings; stripe rust; virulence; winter wheat; Washington (state);     Show all 25 Subjects
Abstract:
... Pectobacterium spp. are a major cause of loss in vegetable and ornamental plant production. One of these species, Pectobacterium carotovorum, can cause soft rot disease on many plants, particularly potato. These diseases lead to significant economic loss and pose food security threats by reducing crop yields in the field, in transit, and during storage. The Gram-negative enterobacterium P. carotov ...
Handle:
10113/7071259
DOI:
10.1094/PDIS-05-20-1059-A

4. Silver-nanoparticle and abscisic acid modulate sub1A quantitative trait loci functioning towards submergence tolerance in rice (Oryza sativa L.)

Author:
Saha, Indraneel; Hasanuzzaman, Mirza; Dolui, Debabrata; Sikdar, Debdas; Debnath, Subhas Chandra; Adak, Malay Kumar
Source:
Environmental and experimental botany 2021 v.181 pp. 104276
ISSN:
0098-8472
Subject:
quantitative trait loci,   etc   ; NAD(P)H oxidase (H2O2-forming); NADP (coenzyme); Oryza sativa; abscisic acid; alcohol dehydrogenase; anaerobiosis; beta-fructofuranosidase; chlorophyll; ethylene; flavonoids; flooding tolerance; genotype; hydrogen peroxide; lycopene; nanosilver; net assimilation rate; phenolic compounds; phosphorylase; proline; rice; seedlings; starch; submergence; sucrose synthase; water content;     Show all 26 Subjects
Abstract:
... An experiment was conducted to explore the silver-nanoparticles (Ag-NPs) and abscisic acid (ABA) to elicit sub1A quantitative trait loci (QTL) responses under submergence stress. Rice genotypes cv. Swarna and Swarna Sub1 were pre-treated with 100 mg ml⁻¹Ag-NP [Ag-NP(+)] and 10 μM ABA [ABA(+)] at 7-day-old seedlings for 1 day in two separate sets and subsequent transfer to complete submergence for ...
DOI:
10.1016/j.envexpbot.2020.104276

5. Correction to: Quantitative trait mapping in Diversity Outbred mice identifies two genomic regions associated with heart size

Author:
Shorter, John R.; Huang, Wei; Beak, Ju Youn; Hua, Kunjie; Gatti, Daniel M.; de Villena, Fernando Pardo-Manuel; Pomp, Daniel; Jensen, Brian C.
Source:
Mammalian genome 2019 v.30 no.1-2 pp. 42
ISSN:
0938-8990
Subject:
quantitative traits,   etc   ; genomics; heart; mice;     Show all 4 Subjects
Abstract:
... The original article has been published with an incorrect text in Materials and Methods section. The corrected text should read as. ...
DOI:
10.1007/s00335-018-9789-9

6. CUBIC: an atlas of genetic architecture promises directed maize improvement

Author:
Liu, Hai-Jun; Wang, Xiaqing; Xiao, Yingjie; Luo, Jingyun; Qiao, Feng; Yang, Wenyu; Zhang, Ruyang; Meng, Yijiang; Sun, Jiamin; Yan, Shijuan; Peng, Yong; Niu, Luyao; Jian, Liumei; Song, Wei; Yan, Jiali; Li, Chunhui; Zhao, Yanxin; Liu, Ya; Warburton, Marilyn L.; Zhao, Jiuran; Yan, Jianbing
Source:
Genome biology 2020 v.21 no.1 pp. 20
ISSN:
1474-760X
Subject:
quantitative trait loci; quantitative traits,   etc   ; Zea mays; agronomic traits; case studies; corn; epistasis; genes; genome mining; genotype-phenotype correlation; heritability; leaf width; phenotypic variation; single nucleotide polymorphism;     Show all 14 Subjects
Abstract:
... BACKGROUND: Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we present the Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population, consisting of 1404 individuals created by extensively inter-crossing 24 widely used Chi ...
DOI:
10.1186/s13059-020-1930-x
PubMed:
31980033
PubMed Central:
PMC6979394

7. Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface

Author:
Besnier, Francois; Solberg, Monica F.; Harvey, Alison C.; Carvalho, Gary R.; Bekkevold, Dorte; Taylor, Martin I.; Creer, Simon; Nielsen, Einar E.; Skaala, Øystein; Ayllon, Fernando; Dahle, Geir; Glover, Kevin A.
Source:
BMC genetics 2020 v.21 no.1 pp. 13
ISSN:
1471-2156
Subject:
quantitative trait loci; quantitative traits,   etc   ; Salmo salar; alleles; aquaculture; breeding programs; data collection; epistasis; fish; genetic variation; inheritance (genetics); loci; phenotype; phenotypic variation; prediction; variance;     Show all 16 Subjects
Abstract:
... BACKGROUND: Quantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domest ...
DOI:
10.1186/s12863-020-0816-y
PubMed:
32033538
PubMed Central:
PMC7006396

