Genome-Wide Association Study of Kernel Traits in Aegilops tauschii

Aegilops tauschii is the diploid progenitor of the D subgenome of hexaploid wheat (Triticum aestivum L.). Here, the phenotypic data of kernel length (KL), kernel width (KW), kernel volume (KV), kernel surface area (KSA), kernel width to length ratio (KWL), and hundred-kernel weight (HKW) for 223 A. tauschii accessions were gathered across three continuous years. Based on population structure analysis, 223 A. tauschii were divided into two subpopulations, namely T-group (mainly included A. tauschii ssp. tauschii accessions) and S-group (mainly included A. tauschii ssp. strangulata). Classifications based on cluster analysis were highly consistent with the population structure results. Meanwhile, the extent of linkage disequilibrium decay distance (r2 = 0.5) was about 110 kb and 290 kb for T-group and S-group, respectively. Furthermore, a genome-wide association analysis was performed on these kernel traits using 6,723 single nucleotide polymorphism (SNP) markers. Sixty-six significant markers, distributed on all seven chromosomes, were identified using a mixed linear model explaining 4.82–13.36% of the phenotypic variations. Among them, 15, 28, 22, 14, 21, and 13 SNPs were identified for KL, KW, KV, KSA, KWL, and HKW, respectively. Moreover, six candidate genes that may control kernel traits were identified (AET2Gv20774800, AET4Gv20799000, AET5Gv20005900, AET5Gv20084100, AET7Gv20644900, and AET5Gv21111700). The transfer of beneficial genes from A. tauschii to wheat using marker-assisted selection will broaden the wheat D subgenome improve the efficiency of breeding.

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Genome-Wide Association Mapping of Late Blight Tolerance Trait in Potato (Solanum tuberosum L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.714575 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fang Wang ◽

Meiling Zou ◽

Long Zhao ◽

Zhiqiang Xia ◽

Jian Wang

Keyword(s):

Solanum Tuberosum ◽

Late Blight ◽

Potato Breeding ◽

Genome Wide Association Study ◽

Solanum Tuberosum L ◽

Potato Cultivars ◽

Genome Wide Association ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome

Uncovering the genetic basis and optimizing the late blight tolerance trait in potatoes (Solanum tuberosum L.) are crucial for potato breeding. Late blight disease is one of the most significant diseases hindering potato production. The traits of late blight tolerance were evaluated for 284 potato cultivars to identify loci significantly associated with the late blight tolerance trait. Of all, 37 and 15 were the most tolerant to disease, and 107 and 30 were the most susceptible. A total of 22,489 high-quality single-nucleotide polymorphisms and indels were identified in 284 potato cultivars. All the potato cultivars were clustered into eight subgroups using population structure analysis and principal component analysis, which were consistent with the results of the phylogenetic tree analysis. The average genetic diversity for all 284 potato cultivars was 0.216, and the differentiation index of each subgroup was 0.025–0.149. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about 0.9 kb. A genome-wide association study using a mixed linear model identified 964 loci significantly associated with the late blight tolerance trait. Fourteen candidate genes for late blight tolerance traits were identified, including genes encoding late blight tolerance protein, chitinase 1, cytosolic nucleotide-binding site–leucine-rich repeat tolerance protein, protein kinase, ethylene-responsive transcription factor, and other potential plant tolerance-related proteins. This study provides novel insights into the genetic architecture of late blight tolerance traits and will be helpful for late blight tolerance in potato breeding.

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Genome-wide association study in New York Phytophthora capsici isolates reveals loci involved in mating type and mefenoxam sensitivity

10.1101/2020.04.01.020826 ◽

2020 ◽

Author(s):

Gregory Vogel ◽

Michael A. Gore ◽

Christine D. Smart

Keyword(s):

New York ◽

Population Structure ◽

Association Study ◽

Candidate Genes ◽

Mating Type ◽

Genome Wide Association Study ◽

Phytophthora Capsici ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

AbstractPhytophthora capsici is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) State and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single-nucleotide polymorphism (SNP) genotyped 252 P. capsici isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam insensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FST between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam insensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA Polymerase I, the enzyme that has been hypothesized to be the target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of P. capsici and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.

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Population structure and genetic basis of the stripe rust resistance of 140 Chinese wheat landraces revealed by a genome-wide association study

Plant Science ◽

10.1016/j.plantsci.2020.110688 ◽

2020 ◽

Vol 301 ◽

pp. 110688

Author(s):

Fangjie Yao ◽

Li Long ◽

Yuqi Wang ◽

Luyao Duan ◽

Xuyang Zhao ◽

...

Keyword(s):

Population Structure ◽

Association Study ◽

Rust Resistance ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Stripe Rust Resistance ◽

Genome Wide ◽

A Genome ◽

Chinese Wheat

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Genome-Wide Association Study in New York Phytophthora capsici Isolates Reveals Loci Involved in Mating Type and Mefenoxam Sensitivity

Phytopathology ◽

10.1094/phyto-04-20-0112-fi ◽

2020 ◽

pp. PHYTO-04-20-011

Author(s):

Gregory Vogel ◽

Michael A. Gore ◽

Christine D. Smart

Keyword(s):

New York ◽

Population Structure ◽

Association Study ◽

Candidate Genes ◽

Mating Type ◽

Genome Wide Association Study ◽

Phytophthora Capsici ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

Phytophthora capsici is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) state and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single nucleotide polymorphism (SNP) genotyped 252 P. capsici isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam sensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FST between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam sensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA polymerase I, the hypothesized target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of P. capsici and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.

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Genome-Wide Association Study in Wheat Identifies Resistance to the Cereal Cyst Nematode Heterodera filipjevi

Phytopathology ◽

10.1094/phyto-02-16-0054-fi ◽

2016 ◽

Vol 106 (10) ◽

pp. 1128-1138 ◽

Cited By ~ 21

Author(s):

Shree R. Pariyar ◽

Abdelfattah A. Dababat ◽

Wiebke Sannemann ◽

Gul Erginbas-Orakci ◽

Abdelnaser Elashry ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Phenotypic Diversity ◽

Cyst Nematode ◽

Genome Wide Association ◽

Cyst Nematodes ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome ◽

Heterodera Filipjevi

The cyst nematode Heterodera filipjevi is a plant parasite causing substantial yield loss in wheat. Resistant cultivars are the preferred method of controlling cyst nematodes. Association mapping is a powerful approach to detect associations between phenotypic variation and genetic polymorphisms; in this way favorable traits such as resistance to pathogens can be located. Therefore, a genome-wide association study of 161 winter wheat accessions was performed with a 90K iSelect single nucleotide polymorphism (SNP) chip. Population structure analysis grouped into two major subgroups and first principal component accounted 6.16% for phenotypic diversity. The genome-wide linkage disequilibrium across wheat was 3 cM. Eleven quantitative trait loci (QTLs) on chromosomes 1AL, 2AS, 2BL, 3AL, 3BL, 4AS, 4AL, 5BL, and 7BL were identified using a mixed linear model false discovery rate of P < 0.01 that explained 43% of total genetic variation. This is the first report of QTLs conferring resistance to H. filipjevi in wheat. Eight QTLs on chromosomes 1AL, 2AS, 2BL, 3AL, 4AL, and 5BL were linked to putative genes known to be involved in plant−pathogen interactions. Two other QTLs on 3BL and one QTL on 7BL linked to putative genes known to be involved in abiotic stress.

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