Linkage and association study discovered loci and candidate genes for glycinin and β-conglycinin in soybean (Glycine max L. Merr.)

2021 ◽  
Author(s):  
Shanshan Zhang ◽  
Hongyang Du ◽  
Yujie Ma ◽  
Haiyang Li ◽  
Guizhen Kan ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Candidate Genes ◽  
Glycine Max L

scholarly journals Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine max L.)

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1335
Author(s):  
Taeklim Lee ◽  
Kyung Do Kim ◽  
Ji-Min Kim ◽  
Ilseob Shin ◽  
Jinho Heo ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Leaf Shape ◽  
Ultraviolet B ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Glycine Max L

The depletion of the stratospheric ozone layer is a major environmental issue and has increased the dosage of ultraviolet-B (UV-B) radiation reaching the Earth’s surface. Organisms are negatively affected by enhanced UV-B radiation, and especially in crop plants this may lead to severe yield losses. Soybean (Glycine max L.), a major legume crop, is sensitive to UV-B radiation, and therefore, it is required to breed the UV-B-resistant soybean cultivar. In this study, 688 soybean germplasms were phenotyped for two categories, Damage of Leaf Chlorosis (DLC) and Damage of Leaf Shape (DLS), after supplementary UV-B irradiation for 14 days. About 5% of the germplasms showed strong UV-B resistance, and GCS731 was the most resistant genotype. Their phenotypic distributions showed similar patterns to the normal, suggesting UV-B resistance as a quantitative trait governed by polygenes. A total of 688 soybean germplasms were genotyped using the Axiom® Soya 180K SNP array, and a genome-wide association study (GWAS) was conducted to identify SNPs significantly associated with the two traits, DLC and DLS. Five peaks on chromosomes 2, 6, 10, and 11 were significantly associated with either DLC or DLS, and the five adjacent genes were selected as candidate genes responsible for UV-B resistance. Among those candidate genes, Glyma.02g017500 and Glyma.06g103200 encode cryptochrome (CRY) and cryptochrome 1 (CRY1), respectively, and are known to play a role in DNA repair during photoreactivation. Real-time quantitative RT-PCR (qRT-PCR) results revealed that CRY1 was expressed significantly higher in the UV-B-resistant soybean compared to the susceptible soybean after 6 h of UV-B irradiation. This study is the first GWAS report on UV-B resistance in soybean, and the results will provide valuable information for breeding UV-B-resistant soybeans in preparation for climate change.

Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes

2014 ◽  
Vol 128 (1) ◽  
pp. 73-91 ◽  
Author(s):  
Arun Prabhu Dhanapal ◽  
Jeffery D. Ray ◽  
Shardendu K. Singh ◽  
Valerio Hoyos-Villegas ◽  
James R. Smith ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Carbon Isotope ◽  
Isotope Ratio ◽  
Genome Wide Association Study ◽  
Carbon Isotope Ratio ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Glycine Max L

scholarly journals Genome-Wide Association Study of Ureide Concentration in Diverse Maturity Group IV Soybean [Glycine max (L.) Merr.] Accessions

2015 ◽  
Vol 5 (11) ◽  
pp. 2391-2403 ◽  
Author(s):  
Jeffery D. Ray ◽  
Arun Prabhu Dhanapal ◽  
Shardendu K. Singh ◽  
Valerio Hoyos-Villegas ◽  
James R. Smith ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Group Iv ◽  
Genome Wide Association ◽  
Maturity Group ◽  
Genome Wide ◽  
Glycine Max L

scholarly journals Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [ Glycine max (L.) Merrill ]

2019 ◽  
Author(s):  
Xue Zhao ◽  
Hairan Dong ◽  
Hong Chang ◽  
Jingyun Zhao ◽  
Weili Teng ◽  
...  
Keyword(s):  
Glycine Max ◽  
Candidate Genes ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Starch Accumulation ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Glycine Max L ◽  
Soybean Food

