Genome-Wide Association Mapping of Seedling Vigor and Regrowth Vigor in Winter Wheat

Seedling vigor and regrowth ability are important traits for the forage production of winter wheat. The objectives of this study were to map quantitative trait loci (QTL) associated with seedling vigor and regrowth vigor traits using a genome-wide association mapping study (GWAS). Seedling vigor and regrowth vigor were evaluated with shoot length, the number of shoots per plant and shoot dry weight per plant 45 days after planting and 15 days after cutting. A large phenotypic variation was observed for all the traits studied. In total, 12 significant QTL for seedling vigor and 16 for regrowth vigor traits were detected on various chromosomes. Four QTL on chromosomes 2B, 4B, 5A and 7A for seedling vigor co-localized with QTL for regrowth vigor due to significant correlations between corresponding traits of the initial growth and regrowth. A BLAST search using DNA sequences of the significant loci revealed candidate genes playing roles in vegetative and reproductive development in different crop species. The QTL and single-nucleotide polymorphism (SNP) markers identified in this study will be further validated and used for marker-assisted selection of the traits during forage wheat breeding.

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Genome-Wide Association Mapping for Heat and Drought Adaptive Traits in Pea

Genes ◽

10.3390/genes12121897 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1897

Author(s):

Endale G. Tafesse ◽

Krishna K. Gali ◽

V. B. Reddy Lachagari ◽

Rosalind Bueckert ◽

Thomas D. Warkentin

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Vegetation Index ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Adaptive Traits ◽

Flowering Duration ◽

Genome Wide ◽

A Genome

Heat and drought, individually or in combination, limit pea productivity. Fortunately, substantial genetic diversity exists in pea germplasm for traits related to abiotic stress resistance. Understanding the genetic basis of resistance could accelerate the development of stress-adaptive cultivars. We conducted a genome-wide association study (GWAS) in pea on six stress-adaptive traits with the aim to detect the genetic regions controlling these traits. One hundred and thirty-five genetically diverse pea accessions were phenotyped in field studies across three or five environments under stress and control conditions. To determine marker trait associations (MTAs), a total of 16,877 valuable single nucleotide polymorphisms (SNPs) were used in association analysis. Association mapping detected 15 MTAs that were significantly (p ≤ 0.0005) associated with the six stress-adaptive traits averaged across all environments and consistent in multiple individual environments. The identified MTAs were four for lamina wax, three for petiole wax, three for stem thickness, two for the flowering duration, one for the normalized difference vegetation index (NDVI), and two for the normalized pigment and chlorophyll index (NPCI). Sixteen candidate genes were identified within a 15 kb distance from either side of the markers. The detected MTAs and candidate genes have prospective use towards selecting stress-hardy pea cultivars in marker-assisted selection.

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Genome-wide association mapping of the ‘super-soft’ kernel texture in white winter wheat

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03841-y ◽

2021 ◽

Author(s):

Meriem Aoun ◽

Arron H Carter ◽

Brian P Ward ◽

Craig F Morris

Keyword(s):

Winter Wheat ◽

Association Mapping ◽

Genome Wide Association ◽

Kernel Texture ◽

Genome Wide

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Genomic Regions Associated with Virulence in Pyrenophora teres f. teres Identified by Genome-Wide Association Analysis and Biparental Mapping

Phytopathology ◽

10.1094/phyto-10-19-0372-r ◽

2020 ◽

Vol 110 (4) ◽

pp. 881-891 ◽

Cited By ~ 5

Author(s):

Anke Martin ◽

Paula Moolhuijzen ◽

Yongfu Tao ◽

Judy McIlroy ◽

Simon R. Ellwood ◽

...

Keyword(s):

Association Mapping ◽

Population Level ◽

Genome Wide Association ◽

Pyrenophora Teres ◽

Barley Cultivars ◽

Genome Wide ◽

A Genome ◽

Sexual Recombination ◽

Parastagonospora Nodorum ◽

Genomic Regions

Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australian barley cultivars. One hundred eighty-eight P. teres f. teres isolates collected across five Australian states were genotyped using Diversity Arrays Technology sequence markers and phenotyped across 20 different barley genotypes. Association mapping identified 14 different genomic regions associated with virulence, with the majority located on P. teres f. teres chromosomes 3 and 5 and one each present on chromosomes 1, 6, and 9. Four of the regions identified were confirmed by quantitative trait loci (QTL) mapping. The QTL regions are discussed in the context of their genomic architecture together with examination of their gene contents, which identified 20 predicted effectors. The number of QTL shown in this study at the population level clearly illustrates a complex genetic basis of P. teres f. teres virulence compared with pure necrotrophs, such as the wheat pathogens Parastagonospora nodorum and Parastagonospora tritici-repentis.

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Genome-wide association mapping of tan spot resistance (Pyrenophora tritici-repentis) in European winter wheat

Molecular Breeding ◽

10.1007/s11032-014-0039-x ◽

2014 ◽

Vol 34 (2) ◽

pp. 363-371 ◽

Cited By ~ 31

Author(s):

Sonja Kollers ◽

Bernd Rodemann ◽

Jie Ling ◽

Viktor Korzun ◽

Erhard Ebmeyer ◽

...

Keyword(s):

Winter Wheat ◽

Association Mapping ◽

Tan Spot ◽

Genome Wide Association ◽

Pyrenophora Tritici Repentis ◽

Genome Wide ◽

European Winter Wheat

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Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes

PLoS ONE ◽

10.1371/journal.pone.0190964 ◽

2018 ◽

Vol 13 (1) ◽

pp. e0190964 ◽

Cited By ~ 13

Author(s):

Julien Frouin ◽

Antoine Languillaume ◽

Justine Mas ◽

Delphine Mieulet ◽

Arnaud Boisnard ◽

...

Keyword(s):

Association Mapping ◽

Calcium Signaling ◽

Salinity Stress ◽

Genome Wide Association ◽

Japonica Rice ◽

Mapping Study ◽

Genome Wide ◽

A Genome ◽

Association Mapping Study

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Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data

10.21203/rs.2.14709/v2 ◽

2019 ◽

Author(s):

Chiheb Boudhrioua ◽

Maxime Bastien ◽

Davoud Torkamaneh ◽

François Belzile

Keyword(s):

Association Mapping ◽

Sclerotinia Sclerotiorum ◽

Single Gene ◽

Genome Wide Association ◽

Chromosome 1 ◽

Whole Genome ◽

Sclerotinia Stem Rot ◽

Genome Wide ◽

A Genome ◽

The Impact

Abstract Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Chr01) where resistant lines had shorter lesions on the stem by 29 mm . A single gene (Glyma.01g048000) resided in the same LD block as the peak SNP, but it is of unknown function. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Chr01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. These results suggest that this region harbors a promising resistance QTL to SSR that can be used in soybean breeding program.

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