8. Combining Random Forests and a Signal Detection Method Leads to the Robust Detection of Genotype-Phenotype Associations

Author:
Ramzan, Faisal; Gültas, Mehmet; Bertram, Hendrik; Cavero, David; Schmitt, Armin Otto
Source:
Genes 2020 v.11 no.8
ISSN:
2073-4425
Subject:
quantitative trait loci; quantitative traits,   etc   ; case studies; egg quality; genes; genome-wide association study; genomics; genotype-phenotype correlation; loci; phenotype; single nucleotide polymorphism;     Show all 11 Subjects
Abstract:
... Genome wide association studies (GWAS) are a well established methodology to identify genomic variants and genes that are responsible for traits of interest in all branches of the life sciences. Despite the long time this methodology has had to mature the reliable detection of genotype–phenotype associations is still a challenge for many quantitative traits mainly because of the large number of ge ...
DOI:
10.3390/genes11080892

9. Spike morphology alternations in androgenic progeny of hexaploid triticale (× Triticosecale Wittmack) caused by nullisomy of 2R and 5R chromosomes

Author:
Kwiatek, Michał T.; Banaszak, Zofia; Skowrońska, Roksana; Kurasiak-Popowska, Danuta; Mikołajczyk, Sylwia; Niemann, Janetta; Tomkowiak, Agnieszka; Weigt, Dorota; Nawracała, Jerzy
Source:
In vitro cellular & developmental biology 2020 v.56 no.2 pp. 150-158
ISSN:
1054-5476
Subject:
quantitative trait loci; quantitative traits,   etc   ; Triticosecale; androgenesis; chromosomes; doubled haploids; epigenetics; fluorescence in situ hybridization; hexaploidy; homozygosity; karyotyping; nullisomics; progeny; spikelets; spikes (plant); triticale;     Show all 16 Subjects
Abstract:
... Induction of androgenesis, followed by chromosome doubling, is a crucial method to obtain complete homozygosity in one-generation route. However, in vitro androgenesis can result in various genetic and epigenetic changes in derived triticale plants. In this study, we evaluated chromosome alternations and we associated them with the changes of spike morphology in androgenic progeny of triticale. We ...
DOI:
10.1007/s11627-019-10021-7

10. Linkage‐linkage disequilibrium dissection of the epigenetic quantitative trait loci (epiQTLs) underlying growth and wood properties in Populus

Author:
Lu, Wenjie; Xiao, Liang; Quan, Mingyang; Wang, Qingshi; El‐Kassaby, Yousry A.; Du, Qingzhang; Zhang, Deqiang
Source:
Thenew phytologist 2020 v.225 no.3 pp. 1218-1233
ISSN:
0028-646X
Subject:
quantitative trait loci; quantitative traits,   etc   ; DNA methylation; Populus; epigenetics; forest trees; gene expression; genes; linkage groups; phenotype; phenotypic variation; progeny; wood; wood properties;     Show all 14 Subjects
Abstract:
... Increasing evidence indicates that DNA methylation is heritable and serves as an essential marker contributing to phenotypic variation. Linkage‐linkage disequilibrium mapping was used to decipher the epigenetic architecture underlying nine growth and wood property traits in a linkage population (550 F₁ progeny) and a natural population (435 unrelated individuals) of Populus using methylation‐sensi ...
DOI:
10.1111/nph.16220

11. Whole-genome sequencing identifies potential candidate genes for reproductive traits in pigs

Author:
Li, Xinjian; Ye, Jianwei; Han, Xuelei; Qiao, Ruimin; Li, Xiuling; Lv, Gang; Wang, Kejun
Source:
Genomics 2020 v.112 no.1 pp. 199-206
ISSN:
0888-7543
Subject:
quantitative trait loci; quantitative traits,   etc   ; environmental factors; litter size; major genes; reproductive performance; reproductive traits; sequence analysis; signal transduction; single nucleotide polymorphism; sows; transforming growth factor beta;     Show all 12 Subjects
Abstract:
... Reproductive performance is a complex quantitative trait, that is determined by multiple genes, regulatory pathways and environmental factors. A list of major genes with large effect have been detected, although multiple QTLs are identified. To identify candidate genes for pig prolificacy, whole genome variants from five high- and five low-prolificacy Yorkshire sows were collected using whole-geno ...
DOI:
10.1016/j.ygeno.2019.01.014

