Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis
文献类型： 外文期刊
作者： Chen, Yuehan 1 ; Liu, Zhi 2 ; Han, Dezhi 3 ; Yang, Qing 2 ; Li, Chenhui 2 ; Shi, Xiaolei 2 ; Zhang, Mengchen 2 ; Yang, Chunyan 2 ; Qiu, Lijuan 4 ; Jia, Hongchang 3 ; Wang, Shu 3 ; Lu, Wencheng 3 ; Ma, Qian 1 ; Yan, Long 2 ;
作者机构： 1.Qingdao Agr Univ, Coll Life Sci, Qingdao 266109, Peoples R China
2.Hebei Acad Agr & Forestry Sci, Minist Agr & Rural Affairs,Inst Cereal & Oil Crops, Natl Soybean Improvement Ctr Shijiazhuang Sub Ctr, Hebei Lab Crop Genet & Breeding,Hebei Huai Hai Key, Shijiazhuang 050035, Hebei, Peoples R China
3.Heilongjiang Acad Agr Sci, Heihe Branch, Heihe 164300, Peoples R China
4.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Gene Resources & Genet Improve, Key Lab Germplasm & Biotechnol MARA, Beijing 100081, Peoples R China
期刊名称：THEORETICAL AND APPLIED GENETICS （ 影响因子：4.4； 五年影响因子：5.0 ）
ISSN： 0040-5752
年卷期： 2024 年 137 卷 8 期
页码：
收录情况： SCI
摘要： Key messageThree QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses.AbstractLow temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD) analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.
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