镉胁迫下野生大豆苗期性状全基因组关联分析及耐镉候选基因筛选

doi:10.15933/j.cnki.1004-3268.2025.01.005

河南农业科学 ›› 2025, Vol. 54 ›› Issue (1): 40-54.DOI: 10.15933/j.cnki.1004-3268.2025.01.005

镉胁迫下野生大豆苗期性状全基因组关联分析及耐镉候选基因筛选

车雅丽¹，吴苏峻¹，王坤杨²，王艳丽¹，张锴¹，乔亚科¹，袁泉³

（1.河北科技师范学院农学与生物科技学院/河北省作物逆境生物学重点实验室，河北秦皇岛 066000；2.河北科技师范学院分析测试中心，河北秦皇岛066000；3. 集发农业梦想王国，河北秦皇岛 066000）

收稿日期:2024-04-08 出版日期:2025-01-15 发布日期:2025-02-26
通讯作者: 王艳丽（1985-），女，黑龙江哈尔滨人，讲师，博士，主要从事大豆遗传育种研究。E-mail：yanliwang0720@163.com 张锴（1987-），男，山东聊城人，副教授，博士，主要从事大豆遗传育种研究。E-mail：zhangkai0779@163.com
作者简介:车雅丽（1996-），女，山西长治人，在读硕士研究生，研究方向：作物遗传育种。E-mail：cyl51000@163.com
基金资助:
河北科技师范学院科学研究基金项目（2021YB005）；河北省科技厅现代种业科技创新专项基金（21326313D）

Genome‑wide Association Analysis of Wild Soybean Seedling Traits and Screening of Candidate Cadmium‑tolerant Genes

CHE Yali¹，WU Sujun¹，WANG Kunyang²，WANG Yanli¹，ZHANG Kai¹，QIAO Yake¹，YUAN Quan³

（1.College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology，Hebei Normal University of Science & Technology，Qinhuangdao 066000，China；2.Analysis and Testing Center，Hebei Normal University of Science & Technology，Qinhuangdao 066000，China；3.The Kingdom of Dreams，Qinhuangdao 066000，China）

Received:2024-04-08 Published:2025-01-15 Online:2025-02-26

摘要/Abstract

摘要： 野生大豆是栽培大豆的近源种，具有丰富的耐逆等位基因。为筛选耐镉野生大豆种质资源并解析其耐镉分子机制，以冀东地区205份野生大豆品系作为研究材料，采用水培试验，设置镉胁迫和对照（不进行镉胁迫）2个处理以及2022年11月和2023年7月2个环境重复，测定苗期地上部鲜质量（SFW）、地下部鲜质量（RFW）、株高（PH）、根长（RL），计算鲜质量根冠比（RSR）、各性状对应的耐镉系数（CTC）及各个野生大豆材料的耐镉综合评价值（D值），同时进行全基因组关联分析（GWAS），并对15号染色体上的显著单核苷酸多态性（SNP）进行单倍型分析。结果表明，除RSR外，镉胁迫处理幼苗性状平均值均低于对照；频率分析结果显示，2个环境下的CTC均表现为正态分布，呈现数量性状遗传特性；参照D值筛选出13份耐镉野生大豆种质。主成分分析显示，205份野生大豆材料可被分为3个类群；连锁不平衡（LD）分析发现，205份野生大豆自然群体在100 kb处出现衰减。GWAS分析共检测到195个与野生大豆耐镉性状显著相关的SNP，单个SNP可解释1.95%~25.43%的表型变异。根据SNP的物理位置共鉴定到591个候选基因，其中11个候选基因分别由多个SNP重复关联到，属于一因多效。更重要的是，根据功能注释发现了2 个金属耐性蛋白（MTPs）基因和2 个重金属相关蛋白（HIPPs）基因，分别是LOC114386540（MTP 10-like）、LOC114388453（MTP 10-like）、LOC114369981（HIPP 36-like）和LOC114381753（HIPP 37-like），这4个基因为阐明野生大豆耐镉性状遗传的分子机制奠定了基础。单倍型分析发现，15号染色体上的单倍型2的平均耐镉系数最大，属于优异单倍型。

