Association analysis of cowpea bacterial blight resistance in USDA cowpea germplasm

Shi, Ainong; Buckley, Blair; Mou, Beiquan; Motes, Dennis; Morris, J. B.; Ma, Jianbing; Xiong, Haizheng; Qin, Jun; Yang, Wei; Chitwood, Jessica; Wang, Yuejin; Lu, Weiguo

doi:10.1007/s10681-015-1610-1

Cited by 46 publications

(36 citation statements)

References 37 publications

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“…This suggests that the cowpea accessions may be grouped into 3 or 4 clusters. Most SNP-based population structure studies in a wide collection of cowpea (size = 116-768 accesions) infered between 2 [32] to 3 clusters [18,25,33].…”

Section: Population Structure and Relationships Between Accessionsmentioning

confidence: 99%

DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

Sodedji

Agbahoungba

Agoyi

et al. 2020

Preprint

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Background: Genetic diversity in a germplasm is crucial for continuous improvement of crop varieties. A panel of 274 cowpea (Vigna unguiculata L.) accessions of unknown genetic diversity was assembled from diverse sources. This study used 3127 SNP markers, generated with the diversity array technology (DArT), to assess genetic diversity, population structure and linkage disequilibrium (LD) in the assembled germplasm.Results: The structure analysis inferred three subpopulations within the germplasm, which was confirmed by Neighbour-Joining (NJ) clustering and principal component analysis (PCA). Low genetic distances (0.005 to 0.44) were observed between accessions. Accessions from Africa; West and Central Africa (113 accessions), East and Central Africa (93 accessions), and Asia (53 accessions) were predominant in the germplasm; and distributed across all subpopulations. High fixation indexes (0.48 ≤ FST≤0.56) were obtained for the inferred subpopulations. AMOVA revealed a very large contribution (99%) of within subpopulations variation to the observed genetic variation in the germplasm. However, the expected heterozygosity (He) was higher than the observed heterozygosity (Ho), indicating high proportion of inbred lines in the germplasm. Linkage Disequilibrium (LD) was observed in the germplasm, particularly on chromosome 6, which showed a low decay along the physical genetic distance between markers in the genome.Conclusions: Significant genetic structuration exists in the assembled cowpea germplasm which shows there is a potential for improvement of the crop. The subgroups consisted mainly of inbred lines which, although from different geographical regions shared alleles in common reflecting high movement of seeds and exchange of germplasm between regions. The presence of linkage disequilibrium in the germplasm paves a way for prospective whole genome-wide association studies in cowpea for quality attributes and important agronomic traits.

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Section: Population Structure and Relationships Between Accessionsmentioning

confidence: 99%

DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

Sodedji

Agbahoungba

Agoyi

et al. 2020

Preprint

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“…Using a randomly selected SNP for conducting a population structure analysis is a valid approach when the use of the complete set of SNPs is computationally heavy as described by Huang et al [52]. Analysis was run using an admixture model along with a correlated allele frequency model, which was independent of each run [53].…”

Section: Population Structure Analysismentioning

confidence: 99%

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Ravelombola¹,

Qin²,

Shi³

et al. 2020

Preprint

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BackgroundSoybean [Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy.Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). Population structure was inferred using STRUCTURE 2.3.4, GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that: a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci (E2, E4, and Dt1) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900, Glyma.19g200800, Glyma.09g196700, and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP (if no annotated genes found close the top one) for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent.Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits in soybean through marker-assisted selection (MAS) and GS in breeding programs. After validation, the candidate genes can be transferred to new cultivars using the linked SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

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“…Out of the 10,259 filtered SNPs, a total of randomly chosen 5,129 SNPs were used for inferring population structure (K).. Analysis was run using an admixture model along with a correlated allele frequency model, which was independent of each run (Shi et al 2016).…”

Section: Population Structure Analysismentioning

confidence: 99%

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Ravelombola

Qin²,

Shi

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci ( E2 , E4 , and Dt1 ) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent. Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

show abstract

Association analysis of cowpea bacterial blight resistance in USDA cowpea germplasm

Cited by 46 publications

References 37 publications

DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

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