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

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.

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Genetic dissection of 2-heptenal content in soybean (Glycine max) seed through genome-wide association study

Crop and Pasture Science ◽

10.1071/cp20237 ◽

2020 ◽

Vol 71 (10) ◽

pp. 884

Author(s):

Zhikun Wang ◽

Mingming Yang ◽

Yuanzhuo Wang ◽

Chao Yang ◽

Xue Zhao ◽

...

Keyword(s):

Glycine Max ◽

Association Study ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Fatty Acid Content ◽

Soybean Seed ◽

Genome Wide Association ◽

Quality Characteristic ◽

Genome Wide ◽

A Genome

Association analysis is an alternative to conventional, family-based methods for detecting the location of gene(s) or quantitative trait loci (QTLs), and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Flavour is an essential quality characteristic of soymilk; however, soymilk contains volatile compounds unacceptable to consumers. One of main constituents in the volatiles of normal soymilk is 2-heptenal, which is thought to be a degradative oxidation product of polyunsaturated acids. In this study, a genome-wide association study using 24651 single-nucleotide polymorphisms (SNPs) was performed to identify quantitative trait nucleotides (QTNs) controlling 2-heptenal content in soybean (Glycine max (L.) Merr.) seed from a natural population of 110 soybean germplasm accessions. We detected 62 significant QTNs located on 18 different chromosomes that are significantly associated with 2-heptenal content in soybean seed. Among these, 17 QTNs co-localised with QTLs previously found to be related to protein, oil and/or fatty acid content in soybean seed. We also identified some candidate genes involved in lipid metabolism. These findings further our understanding of the genetic basis of 2-heptenal content in soybean seed and the improvement of marker-assisted breeding efficiency, which will be important for breeding soybean cultivars with low 2-heptenal content.

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Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm

BMC Genomics ◽

10.1186/s12864-015-1441-4 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 98

Author(s):

Jiaoping Zhang ◽

Qijian Song ◽

Perry B Cregan ◽

Randall L Nelson ◽

Xianzhi Wang ◽

...

Keyword(s):

Glycine Max ◽

Association Study ◽

Flowering Time ◽

Plant Height ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

Early Maturing

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Genome‐wide association study of soybean ( Glycine Max ) phosphorus deficiency tolerance during the seedling stage

Plant Breeding ◽

10.1111/pbr.12901 ◽

2021 ◽

Author(s):

Shengqian Chao ◽

Wenkai Du ◽

Tian Lu ◽

Yuming Yang ◽

Kaiqiang Wang ◽

...

Keyword(s):

Glycine Max ◽

Association Study ◽

Genome Wide Association Study ◽

Phosphorus Deficiency ◽

Seedling Stage ◽

Genome Wide Association ◽

Genome Wide

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

10.21203/rs.2.9598/v1 ◽

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.

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