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

CHE Yali; WU Sujun; WANG Kunyang; WANG Yanli; ZHANG Kai; QIAO Yake; YUAN Quan

doi:10.15933/j.cnki.1004-3268.2025.01.005

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 L0C114386540(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.