Genetic dissection of yield-related traits via genome-wide association analysis across multiple environments in wild soybean (Glycine soja Sieb. and Zucc.)

Dezhou Hu; Huairen Zhang; Qing Du; Zhenbin Hu; Zhongyi Yang; Xiao Li; Jiao Wang; Fang Huang; Deyue Yu; Hui Wang; Guizhen Kan

doi:10.1007/s00425-019-03329-6

Genetic dissection of yield-related traits via genome-wide association analysis across multiple environments in wild soybean (Glycine soja Sieb. and Zucc.)

Planta. 2020 Jan 6;251(2):39. doi: 10.1007/s00425-019-03329-6.

Authors

Dezhou Hu¹, Huairen Zhang^{1

2}, Qing Du¹, Zhenbin Hu³, Zhongyi Yang¹, Xiao Li¹, Jiao Wang¹, Fang Huang¹, Deyue Yu^{1

4}, Hui Wang¹, Guizhen Kan⁵

Affiliations

¹ National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
² Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
³ Department of Agronomy, Kansas State University, Manhattan, KS, USA.
⁴ School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
⁵ National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China. kanguizhen@njau.edu.cn.

PMID: 31907621
DOI: 10.1007/s00425-019-03329-6

Abstract

A total of 41 SNPs were identified as significantly associated with five yield-related traits in wild soybean populations across multiple environments, and the candidate gene GsCID1 was found to be associated with seed weight. These results may facilitate improvements in cultivated soybean. Crop-related wild species contain new sources of genetic diversity for crop improvement. Wild soybean (Glycine soja Sieb. and Zucc.) is the progenitor of cultivated soybean [Glycine max (L.) Merr.] and can be used as an essential genetic resource for yield improvements. In this research, using genome-wide association study (GWAS) in 96 out of 113 wild soybean accessions with 114,090 single nucleotide polymorphisms (SNPs) (with minor allele frequencies ≤ 0.05), SNPs associated with five yield-related traits were identified across multiple environments. In total, 41 SNPs were significantly associated with the traits in two or more environments (significance threshold P ≤ 8.76 × 10^-6), with 29, 7, 3, and 2 SNPs detected for 100-seed weight (SW), maturity time (MT), seed yield per plant (SY) and flowering time (FT), respectively. BLAST search against the Glycine soja W05 reference genome was performed, 20 candidate genes were identified based on these 41 significant SNPs. One candidate gene, GsCID1 (Glysoja.04g010563), harbored two significant SNPs-AX-93713187, with a non-synonymous mutation, and AX-93713188, with a synonymous mutation. GsCID1 was highly expressed during seed development based on public information resources. The polymorphisms in this gene were associated with SW. We developed a derived cleaved amplified polymorphic sequence (dCAPS) marker for GsCID1 that was highly associated with SW and was validated as a functional marker. In summary, the revealed SNPs/genes are useful for understanding the genetic architecture of yield-related traits in wild soybean, which could be used as a potential exotic resource to improve cultivated soybean yields.

Keywords: Crop wild relatives; GWAS; GsCID1; Marker-assisted selection; Wild soybean.

MeSH terms

Genome, Plant / genetics
Genome-Wide Association Study / methods*
Genotype
Glycine max / genetics*
Linkage Disequilibrium / genetics*
Polymorphism, Single Nucleotide / genetics
Quantitative Trait Loci / genetics

Abstract

MeSH terms

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