Genome-wide Association Analysis Of Height Related Traits And Breeding Prediction In Soybean Under Low Light Stress

Plant height is an important trait that affects soybean yield,and cultivating soybean varieties with suitable plant height is an important measure to achieve high yield soybean breeding.The traits related to soybean plant height are complex quantitative traits,and their inheritance is greatly influenced by the environment.Previous studies have shown that soybean plant height related traits will change under the maizesoybean strip intercropping,resulting in severe soybean lodging,ultimately affecting soybean yield and quality.However,there are few studies on the genetic mechanism of soybean plant height traits changes under low light stress.Therefore,in this study,by setting two treatments of normal light and low light at seedling stage(simulated the maize-soybean strip intercropping),base on the 77,511 SNP markers obtained from microarray sequencing and 11,464 SNPLDB markers constructed by RTM-GWAS computational program were analyzed by two association analysis methods,MLMGWAS and RTM-GWAS,for three environments(E1: Renshou in 2021;E2: Renshou in 2022;E3: Chongzhou in 2022)of 181 soybean materials at seedling stage and at maturity after restoration of light,genome-wide association analysis was performed to mine stable loci controlling plant height and to predict the functions of candidate genes within the stable interval,and finally,based on the SNPLDB markers localized by RTM-GWAS for low light Finally,the design of soybean plant height breeding under low light stress was based on the SNPLDB markers located by RTM-GWAS.The main results are as follows:1.Different environments and light treatments have a significant effects on plant height related traits in soybean,and plant height,average internode length,and hypocotyl length increased after low light treatment;a three factor variance analysis was conducted on 181 soybean samples for plant height related traits at two stages.Except for the hypocotyl length at maturing stage,which was not significantly different under the two light treatments,the differences in other traits were extremely significant under the interaction of various factors such as environment,treatment,variety,and the three factors.2.A total of 503 QTL loci significantly associated with height-related traits were obtained by both mixed linear model(MLM)and restricted two-stage genome-wide multi-locus association analysis(RTM-GWAS)for 181 soybean plant height related traits under normal light and low light treatment at seedling and maturity stages in three environments,144 for plant height,85 for number of main stem nodes,190 for average internode lengths and 84 for hypocotyl length.Three significantly associated SNP loci/intervals,13＿35823484...35823553,13＿39150318...39150447 and 13＿39473397,were stably detected under multiple environments,multiple traits,two treatments and two association analysis methods.These three stably present intervals were used for the screening of candidate genes for height-related traits.3.According to the soybean reference genome Wm82.a1 information,a total of 77 genes were detected in three co-localized segments,which were converted into the Wm82.a2 version of gene names,and genes that were specifically expressed on stalks or expressed at relatively high levels were screened using the expression data of each gene on soybean tissues published on the Phyzome website,and finally four candidates for plant height related traits were screened based on the annotation information Glyma.13g266300,Glyma.13g266500,Glyma.13g310300,and Glyma.13g308100.4.Based on the phenotype values of 181 soybean materials under low light conditions and the association results of SDPLDB markers,the plant height QTL-allele matrix was established,and then the hybridization was calculated according to the formula yij=gij+(yi-gi+yj-gj)/2 Phenotype predictors of combined offspring.Set the predicted values of the combined offspring generated by continuous self-crossing of F1 as the 25 th percentile,50 th percentile,and 75 th percentile,respectively.Taking tall pole breeding as an example,when the predicted value of the combined progeny is the 75 th percentile,some single-cross combined offspring show superparental dominance.When the predicted value of the progeny is the 25 th percentile,the predicted plant height of the offspring of some single-cross combinations is relatively short.For example,when the parents ZY121 and ZY108 are crossed,the predicted plant height of the offspring is 35.91 cm.