Population Genetic Analysis Of Main Soybean Cultivars From Northern Huang-Huai-Hai Based On Whole Genome Resequencing

Soybean [Glycine max(L.)Merr.] is an important source of plant protein and edible vegetable oil,and plays an important role in the development of the national economy.Breeding soybean varieties is the most important part of soybean production.Researching the genetic diversity and population genetic structure of soybean bred varieties and their germplasm resources has important guiding significance for soybean breeding and variety improvement.Huang-Huai-Hai is the second largest producing area in my country and has played a key role in China’s soybean production.In recent years,genome sequencing has gradually entered a high-throughput and high-precision stage,which has played a great role in crop germplasm resources and breeding improvement.This thesis uses high-throughput sequencing methods to sequence the whole genome of a total of 123 soybean materials in the northern Huang-Huai-Hai region,including Beijing,Shandong,Hebei,and Henan,including newly bred varieties and related germplasm in recent years.Statistical analysis of variation results and population genetic analysis were carried out to provide references for soybean breeding and soybean molecular biology research.The main research contents are as follows:1.Re-sequencing 123 cultivars of Huang-Huai-Hai soybeans obtained 743 G of original data.Using Williams 82(v2.1)as the reference genome,the average sequencing depth was 10.31 X,and the average genome coverage of each sample after being compared to the reference genome.It was 95.56%.The population variation detection yielded a total of 3105465 SNPs and 691571 In Dels.There were an average of 32.83 SNPs per kb in the genome.SNP annotation statistics showed 51749 synonymous mutations and 65142 non-synonymous mutations in the CDS region.These SNPs resulted in 37754 gene mutations.In Del annotations show that the codon insertion mutations that occur in the CDS region are the most,2887,and the start codon and stop codon mutations are the least,318 in total.These In Dels caused 9339 gene mutations in total.5871 SVs were detected resulting in 8871 gene mutations.2.The analysis of population genetic structure can be divided into three categories according to cluster analysis.Among them,group Ⅰ contains 47 samples,except for one in Beijing and Hebei,all from Henan and Shandong provinces;group Ⅱ contains 23 samples,which can be Divided into two subgroups,one of which is mainly composed of samples from Beijing,forming a small-scale cluster;Group III contains 53 samples,which can be divided into four subgroups,with samples from all provinces.Obvious clustering related to the source.The STRUCTURE clustering results show that there are nine categories.The first,second,eighth,and ninth groups are from Henan and Shandong,except for one from Hebei,which corresponds to the cluster analysis of group I.The third group is from Beijing Two provinces of Henan.The 18 samples in the fourth group include all provinces.The fifth group consists entirely of Beijing samples,which corresponds to the subgroup of Beijing samples in group Ⅱ.Except for a Beijing sample,the sixth and seventh groups are from Hebei Province.In the results of STRUCTURE analysis,samples from the same Beijing and Hebei have obvious independent clustering.In PCA analysis,this result was partially confirmed.In PC1,some samples from Beijing had obvious small-scale clustering,while samples from Hebei Province were all in the second and third quadrants.In contrast,the samples from Henan and Shandong have no obvious distribution pattern3.The calculation and analysis of Fst and π values based on SNP data show that the average nucleic acid diversity of soybean cultivars in the four provinces is the highest(π=0.0027),Beijing Province is the least(π=0.0017),and the genetic diversity of soybean cultivars in Henan Province Sex is the most abundant,followed by Shandong Province,and Beijing Province has the lowest genetic diversity.The Fst value reveals that the population differentiation coefficients of Shandong and Henan provinces are the lowest at 0.031,while the differentiation coefficients of Shandong Province,Beijing and Hebei provinces are 0.034 and 0.033,respectively,indicating that the bred varieties in Shandong Province are not very different from these three provinces.It is speculated that it is caused by the selection and breeding of Shandong varieties as parents.The differentiation coefficient between Henan and Beijing,Henan and Hebei is the highest,which means that the bred varieties of Henan Province have fewer crosses with Beijing and Hebei.For the bred soybean varieties of Beijing and Hebei provinces,the bred varieties of Henan Province are more abundant.At the same time,linkage disequilibrium analysis also verified that the genetic diversity of bred varieties in Henan Province is the highest,and can be used as a candidate parent for excellent breeding.