Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping

Tuyen D. Do, Tri D. Vuong, David Dunn, Michael Clubb, Babu Valliyodan, Gunvant Patil, Pengyin Chen, Dong Xu, Henry T. Nguyen, J. Grover Shannon

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm. In this study, a genome-wide association study (GWAS) was performed to map genomic regions for salt tolerance in a diverse panel of 305 soybean accessions using a single nucleotide polymorphism (SNP) dataset derived from the SoySNP50K iSelect BeadChip. A second GWAS was also conducted in a subset of 234 accessions using another 3.7 M SNP dataset derived from a whole-genome resequencing (WGRS) study. In addition, three gene-based markers (GBM) of the known gene, Glyma03g32900, on Chr. 3 were also integrated into the two datasets. Salt tolerance among soybean lines was evaluated by leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC). Results: For both association studies, a major locus for salt tolerance on Chr. 3 was confirmed by a number of significant SNPs, of which three gene-based SNP markers, Salt-20, Salt14056 and Salt11655, had the highest association with all four traits studied. Also, additional genomic regions on Chrs. 1, 8, and 18 were found to be associated with various traits measured in the second GWAS using the WGRS-derived SNP dataset. Conclusions: A region identified on Chr. 8 was identified to be associated with all four traits and predicted as a new minor locus for salt tolerance in soybean. The candidate genes harbored in this minor locus may help reveal the molecular mechanism involved in salt tolerance and to improve tolerance in soybean cultivars. The significant SNPs will be useful for marker-assisted selection for salt tolerance in soybean breeding programs.

Original languageEnglish (US)
Article number318
JournalBMC Genomics
Volume20
Issue number1
DOIs
StatePublished - Apr 25 2019

Fingerprint

Salt-Tolerance
Soybeans
Genome
Single Nucleotide Polymorphism
Chromosomes, Human, Pair 3
Genome-Wide Association Study
Genes
Chromosomes, Human, Pair 8
Chromosome Mapping
Salinity
Chlorophyll
Breeding
Chlorides
Seeds
Salts
Sodium
Datasets

Keywords

  • Candidate genes
  • Gene-based marker
  • Genome-wide association study (GWAS)
  • Salt tolerance
  • Single nucleotide polymorphism (SNP)
  • Soybean [Glycine max (L.) Merr.)]

PubMed: MeSH publication types

  • Journal Article

Cite this

Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping. / Do, Tuyen D.; Vuong, Tri D.; Dunn, David; Clubb, Michael; Valliyodan, Babu; Patil, Gunvant; Chen, Pengyin; Xu, Dong; Nguyen, Henry T.; Shannon, J. Grover.

In: BMC Genomics, Vol. 20, No. 1, 318, 25.04.2019.

Research output: Contribution to journalArticle

Do, TD, Vuong, TD, Dunn, D, Clubb, M, Valliyodan, B, Patil, G, Chen, P, Xu, D, Nguyen, HT & Shannon, JG 2019, 'Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping', BMC Genomics, vol. 20, no. 1, 318. https://doi.org/10.1186/s12864-019-5662-9
Do, Tuyen D. ; Vuong, Tri D. ; Dunn, David ; Clubb, Michael ; Valliyodan, Babu ; Patil, Gunvant ; Chen, Pengyin ; Xu, Dong ; Nguyen, Henry T. ; Shannon, J. Grover. / Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping. In: BMC Genomics. 2019 ; Vol. 20, No. 1.
@article{381a75525cc14e0580e74fc062536b9d,
title = "Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping",
abstract = "Background: Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm. In this study, a genome-wide association study (GWAS) was performed to map genomic regions for salt tolerance in a diverse panel of 305 soybean accessions using a single nucleotide polymorphism (SNP) dataset derived from the SoySNP50K iSelect BeadChip. A second GWAS was also conducted in a subset of 234 accessions using another 3.7 M SNP dataset derived from a whole-genome resequencing (WGRS) study. In addition, three gene-based markers (GBM) of the known gene, Glyma03g32900, on Chr. 3 were also integrated into the two datasets. Salt tolerance among soybean lines was evaluated by leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC). Results: For both association studies, a major locus for salt tolerance on Chr. 3 was confirmed by a number of significant SNPs, of which three gene-based SNP markers, Salt-20, Salt14056 and Salt11655, had the highest association with all four traits studied. Also, additional genomic regions on Chrs. 1, 8, and 18 were found to be associated with various traits measured in the second GWAS using the WGRS-derived SNP dataset. Conclusions: A region identified on Chr. 8 was identified to be associated with all four traits and predicted as a new minor locus for salt tolerance in soybean. The candidate genes harbored in this minor locus may help reveal the molecular mechanism involved in salt tolerance and to improve tolerance in soybean cultivars. The significant SNPs will be useful for marker-assisted selection for salt tolerance in soybean breeding programs.",
keywords = "Candidate genes, Gene-based marker, Genome-wide association study (GWAS), Salt tolerance, Single nucleotide polymorphism (SNP), Soybean [Glycine max (L.) Merr.)]",
author = "Do, {Tuyen D.} and Vuong, {Tri D.} and David Dunn and Michael Clubb and Babu Valliyodan and Gunvant Patil and Pengyin Chen and Dong Xu and Nguyen, {Henry T.} and Shannon, {J. Grover}",
year = "2019",
month = "4",
day = "25",
doi = "10.1186/s12864-019-5662-9",
language = "English (US)",
volume = "20",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping

