Genome-wide association study (GWAS) of salt tolerance in worldwide soybean germplasm lines View Full Text


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Article Info

DATE

2017-03-06

AUTHORS

A. Zeng, P. Chen, K. Korth, F. Hancock, A. Pereira, K. Brye, C. Wu, A. Shi

ABSTRACT

Salt is a severe abiotic stress causing soybean yield loss in saline soils and irrigated fields. Marker-assisted selection (MAS) is a powerful genomic tool for improving the efficiency of breeding salt-tolerant soybean varieties. The objectives of this study were to uncover novel single-nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs) associated with salt tolerance and to confirm the previously identified genomic regions and SNPs for salt tolerance. A total of 283 diverse soybean plant introductions (PIs) were screened for salt tolerance in the greenhouse based on leaf chloride concentrations and leaf chlorophyll concentrations after 12–18 days of 120-mM NaCl treatment. A total of 33,009 SNPs across 283 genotypes from the Illumina Infinium SoySNP50K BeadChip database were employed in the association analysis with leaf chloride concentrations and leaf chlorophyll concentrations. Genome-wide association mapping showed that 45 SNPs representing nine genomic regions on chromosomes (Chr.) 2, 3, 7, 8, 10, 13, 14, 16, and 20 were significantly associated with both leaf chloride concentrations and leaf chlorophyll concentrations in 2014, 2015, and combined years. A total of 31 SNPs on Chr. 3 were mapped at or near the previously reported major salt tolerance QTL. The significant SNP on Chr. 2 was also in proximity to the previously reported SNP for salt tolerance. The other significant SNPs represent seven putative novel QTLs for salt tolerance. The significant SNP markers on Chr. 2, 3, 14, 16, and 20, which were identified in both general linear model and mixed linear model, were highly recommended for MAS in breeding salt-tolerant soybean varieties. More... »

PAGES

30

References to SciGraph publications

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  • 2011-01-14. Identification and validation of a major QTL for salt tolerance in soybean in EUPHYTICA
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  • 2004-09-09. A major QTL conditioning salt tolerance in S-100 soybean and descendent cultivars in THEORETICAL AND APPLIED GENETICS
  • 2014-07-09. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing in NATURE COMMUNICATIONS
  • 2015-10-30. Genome-wide association study, genomic prediction and marker-assisted selection for seed weight in soybean (Glycinemax) in THEORETICAL AND APPLIED GENETICS
  • 2014-09-23. Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean in BMC GENOMICS
  • 2005-12-25. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness in NATURE GENETICS
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  • 2012-04-25. Genome-wide association analysis detecting significant single nucleotide polymorphisms for chlorophyll and chlorophyll fluorescence parameters in soybean (Glycine max) landraces in EUPHYTICA
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    http://scigraph.springernature.com/pub.10.1007/s11032-017-0634-8

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    52 diverse soybean plant introductions
    53 efficiency
    54 field
    55 general linear model
    56 genome-wide association mapping
    57 genome-wide association studies
    58 genomic regions
    59 genomic tools
    60 genotypes
    61 germplasm lines
    62 greenhouse
    63 introduction
    64 leaf chloride concentrations
    65 leaf chlorophyll concentration
    66 linear model
    67 lines
    68 loci
    69 loss
    70 major salt tolerance QTL
    71 mapping
    72 markers
    73 model
    74 novel quantitative trait loci
    75 novel single-nucleotide polymorphisms
    76 objective
    77 plant introductions
    78 polymorphism
    79 powerful genomic tools
    80 proximity
    81 putative novel QTLs
    82 quantitative trait loci
    83 region
    84 saline soils
    85 salt
    86 salt tolerance
    87 salt tolerance quantitative trait locus
    88 salt-tolerant soybean varieties
    89 selection
    90 severe abiotic stresses
    91 significant SNP markers
    92 significant single-nucleotide polymorphisms
    93 single-nucleotide polymorphisms
    94 soil
    95 soybean germplasm lines
    96 soybean plant introductions
    97 soybean varieties
    98 soybean yield loss
    99 stress
    100 study
    101 tolerance
    102 tolerance quantitative trait locus
    103 tool
    104 total
    105 trait loci
    106 treatment
    107 variety
    108 worldwide soybean germplasm lines
    109 years
    110 yield loss
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