Identification Of QTNs And QTN-by-envitonment Interactions And Their Candidate Genes For Flowering Time And Plant Height In Soybean

Soybean(Glycine max L.Merr.)is an important food and oil crop which grows widely.And it is of great value in fields such as food,feeding,and industry.Flowering time and plant height of soybean are complex quantitative traits with complex genetic mechanisms and important factors of soybean yield and fitness.These phenotypes are not only influenced by genotype but also has a close relationship with the environment and the interaction of genes and environment.Detecting environmental interactions of quantitative trait nucleotides(QTNs)can reveal the interactions of gene and environment.Therefore,detecting the QEIs(QTN-by-environment interactions)of flowering time and plant height of soybean is of great significance.There are significant differences between different environments in flowering time and plant height phenotypes of soybean,but few QEIs studies on these traits in soybean repoted,because of the lack of methodology of detecting GEIs by GWAS(genome-wide association studies).The new GWAS methodological framework 3Vmr MLM and its software package developed in our laboratory,that can detect QEIs.And previous studies using this methodological framework for QEIs of crops have been reported.Therefore,in this study,using 3Vmr MLM and its software package,we associate 740,754 SNPs in 286 soybean accessions with the phenotypic values of first flowering time,full flowering time and plant height contents under 5 environments and their BLUP values.(First and full flowering time: 2011 Nanjing,2012 Nanjing,2017 Ezhou,2017 Wuhan and 2022 Wuhan,plant height: 2014 Nanjing,2012 Nanjing,2017 Ezhou,2017 Wuhan and 2022 Wuhan).We used single environment analysis and multi environment association analysis in five environments to detect of their main-effect QTNs and QEIs.After that,mining potential candidate genes around main-effect QTNs and QEIs by differential expression analys,GO annotations,KEGG and comparison with homologous genes in arabidopsis.We can determine the candidate genes and its influences on phenotypes.Finally,the elite alleles for main-effect QTNs were mined to design the best cross combinations for soybean early flowering trait improvement.The main results are as follows:1.There was significant genetic variation among cultivars and years for first flowering times,full flowering times,and plant height,with broad sense heritabilities of0.960,0.956,and 0.926.2.Single environment analysis and multi-environment joint analysis were performed using 3Vmr MLM method.A total of 136,127,and 125 significant and suggestive QTNs were identified in the single environment analysis.41,40,44 QTNs and 22,24,19 QEIs were identified in the multi environment analysis.These QTNs and QEIs identified under the conditions of LOD scores ≥ 3.And a total of 12 known genes were identified within100 kb around these QTNs and QEIs,including 1 known gene near plant height QEI with evidence of environmental interaction.3.We performed differential expression analysis to the genes that searched within100 kb around the detected QTNs and QEIs,to select genes with significant differences in expressions of shoot apical meristem(SAM),flower,stem and node for first flowering times,full flowering times and plant height traits.26,40,and 40 differentially expressed genes were selected.KEGG and GO annotation of these differentially expressed genes identified 14 potential candidate genes,including 1 potential candidate GEI(gene-byenvironment interaction)with evidence of environmental interaction.Haplotype analysis of these candidate genes finally identified 2 significant candidate genes,glyma.15g022300 and glyma.02g125600,and a significant candidate GEI,glyma.13g292800,with evidence of environmental interactions in both arabidopsis and soybean.4.Using the effect values of QTNs and genotype informatio of the first flowering times and full flowering times,we determined the elite alleles that are able to make soybean flowering early and their distributions among 286 soybean accessions.And we found that the average number of elite alleles ranged from 58 to 119 and from 58 to 103,and the average number of elite alleles ranged from 86.97 and 77.38.Respectively,the number of elite alleles was significantly negatively correlated with the phenotypic values at the first flowering times and full flowering times stages,the correlation coefficients were-0.574 and-0.525,with P < 0.01.The elite allele was used for breeding design.We select 20 varieties with the earliest floweing time.Among them,Qinyan 1,Heihe 54,Shang 7608,Qingcha-1,Fengshou,and Shangqiu 73 are likely to be excellent parents for the improvement of the flowering time of soybean.Five crosses with the highest number of elite alleles were proposed for each of the first and full flowering time.The progeny of a cross between the combination of heihe54 and Shang7608 may aggregate the highest number of 125 elite alleles for the first flowering time and may flowering earliest.The combination of Shangqiu73 and Shang7608 may aggregate a maximum number of 116 elite anthesis alleles for the full flowering time and may full flowering earliest.