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A genome-wide association analysis for salt tolerance during the soybean germination stage and development of KASP markers

文献类型： 外文期刊

作者： Wang, Junyan 1 ; Zhou, Miaomiao 1 ; Zhang, Hongmei 2 ; Liu, Xiaoqing 2 ; Zhang, Wei 2 ; Wang, Qiong 2 ; Jia, Qianru 2 ; Xu, Donghe 3 ; Chen, Huatao 2 ; Su, Chengfu 1 ;

作者机构： 1.Qingdao Agr Univ, Coll Agron, Qingdao, Peoples R China

2.Jiangsu Acad Agr Sci, Inst Ind Crops, Nanjing, Peoples R China

3.Japan Int Res Ctr Agr Sci JIRCAS, Tsukuba, Ibaraki, Japan

4.Zhongshan Biol Breeding Lab ZSBBL, Nanjing, Peoples R China

关键词： soybean; salt tolerance; germination stage; genome-wide association analysis; KASP marker

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.6； 五年影响因子：6.8 ）

ISSN： 1664-462X

年卷期： 2024 年 15 卷

页码：

收录情况： SCI

摘要： Salt stress poses a significant challenge to crop productivity, and understanding the genetic basis of salt tolerance is paramount for breeding resilient soybean varieties. In this study, a soybean natural population was evaluated for salt tolerance during the germination stage, focusing on key germination traits, including germination rate (GR), germination energy (GE), and germination index (GI). It was seen that under salt stress, obvious inhibitions were found on these traits, with GR, GE, and GI diminishing by 32% to 54% when compared to normal conditions. These traits displayed a coefficient of variation (31.81% to 50.6%) and a substantial generalized heritability (63.87% to 86.48%). Through GWAS, a total of 1841 significant single-nucleotide polymorphisms (SNPs) were identified to be associated with these traits, distributed across chromosome 2, 5, 6, and 20. Leveraging these significant association loci, 12 candidate genes were identified to be associated with essential functions in coordinating cellular responses, regulating osmotic stress, mitigating oxidative stress, clearing reactive oxygen species (ROS), and facilitating heavy metal ion transport - all of which are pivotal for plant development and stress tolerance. To validate the candidate genes, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was conducted, revealing three highly expressed genes (Glyma.02G067700, Glyma.02G068900, and Glyma.02G070000) that play pivotal roles in plant growth, development, and osmoregulation. In addition, based on these SNPs related with salt tolerance, KASP (Kompetitive Allele-Specific PCR)markers were successfully designed to genotype soybean accessions. These findings provide insight into the genetic base of soybean salt tolerance and candidate genes for enhancing soybean breeding programs in this study.

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