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Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population

文献类型： 外文期刊

作者： Yang, Guang 1 ; Li, Wei 2 ; Fan, Chao 2 ; Liu, Miao 2 ; Liu, Jianxin 2 ; Liang, Wenwei 2 ; Wang, Ling 2 ; Di, Shufeng 2 ; Fang, Chao 3 ; Li, Haiyang 3 ; Ding, Guohua 2 ; Bi, Yingdong 2 ; Lai, Yongcai 2 ;

作者机构： 1.Heilongjiang Acad Agr Sci, Postdoctoral Sci Res Stn, Harbin 150028, Heilongjiang, Peoples R China

2.Heilongjiang Acad Agr Sci, Inst Crop Cultivat & Tillage, Harbin 150028, Heilongjiang, Peoples R China

3.Guangzhou Univ, Innovat Ctr Mol Genet & Evolut, Sch Life Sci, Guangzhou 510405, Peoples R China

关键词： Genome-wide association study; Flowering time; Active accumulated temperature; Glycine soja; Haplotypes

期刊名称：BMC GENOMICS （ 影响因子：4.547； 五年影响因子：4.931 ）

ISSN： 1471-2164

年卷期： 2022 年 23 卷 1 期

页码：

收录情况： SCI

摘要： Flowering time and active accumulated temperature (AAT) are two key factors that limit the expanded production especially for soybean across different regions. Wild soybean provides an important germplasm for functional genomics study in cultivar soybean. However, the studies on genetic basis underlying flowering time in response to AAT especially in wild soybean were rarely reported. In this study, we used 294 wild soybean accessions derived from major soybean production region characterized by different AAT in Northeast of China. Based on genome-wide association study (GWAS), we identified 96 SNPs corresponded to 342 candidate genes that significantly associated with flowering time recorded in two-year experiments. Gene Ontology enrichment analysis suggests that the pathways of photosynthesis light reaction and actin filament binding were significantly enriched. We found three lead SNPs with -log(10)(p-value) > 32 across the two-year experiments, i.e., Chr02:9490318, Chr04:8545910 and Chr09:49553555. Linkage disequilibrium block analysis shows 28 candidate genes within the genomic region centered on the lead SNPs. Among them, expression levels of three genes (aspartic peptidase 1, serine/threonine-protein kinase and protein SCAR2-like) were significantly differed between two subgroups possessing contrasting flowering time distributed at chromosome 2, 4 and 9, respectively. There are 6, 7 and 3 haplotypes classified on the coding regions of the three genes, respectively. Collectively, accessions with late flowering time phenotype are typically derived from AAT zone 1, which is associated with the haplotypic distribution and expression levels of the three genes. This study provides an insight into a potential mechanism responsible for flowering time in response to AAT in wild soybean, which could promote the understanding of genetic basis for other major crops.

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