Genome-Wide Association Analysis For Yield-Related Agronomic Traits Of Soybean Mini Core Collection

Soybean[Glycine Max（L.）Merr.]is a very important grain and oil crop in China.Its yield is indirectly or directly related to most agronomic traits,such as plant height,number of notes on main stem,branching and so on.Compared to rice,wheat and other crops,the yield of soybean is lower and the breeding progress is much slower.Through the association between molecular makers and target traits and through analysis of the genetic basis of phenotypic diversity,we can located the yield-related genes.Therefore,this work paves the way for marker-assisted selection and improves the efficiency of soybean high-yield breeding.Soybean mini core collection represents of the genetic diversity about 63.5%of 230 thousands cultivated soybean germplasm resources in China.It is an excellent material for soybean gene excavation and variety improvement.In this study,224 of this soybean mini core collection were used as experimental materials to do descriptive statistical analysis and variance analysis for phenotypic data.A total genome-wide association analysis was performed on six traits of plant height,number of nodes on main stem,branching,stem diameter,average internode length and number of effective pods six traits with 1749 single nucleotide polymorphisms（SNPs）covering whole genome.On the basis of this,the agronomic trait SNPs loci co-located using the two models were excavated with excellent allelic variation and the selection of excellent germplasm.The whole genome identification of SNPs closely related to soybean yield-related traits was carried out to lay the foundation for further screening and functional marker-assisted breeding of soybean related candidate genes.The main results of this study are as follows:1.All the six yield-related traits（plant height,number of nodes on main stem,branching,stem diameter,average internode length and number of effective pods）of soybean mini core collection are of great variety,the phenotypic coefficient of variation from 16,96%to 45.55%.The variance analysis showed that there were significant differences among varieties.And the generalized heritability of each trait was high,all above 82.09%.In the simple correlation analysis,almost all traits significantly related to the others,though that the average internode length was not related to brancheing and number of effective pods.The correlation coefficient between plant height and main stem number was the highest,reaching 0.885.2.Under the condition of P<10-3（-1gP>3.00）,the six traits were associated to 36 SNPs using GLM model and MLM model.Hight was related to 13 SNPs loci,located on chromosomes 2,6,8,10,11,15 and 18,respectively.The number of nodes on main stem was related to 4 loci,located on chromosomes 5,6,10 and 11,respectively.The branching were associated with 7 loci,located on chromosomes 2,6,7,8,13 and 18,respectively.Stem diameter were associated with 9 loci,located at chromosomes 2,5,10,14,15 and 18,respectively.The average internode length was associated with one loci,located on chromosome 18;the two SNPs associated with the number of effective pods r were located on chromosome 7.The marker Map-1899 has the highest P value in both plant height,number of nodes on main stem and stem diameter,and also average internode length by using GLM model on the 10 chromosome.3.The 36 excellent alleles with synergistic or reduced effect were identified through screening the SNPs associated by using GLM model and the MLM model.Among them,the plant height was screened for 6 synergistic alleles and 7 alleles were changed,respectively.The number of nodes on main stem was screened to one potency allele mutation,and three alleles were reduced.（P<0.05）.There were no significant differences in the allelic variation between the two cultivars（Gm18₄309759-A）;the number of effective pods was screened to a synergistic allele variability,and one allele was reduced.And then explored the distribution of excellent allelic variation in 20 extremes of 20 properties（high or low）.The results showed that there were the most significant alleles in the four traits of plant height,number nodes on main stem,stem diameter and average internode length for Huang mao dou.Sui Nong 1 contains the highest number of alleles with plant height,main stem number and stem diameter,Niu mao huang（Liaoning）contains the highest number of alleles with number nodes on main stem,stem diameter and branching.