AU - Do, Tuyen D.

AU - Vuong, Tri D.

AU - Dunn, David

AU - Clubb, Michael

AU - Valliyodan, Babu

AU - Patil, Gunvant

AU - Chen, Pengyin

AU - Xu, Dong

AU - Nguyen, Henry T.

AU - Shannon, J. Grover

PY - 2019/4/25

Y1 - 2019/4/25

N2 - Background: Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm. In this study, a genome-wide association study (GWAS) was performed to map genomic regions for salt tolerance in a diverse panel of 305 soybean accessions using a single nucleotide polymorphism (SNP) dataset derived from the SoySNP50K iSelect BeadChip. A second GWAS was also conducted in a subset of 234 accessions using another 3.7 M SNP dataset derived from a whole-genome resequencing (WGRS) study. In addition, three gene-based markers (GBM) of the known gene, Glyma03g32900, on Chr. 3 were also integrated into the two datasets. Salt tolerance among soybean lines was evaluated by leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC). Results: For both association studies, a major locus for salt tolerance on Chr. 3 was confirmed by a number of significant SNPs, of which three gene-based SNP markers, Salt-20, Salt14056 and Salt11655, had the highest association with all four traits studied. Also, additional genomic regions on Chrs. 1, 8, and 18 were found to be associated with various traits measured in the second GWAS using the WGRS-derived SNP dataset. Conclusions: A region identified on Chr. 8 was identified to be associated with all four traits and predicted as a new minor locus for salt tolerance in soybean. The candidate genes harbored in this minor locus may help reveal the molecular mechanism involved in salt tolerance and to improve tolerance in soybean cultivars. The significant SNPs will be useful for marker-assisted selection for salt tolerance in soybean breeding programs.

AB - Background: Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm. In this study, a genome-wide association study (GWAS) was performed to map genomic regions for salt tolerance in a diverse panel of 305 soybean accessions using a single nucleotide polymorphism (SNP) dataset derived from the SoySNP50K iSelect BeadChip. A second GWAS was also conducted in a subset of 234 accessions using another 3.7 M SNP dataset derived from a whole-genome resequencing (WGRS) study. In addition, three gene-based markers (GBM) of the known gene, Glyma03g32900, on Chr. 3 were also integrated into the two datasets. Salt tolerance among soybean lines was evaluated by leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC). Results: For both association studies, a major locus for salt tolerance on Chr. 3 was confirmed by a number of significant SNPs, of which three gene-based SNP markers, Salt-20, Salt14056 and Salt11655, had the highest association with all four traits studied. Also, additional genomic regions on Chrs. 1, 8, and 18 were found to be associated with various traits measured in the second GWAS using the WGRS-derived SNP dataset. Conclusions: A region identified on Chr. 8 was identified to be associated with all four traits and predicted as a new minor locus for salt tolerance in soybean. The candidate genes harbored in this minor locus may help reveal the molecular mechanism involved in salt tolerance and to improve tolerance in soybean cultivars. The significant SNPs will be useful for marker-assisted selection for salt tolerance in soybean breeding programs.

KW - Candidate genes

KW - Gene-based marker

KW - Genome-wide association study (GWAS)

KW - Salt tolerance

KW - Single nucleotide polymorphism (SNP)

KW - Soybean [Glycine max (L.) Merr.)]

UR - http://www.scopus.com/inward/record.url?scp=85065025570&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85065025570&partnerID=8YFLogxK

U2 - 10.1186/s12864-019-5662-9

DO - 10.1186/s12864-019-5662-9

M3 - Article

C2 - 31023240

AN - SCOPUS:85065025570

VL - 20

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 318

ER -