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

Zeng, Ailan; Chen, P.; Korth, Kenneth L.; Hancock, Floyd; Pereira, Andy; Brye, Kristofor R.; Wu, Cunxiang; Shi, Ainong

doi:10.1007/s11032-017-0634-8

Cited by 92 publications

(65 citation statements)

References 36 publications

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“…Due to the high genetic diversity of the selected G. soja PIs in this collection, the extent of LD was lower than in other GWAS studies (Hwang et al, 2014;Zhou et al, 2015;Leamy et al, 2017;Zeng et al, 2017), and a higher marker density could be required to make sure that the genome was covered adequately for a GWAS study (Nordborg and Tavaré, 2002). Due to the high genetic diversity of the selected G. soja PIs in this collection, the extent of LD was lower than in other GWAS studies (Hwang et al, 2014;Zhou et al, 2015;Leamy et al, 2017;Zeng et al, 2017), and a higher marker density could be required to make sure that the genome was covered adequately for a GWAS study (Nordborg and Tavaré, 2002).…”

Section: Correlations Among Traitsmentioning

confidence: 66%

“…soja collection used in this study was chosen to represent a maximum genetic diversity of 806 G. soja accessions; therefore, it could have low frequency of specific alleles. Due to the high genetic diversity of the selected G. soja PIs in this collection, the extent of LD was lower than in other GWAS studies (Hwang et al, 2014;Zhou et al, 2015;Leamy et al, 2017;Zeng et al, 2017), and a higher marker density could be required to make sure that the genome was covered adequately for a GWAS study (Nordborg and Tavaré, 2002). In 2011, Ingvarsson and Street (2011) reported that a larger sample size might be required to facilitate the discovery of associations between genetic markers and studied traits.…”

Section: Correlations Among Traitsmentioning

confidence: 99%

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Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

Large

Taliercio

et al. 2019

Crop Science

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The relatively low genetic variation of current US soybean [Glycine max (L.) Merr.] cultivars constrains the improvement of grain yield and other agronomic and seed composition traits. Recently, a substantial effort has been undertaken to introduce novel genetic diversity present in wild soybean (Glycine soja Siebold & Zucc.) into elite cultivars, in both public and private breeding programs. The objectives of this research were to evaluate the phenotypic diversity within a collection of 80 G. soja plant introductions (PIs) in the USDA National Genetic Resources Program and to analyze the correlations between agronomic and seed composition traits. Field tests were conducted in Missouri and North Carolina during 3 yr (2013, 2014, and 2015) in a randomized complete block design. The phenotypic data collected included plant maturity date, seed weight, and the seed concentration of protein, oil, essential amino acids, fatty acid, and soluble carbohydrates. We found that genotype was a significant (P < 0.0001) source of variation for maturity date, seed weight, seed protein and amino acids, seed oil and fatty acids, and seed carbohydrates, and significant correlations were observed between numerous traits. The G. soja PIs generally had lower seed weight, higher seed contents of protein, linolenic acid, raffinose, and stachyose, and lower seed contents of oil and oleic acid than the cultivated soybean G. max lines. The information and data collected in this study will be invaluable in guiding soybean breeders and geneticists in selecting promising G. soja PIs for research and cultivar improvement.

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Section: Correlations Among Traitsmentioning

confidence: 66%

Section: Correlations Among Traitsmentioning

confidence: 99%

Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

Large

Taliercio

et al. 2019

Crop Science

View full text Add to dashboard Cite

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“…Failure to correct for population stratification in GWAS models can lead to false positives, especially if the trait of interest is correlated with the structure of the panel (Wang et al 2005). Several studies in soybean have been reported using the GWAS approach with SNP markers for many different traits, such as seed composition (Hwang et al 2014;Vaughn et al 2014;Bandillo et al 2015;Cao et al 2017), salt tolerance (Patil et al 2016;Zeng et al 2017), carbon isotope composition (Dhanapal et al 2015;Kaler et al 2017a), ureide concentration (Ray et al 2015), agronomic traits (Zhang et al 2015;Contreras-Soto et al 2017;Li et al 2017), chlorophyll traits (Dhanapal et al 2016), local adaptation (Bandillo et al 2017), insect resistance (Chang and Hartman 2017), and canopy wilting (Kaler et al 2017b). These studies have provided a useful way to identify potential genomic regions with high resolution and candidate genes or QTL for traits of interest.…”

mentioning

confidence: 99%

Genome-Wide Association Analyses Reveal Genomic Regions Controlling Canopy Wilting in Soybean

Steketee

Schapaugh

Carter

et al. 2020

G3 Genes|Genomes|Genetics

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Drought stress causes the greatest soybean [Glycine max (L.) Merr.] yield losses among the abiotic stresses in rain-fed U.S. growing areas. Because less than 10% of U.S. soybean hectares are irrigated, combating this stress requires soybean plants which possess physiological mechanisms to tolerate drought for a period of time. Phenotyping for these mechanisms is challenging, and the genetic architecture for these traits is poorly understood. A morphological trait, slow or delayed canopy wilting, has been observed in a few exotic plant introductions (PIs), and may lead to yield improvement in drought stressed fields. In this study, we visually scored wilting during stress for a panel of 162 genetically diverse maturity group VI-VIII soybean lines genotyped with the SoySNP50K iSelect BeadChip. Field evaluation of canopy wilting was conducted under rain-fed conditions at two locations (Athens, GA and Salina, KS) in 2015 and 2016. Substantial variation in canopy wilting was observed among the genotypes. Using a genome-wide association mapping approach, 45 unique SNPs that tagged 44 loci were associated with canopy wilting in at least one environment with one region identified in a single environment and data from across all environments. Several new soybean accessions were identified with canopy wilting superior to those of check genotypes. The germplasm and genomic regions identified can be used to better understand the slow canopy wilting trait and be incorporated into elite germplasm to improve drought tolerance in soybean.

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“…Genome-wide analysis showed that natural variation associated with the Glyma03g32900 gene has a major impact on salt tolerance in soybean. A total of 283 worldwide soybean germplasm lines and the SoySNP50K BeadChip database were used to perform the GWAS for salt tolerance (Zeng et al 2017). A total of 45 SNPs representing nine genomic regions on nine chromosomes were significantly associated with salt tolerance based on GWAS analysis.…”

Section: Gwas For Salt Tolerance In Soybeanmentioning

confidence: 99%

Advances in salinity tolerance of soybean: Genetic diversity, heredity, and gene identification contribute to improving salinity tolerance

Chen

Liu

Zhang

et al. 2018

Journal of Integrative Agriculture

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Salt stress is one of the major abiotic stresses affecting soybean growth. Genetic improvement for salt tolerance is an effective way to protect soybean yield under salt stress conditions. Successful improvement of salt tolerance in soybean relies on identifying genetic variation that confers tolerance in soybean germplasm and subsequently incorporating these genetic resources into cultivars. In this review, we summarize the progress in genetic diversity and genetics of salt tolerance in soybean, which includes identifying genetic diversity for salt tolerant germplasm; mapping QTLs conferring salt tolerance; map-based cloning; and conducting genome-wide association study (GWAS) analysis in soybean. Future research avenues are also discussed, including high throughput phenotyping technology, the CRISPR/Cas9 Genome-Editing System, and genomic selection technology for molecular breeding of salt tolerance.

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

Cited by 92 publications

References 36 publications

Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

Genome-Wide Association Analyses Reveal Genomic Regions Controlling Canopy Wilting in Soybean

Advances in salinity tolerance of soybean: Genetic diversity, heredity, and gene identification contribute to improving salinity tolerance

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