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Journal of Integrative Agriculture  2022, Vol. 21 Issue (10): 2833-2847    DOI: 10.1016/j.jia.2022.07.031
Special Issue: 油料作物合辑Oil Crops
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Linkage and association mapping of wild soybean (Glycine soja) seeds germinating under salt stress

SHI Mei-qi1, LIAO Xi-liang1, YE Qian1, ZHANG Wei1, LI Ya-kai1, Javaid Akhter BHAT1, KAN Gui-zhen1, YU De-yue1, 2

1 National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, P.R.China

2 Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, P.R.China

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摘要  盐分会损害大豆的萌发、生长和产量。萌发期是大豆生长发育的关键时期。野生大豆中含有许多抗性基因,是大豆遗传改良的宝贵资源。为了确定野生大豆在盐胁迫下种子萌发期间激活的遗传位点,本研究对两个群体的3个耐盐相关性状进行了筛选,其中一个是包含142个家系的大豆种间杂交群体,另一个是包含121份野生大豆材料的自然群体。利用3个耐盐指标的单核苷酸多态性(SNP)标记,在两个环境下通过连锁定位和全基因组关联研究(GWAS)检测到25个数量性状位点(QTLs),21个显著SNPs [-Log10(P)≥4.0]和24个潜在SNPs [3.5<-Log10(P)<4.0]。根据这些SNPs和QTLs鉴定出关键遗传区域。根据W05基因组的基因功能注释和盐诱导基因表达实时荧光定量PCR分析,选择GsAKR1作为野生大豆萌发阶段响应盐胁迫的候选基因。这些结果有助于确定野生大豆耐盐遗传网络,并为耐盐大豆的分子标记辅助选择提供依据。


Salinity threatens soybean germination, growth and production.  The germination stage is a key period in the life of soybean.  Wild soybean contains many genes related to stress resistance that are valuable resources for the genetic improvement of soybean.  To identify the genetic loci of wild soybean that are active during seed germination under salt stress, two populations, a soybean interspecific hybrid population comprising 142 lines and a natural population comprising 121 wild soybean accessions, were screened for three germination-related traits in this study.  By using single-nucleotide polymorphism (SNP) markers with three salt tolerance indices, 25 quantitative trait loci (QTLs), 21 significant SNPs (–log10(P)≥4.0) and 24 potential SNPs (3.5<–log10(P)<4.0) were detected by linkage mapping and a genome-wide association study (GWAS) in two environments.  The key genetic region was identified based on these SNPs and QTLs.  According to the gene functional annotations of the W05 genome and salt-induced gene expression qRT-PCR analysis, GsAKR1 was selected as a candidate gene that responded to salt stress at the germination stage in the wild soybean.  These results could contribute to determining the genetic networks of salt tolerance in wild soybean and will be helpful for molecular marker-assisted selection in the breeding of salt-tolerant soybean.

Keywords:  salt tolerance        wild soybean        QTLs        GWAS        GsAKR1  
Received: 05 January 2021   Accepted: 07 May 2021
Fund: This work was supported by the Natural Science Foundation of Jiangsu Province, China (BK20191313), the Fundamental Research Funds for the Central Universities, China (KYZ201705) and the Bioinformatics Center of Nanjing Agricultural University, China.
About author:  SHI Mei-qi, E-mail:; Correspondence KAN Gui-zhen, E-mail:; YU De-yue, E-mail:

Cite this article: 

SHI Mei-qi, LIAO Xi-liang, YE Qian, ZHANG Wei, LI Ya-kai, Javaid Akhter BHAT, KAN Gui-zhen, YU De-yue. 2022. Linkage and association mapping of wild soybean (Glycine soja) seeds germinating under salt stress. Journal of Integrative Agriculture, 21(10): 2833-2847.

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