12. QTL.gCIMapping.GUI v2.0: An R software for detecting small-effect and linked QTLs for quantitative traits in bi-parental segregation populations

Author:
Zhang, Ya-Wen; Wen, Yang-Jun; Dunwell, Jim M.; Zhang, Yuan-Ming
Source:
Computational and Structural Biotechnology Journal 2020 v.18 pp. 59-65
ISSN:
2001-0370
Subject:
quantitative trait loci; quantitative traits,   etc   ; Bayesian theory; backcrossing; chromosome mapping; computer software; data collection; doubled haploids; genes; inbred lines; probability; rice; user interface;     Show all 13 Subjects
Abstract:
... The methodologies and software packages for mapping quantitative trait loci (QTLs) in bi-parental segregation populations are well established. However, it is still difficult to detect small-effect and linked QTLs. To address this issue, we proposed a genome-wide composite interval mapping (GCIM) in bi-parental segregation populations. To popularize this method, we developed an R package. This pro ...
DOI:
10.1016/j.csbj.2019.11.005
PubMed:
31890145
PubMed Central:
PMC6921137

13. Analysis of QTL for Grain Size in a Rice Chromosome Segment Substitution Line Z1392 with Long Grains and Fine Mapping of qGL-6

Author:
Zhang, Ting; Wang, Shiming; Sun, Shuangfei; Zhang, Yi; Li, Juan; You, Jing; Su, Tian; Chen, Wenbo; Ling, Yinghua; He, Guanghua; Zhao, Fangming
Source:
Rice 2020 v.13 no.1 pp. 40
ISSN:
1939-8425
Subject:
quantitative trait loci,   etc   ; additive effect; alleles; chromosomes; epistasis; genotype; grain yield; inheritance (genetics); rice; substitution lines;     Show all 10 Subjects
Abstract:
... BACKGROUND: Grain size affects not only rice yield but is also an important element in quality of appearance. However, the mechanism for inheritance of grain size is unclear. RESULTS: A rice chromosome segment substitution line Z1392, which harbors three substitution segments and produces grains of increased length, was identified. The three chromosome segments were located on chromosomes 1, 5, an ...
DOI:
10.1186/s12284-020-00399-z

14. Identification of Blast Resistance QTLs Based on Two Advanced Backcross Populations in Rice

Author:
Jiang, Haichao; Feng, Yutao; Qiu, Lei; Gao, Guanjun; Zhang, Qinglu; He, Yuqing
Source:
Rice 2020 v.13 no.1 pp. 31
ISSN:
1939-8425
Subject:
quantitative trait loci,   etc   ; backcrossing; blast disease; phenotypic variation; resistance genes; rice;     Show all 6 Subjects
Abstract:
... BACKGROUND: Rice blast is an economically important and mutable disease of rice. Using host resistance gene to breed resistant varieties has been proven to be the most effective and economical method to control rice blast and new resistance genes or quantitative trait loci (QTLs) are then needed. RESULTS: In this study, we constructed two advanced backcross population to mapping blast resistance Q ...
DOI:
10.1186/s12284-020-00392-6

15. Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits

Author:
Gleason, Kevin J.; Yang, Fan; Pierce, Brandon L.; He, Xin; Chen, Lin S.
Source:
Genome biology 2020 v.21 no.1 pp. 236
ISSN:
1474-760X
Subject:
quantitative trait loci,   etc   ; genes; linkage disequilibrium; loci; pleiotropy; single nucleotide polymorphism; statistics;     Show all 7 Subjects
Abstract:
... To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies. Primo examines association patterns of SNPs to complex and omics traits. In gene regions harboring known susce ...
DOI:
10.1186/s13059-020-02125-w

16. sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression

Author:
He, Yuan; Chhetri, Surya B.; Arvanitis, Marios; Srinivasan, Kaushik; Aguet, François; Ardlie, Kristin G.; Barbeira, Alvaro N.; Bonazzola, Rodrigo; Im, Hae Kyung; Brown, Christopher D.; Battle, Alexis
Source:
Genome biology 2020 v.21 no.1 pp. 235
ISSN:
1474-760X
Subject:
quantitative trait loci,   etc   ; etiology; gene expression regulation; genes; humans; models; tissues; transcription factors;     Show all 8 Subjects
Abstract:
... Genetic regulation of gene expression, revealed by expression quantitative trait loci (eQTLs), exhibits complex patterns of tissue-specific effects. Characterization of these patterns may allow us to better understand mechanisms of gene regulation and disease etiology. We develop a constrained matrix factorization model, sn-spMF, to learn patterns of tissue-sharing and apply it to 49 human tissues ...
DOI:
10.1186/s13059-020-02129-6

17. Natural Variation in Plant Pluripotency and Regeneration

Author:
Lardon, Robin; Geelen, Danny
Source:
Plants 2020 v.9 no.10
ISSN:
2223-7747
Subject:
quantitative trait loci,   etc   ; Arabidopsis; epigenetics; explants; genetic factors; homeotic genes; in vitro regeneration; organogenesis; plant tissues;     Show all 9 Subjects
Abstract:
... Plant regeneration is essential for survival upon wounding and is, hence, considered to be a strong natural selective trait. The capacity of plant tissues to regenerate in vitro, however, varies substantially between and within species and depends on the applied incubation conditions. Insight into the genetic factors underlying this variation may help to improve numerous biotechnological applicati ...
DOI:
10.3390/plants9101261

18. A major and stable QTL controlling wheat thousand grain weight: identification, characterization, and CAPS marker development

Author:
Duan, Xixian; Yu, Haixia; Ma, Wujun; Sun, Jiaqiang; Zhao, Yun; Yang, Rongchang; Ning, Tangyuan; Li, Qingfang; Liu, Qianqian; Guo, Tingting; Yan, Min; Tian, Jichun; Chen, Jiansheng
Source:
Molecular breeding 2020 v.40 no.7 pp. 68
ISSN:
1380-3743
Subject:
quantitative trait loci,   etc   ; Triticum aestivum; cultivars; genes; grain yield; loci; marker-assisted selection; wheat;     Show all 8 Subjects
Abstract:
... Thousand grain weight (TGW) is one of the three crucial determinants of wheat (Triticum aestivum) grain yield. The identification of functional genes and development of closely linked markers are urgently needed for wheat yield improvements. In this study, quantitative trait locus (QTL) mapping for TGW was carried out using one RIL population in four environments. A total of 8 QTL controlling TGW ...
DOI:
10.1007/s11032-020-01147-3

19. Genetic diversity in muskmelon based on SSR markers and morphological traits under well-watered and water-deficit condition

Author:
Ansari, Waquar Akhter; Atri, Neelam; Yang, Luming; Singh, Bijendra; Pandey, Sudhakar
Source:
Biocatalysis and agricultural biotechnology 2020 v.26 pp. 101630
ISSN:
1878-8181
Subject:
quantitative traits,   etc   ; alleles; branching; females; flowering; fruits; genetic variation; genotype; horticulture; loci; males; microsatellite repeats; muskmelons;     Show all 13 Subjects
Abstract:
... In the present study genetic diversity among 48 muskmelon accessions was analyzed employing various morphological traits under well-watered and water-deficit condition and SSR markers. Maximum values for horticultural traits were, 44 cm for fruit polar circumference, 33.2 cm for fruit equatorial circumference, 21 for number of fruits, 41.5 for days to first male flowering, 44 for days to 50% male ...
DOI:
10.1016/j.bcab.2020.101630

20. The genetics of exapted resistance to two exotic pathogens in pedunculate oak

Author:
Bartholomé, Jérôme; Brachi, Benjamin; Marçais, Benoit; Mougou‐Hamdane, Amira; Bodénès, Catherine; Plomion, Christophe; Robin, Cécile; Desprez‐Loustau, Marie‐Laure
Source:
Thenew phytologist 2020 v.226 no.4 pp. 1088-1103
ISSN:
0028-646X
Subject:
quantitative trait loci,   etc   ; Erysiphe alphitoides; Phytophthora cinnamomi; Quercus robur; genomics; hosts; pathogens; phenotypic variation; proteins;     Show all 9 Subjects
Abstract:
... Exotic pathogens cause severe damage in natural populations in the absence of coevolutionary dynamics with their hosts. However, some resistance to such pathogens may occur in naive populations. The objective of this study was to investigate the genetics of this so‐called ‘exapted’ resistance to two pathogens of Asian origin (Erysiphe alphitoides and Phytophthora cinnamomi) in European oak. Host–p ...
DOI:
10.1111/nph.16319