Study On The Genetic Basis Analysis Of Soybean Cultivars In Huang-Huai-Hai A133 Family By Whole Genome Resequencing

Soybean[Glycine Max（L.）Merr.]is an important oil crop,and often used as raw material of plant protein,which plays an important role in our daily life.Huang-Huai-Hai is an important soybean producing area in China,the cultivars in Huang-Huai-Hai region play an important role in production.Ji Mo You Dou is a local soybean in Ji Mo,Shan Dong province,it bred a large number of cultivars as an ancestor,and has abundant soybean germplasm resources.It is of great guiding significance to study the genetic of soybeans of A133 families for soybean breeding,parental selection and parental evaluation.In order to recognize the genetic basis of A133 family,this study analyzed the population structure,genetic diversity,and genetic variation detection of 83 soybeans using whole-genome sequencing（WGS）technology based on the parents of A133 family in Huang-Huai-Hai region and some selected varieties.The main results were as follows:1.The average sequencing depth of 83 soybean varieties in Huang-Huai-Hai was 10.27×,and the average coverage rate of Williams 82.A2.v1 Reads matched to the soybean reference genome was 95.4%.A total of 10,940,802 SNPs and 1,646,155In Dels were obtained by genome-wide sequencing.An average of 2,738,025 SNPs and 443,762 In Dels were detected in each cultivar,and a total of 7,868 SVs were found in the A133 family.The SNPs,In Dels,SVs and other variants resulted in a total of 54,911 mutant genes,with an average number of 17,882 variants per variety.SNPs and In Dels annotation showed that the percentages of SNPs and In Dels in each region of soybean genome were similar,with the highest proportion of intergene region being 40%,and the lowest proportion of exon region being 0.04%.Annotation information of period 2006-2015 was more abundant than that of ancestral parents.2.Correlation coefficient between the genetic contribution value and the breeding age was-0.817,which showing a strong negative correlation.The genetic contribution values of cultivars decreased with age,and most soybean cultivars were lower than 0.125.The sequence of genetic diversity of the three populations was as follows:2005-2015>1970-2005>Ancestral parents,and Nei’s gene diversity（H）was 0.024 to 0.660,with an average of 0.320.Polymorphism information content（PIC）was 0.024 to 0.585,with an average of 0.274.Genetic diversity in A133 family increased,which was contrary to the trend of soybean genetic contribution values in different periods.Both the analysis results of NJ clustering and population structure are divided into 8 classes.Cluster 3,Cluster 4,Cluster 5,Cluster 6 and Cluster 7,which belong to the structure clustering,are also grouped into the same NJ clustering.Clustering of soybeans was correlated with variety consanguinity to a certain extent.Most of the cultivated soybeans were not close to their ancestral parents,and there was no specific clustering pattern according to the specific period.The first three principal components in PCA analysis accounted for 22.7%,13.2%and 11.5%of the total variation,respectively,which also indicated that there was no obvious subgroup differentiation among soybean populations in each period.3.3 differentiation coefficients among the groups were 0.047,0.069 and 0.028,respectively.There was a moderate degree of differentiation between the ancestral parents and period 2006-2015 soybeans.The nucleotide diversity was 0.0019,which means the whole family was low.A total of 202 Windows with F_ST≥0.7 and low level of nucleotide diversity（π）were detected on chromosomes 7,15,16 and 18 with100Kb as the window and 1Kb as the step size.A total of 63 variated genes were screened out in these window regions.GO annotation results showed that most of the mutant genes had molecular functions such as DNA binding,RNA binding and signal transduction.Some agronomic traits related genes such as Glyma.15G029200,Glyma.15G029000,and Glyma.18G066400 showed SNP variation,which expanded the adaptability of soybean population.Through the whole genome sequencing,the genetic information of A133 family was rich,which was suitable for the exchange and cultivation of germplasm and could be used to guide the selection of parents in the future.