关键词: 野生大豆, 镉胁迫, 全基因组关联分析（GWAS）, 耐镉系数, 候选基因

Abstract: Wild soybean is a close relative of cultivated soybean，which has abundant resistance alleles. In order to screen cadmium‑tolerant wild soybean germplasm resources and analyze its molecular mechanism of cadmium‑tolerance，205 wild soybean lines from eastern Hebei Province were selected as research materials.A hydroponic experiment was conducted to set up cadmium stress and control(without cadmium stress)with two environmental replicates in November 2022 and July 2023. The shoot fresh weight(SFW)，root fresh weight(RFW)，plant height(PH)，root length(RL)were determined，and root shoot ratio(RSR)of fresh weight，cadmium tolerance coefficient(CTC)corresponding to each trait and cadmium tolerance evaluation value(D value)of each wild soybean strain were calculated. At the same time，genome‑wide association analysis(GWAS) was carried out，and then haplotype analysis was performed on significant single nucleotide polymorphism(SNP)on chromosome 15.The results showed that the average value of seedlings traits under cadmium stress were lower than those of the control except for RSR. The results of frequency analysis showed that the CTC in the two environments showed normal distribution and genetic characteristics of quantitative traits. According to D value，13 cadmium‑tolerant wild soybean germplasms were screened out. Principal component analysis(PCA)showed that 205 wild soybean lines could be divided into three groups. Linkage disequilibrium(LD)analysis showed that 205 wild soybean natural populations decayed at 100 kb.A total of 195 SNPs significantly associated with cadmium tolerance in wild soybean were detected by GWAS analysis，and a single SNP could explain 1.95% to 25.43% of the phenotypic variation.A total of 591 candidate genes were identified according to the physical location of SNPs，of which 11 candidate genes were repeatedly associated with multiple SNPs，which belonged to pleiotropic effects. More importantly，genes of two metal‑tolerant proteins(MTPs)and two heavy metal‑associated isoprenylated plant proteins(HIPPs)were identified according to functional annotations.They were LOC114386540(MTP 10‑like)，LOC114388453(MTP 10‑like)，LOC114369981(HIPP 36‑like)and LOC114381753(HIPP 37‑like)，laying a foundation for elucidation of the molecular mechanism of the inheritance of cadmium tolerance in wild soybean. Haplotype analysis showed that the average CTC of haplotype 2 on chromosome 15 was the largest，which belonged to the excellent haplotype. This results provide information for analyzing the genetic mechanism of cadmium tolerance in wild soybean and provide important genetic resources for cultivating cadmium‑tolerant soybean varieties.

Key words: Wild soybean；Cadmium stress；Genome?wide association analysis（GWAS）；Cadmium , tolerance coefficient；Candidate gene

中图分类号:

S565.1

车雅丽1, 吴苏峻1, 王坤杨2, 王艳丽1, 张锴1, 乔亚科1, 袁泉3. 镉胁迫下野生大豆苗期性状全基因组关联分析及耐镉候选基因筛选[J]. 河南农业科学, 2025, 54(1): 40-54.

CHE Yali, WU Sujun, WANG Kunyang, WANG Yanli, ZHANG Kai, QIAO Yake, YUAN Quan. Genome‑wide Association Analysis of Wild Soybean Seedling Traits and Screening of Candidate Cadmium‑tolerant Genes[J]. Journal of Henan Agricultural Sciences, 2025, 54(1): 40-54.

图/表 13

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镉胁迫下野生大豆苗期性状全基因组关联分析及耐镉候选基因筛选

Genome‑wide Association Analysis of Wild Soybean Seedling Traits and Screening of Candidate Cadmium‑tolerant Genes

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