Abstract Background The hundred seed weight (HSW) was one of soybean [Glycine max (L.) Merrill] yield components, and was also especially critical for various soybean food types. In this study, a representative sample consisted of 185 accessions, selected from Northeast China, was tested under six tested environments for determination of quantitative trait nucleotide (QTN) of HSW through genome-wide association study (GWAS). Result A total of 24,180 single nucleotide polymorphisms (SNPs) with minor allele frequency more than 0.2 and missing data less than 3% were utilized to the estimate linkage disequilibrium (LD) level in the tested association panel. Thirty-four association signals were identified to be associated with HSW via GWAS. Among them, nineteen QTN were the novel and another fifteen QTN were overlapped or located near the genomic regions of known HSW QTL. A total of 237 genes, derived from 31 QTN, located near peak SNP for six tested environments, were considered as candidate genes, such as plant growing regulation, hormone metabolism, cell, RNA, protein metabolism, development, starch accumulation, secondary metabolism, signaling, and TCA, some of which have been found to participant in the regulation of HSW. A total of 106 SNPs from 16 candidate genes were significantly associated with HSW in soybean. Conclusions The identified loci with beneficial alleles and the candidate genes might be valuable for the molecular network and MAS of HSW.

scholarly journals Erratum to: Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes

2015 ◽  
Vol 128 (2) ◽  
pp. 375-376
Author(s):  
Arun Prabhu Dhanapal ◽  
Jeffery D. Ray ◽  
Shardendu K. Singh ◽  
Valerio Hoyos-Villegas ◽  
James R. Smith ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Carbon Isotope ◽  
Isotope Ratio ◽  
Genome Wide Association Study ◽  
Carbon Isotope Ratio ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Glycine Max L

Identification of loci and candidate genes for plant height in soybean ( Glycine max ) via genome‐wide association study

2019 ◽  
Vol 138 (6) ◽  
pp. 721-732 ◽  
Author(s):  
Yan Jing ◽  
Xue Zhao ◽  
Jun Wang ◽  
Ming Lian ◽  
Weili Teng ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Candidate Genes ◽  
Plant Height ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill]

2019 ◽  
Author(s):  
Xue Zhao ◽  
Hairan Dong ◽  
Hong Chang ◽  
Jingyun Zhao ◽  
Weili Teng ◽  
...  
Keyword(s):  
Glycine Max ◽  
Candidate Genes ◽  
Seed Weight ◽  
Growth Regulation ◽  
Genome Wide Association ◽  
Starch Accumulation ◽  
Genome Wide ◽  
A Genome ◽  
Glycine Max L ◽  
Soybean Food

Abstract Background: The hundred seed weight (HSW) is one of the yield components of soybean [Glycine max (L.) Merrill] and is especially critical for various soybean food types. In this study, a representative sample consisting of 185 accessions was selected from Northeast China and analysed in three tested environments to determine the quantitative trait nucleotide (QTN) of HSW through a genome-wide association study (GWAS). Result: A total of 24,180 single nucleotide polymorphisms (SNPs) with minor allele frequencies greater than 0.2 and missing data less than 3% were utilized to estimate linkage disequilibrium (LD) levels in the tested association panel. Thirty-four association signals were identified as associated with HSW via GWAS. Among them, nineteen QTNs were novel, and another fifteen QTNs were overlapped or located near the genomic regions of known HSW QTL. A total of 237 genes, derived from 31 QTNs and located near peak SNPs from the three tested environments in 2015 and 2016, were considered candidate genes, were related to plant growth regulation, hormone metabolism, cell, RNA, protein metabolism, development, starch accumulation, secondary metabolism, signalling, and the TCA cycle, some of which have been found to participate in the regulation of HSW. A total of 106 SNPs from 16 candidate genes were significantly associated with HSW in soybean. Conclusions: The identified loci with beneficial alleles and candidate genes might be valuable for the molecular network and MAS of HSW.

Prevalence of the pit and antipit in the genus Glycine

1987 ◽  
Vol 45 ◽  
pp. 986-987
Author(s):  
R. W. Yaklich ◽  
E. L. Vigil ◽  
W. P. Wergin
Keyword(s):  
Amino Acids ◽  
Endoplasmic Reticulum ◽  
Glycine Max ◽  
Seed Coat ◽  
Cell Types ◽  
Abaxial Surface ◽  
Legume Seed ◽  
Initial Report ◽  
Cone Cells ◽  
Glycine Max L

The legume seed coat is the site of sucrose unloading and the metabolism of imported ureides and synthesis of amino acids for the developing embryo. The cell types directly responsible for these functions in the seed coat are not known. We recently described a convex layer of tissue on the inside surface of the soybean (Glycine max L. Merr.) seed coat that was termed “antipit” because it was in direct opposition to the concave pit on the abaxial surface of the cotyledon. Cone cells of the antipit contained numerous hypertrophied Golgi apparatus and laminated rough endoplasmic reticulum common to actively secreting cells. The initial report by Dzikowski (1936) described the morphology of the pit and antipit in G. max and found these structures in only 68 of the 169 seed accessions examined.

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