Study On Genetic Structure And Important Family Genetic Basis Of Huang-Huai-Hai Soybean Cultivars Based On Genome Resequencing

Research on the genetic diversity of soybean germplasm resources is crucial for breeding soybean cultivars that are diversified and adaptable to different production needs.The Huang-Huai-Hai is the second largest soybean-producing area in China and has played an important role in soybean production with a large number of soybean cultivars bred there.This paper uses whole-genome sequencing technology to study the population structure and genetic diversity of soybean cultivars from different periods in the Huang-Huai-Hai.It evaluates the population structure and genetic diversity composition of the soybean breeding population in different breeding periods and identifies genomic regions related to artificial selection,providing a reference for soybean genetic improvement,parent selection,and gene discovery.The main research results are as follows:(1)A total of 181 soybean cultivars from the Huang-Huai-Hai underwent whole-genome resequencing,with an average sequencing depth of 10.38 x.In total,4,666,538 single nucleotide polymorphisms(SNPs)and 2,520,208 insertions /deletions(In Dels)were detected on 20 chromosomes.A significant number of putative variants were found in important genomic regions,which could have a significant impact on genes involved in major biological processes.Across all cultivars,50,365 genes had mutations,and enrichment analysis identified 1314 important gene regions with SNPs and 1241 important genes with In Dels.These genes were found to be involved in a wide range of biological processes,including cell processes,metabolic processes,reproductive processes,GTP metabolic processes and regulation.(2)The 181 cultivars were classified into five subgroups based on breeding time:A(1963-1980),B(1983-1988),C(1991-2000),D(2001-2011),and E(2012-2017).Principal component analysis and population structure analysis indicated no clear clustering of subgroups.The LD half-decay distances for the five subgroups were 290 KB,380 k KB 753 KB,182 KB,and 227 KB,respectively.The A subgroup had the highest degree of nucleotide polymorphism,which gradually decreased in the B and C subgroups over time,while the D and E subgroups showed a rapid increase in nucleotide polymorphism in the past 20 years,with relatively lower levels in the B and C subgroups.The genetic differentiation between subgroups A and B,and B and C,increased gradually,while that between C and D,and D and E,decreased sharply,indicating a trend of increasing and then decreasing genetic differentiation among subgroups within similar breeding periods.This could provide guidance for breeders in setting breeding targets during breeding periods.Analysis of the polymorphic information content(PIC)statistics showed results similar to π.Selection signature analysis revealed a large number of artificial selection regions in the Huang-Huai-Hai soybean population genome.SNP variant detection was performed on 18 functional genes involved in soybean photoperiod,seed weight,seed shape,pod habit,and fatty acid synthesis,which can help to understand the photoperiod adaptation mechanism of soybean in the Huang-Huai-Hai and provide genetic resources for soybean molecular breeding.(3)In this paper,the RCI 2 gene family was deeply analyzed using bioinformatics methods,and five RCI 2 genes were identified in soybean,distributed across five chromosomes of the soybean genome.The five RCI 2 genes were of similar length,with instability indices ranging from 19.11 to 46.22.Phylogenetic analysis showed that RCI 2 proteins in soybean,rice,wheat,millet,and maize could be classified into three distinct branches.Almost all RCI 2 genes contained 2-3exons and 1-2 introns.Many cis-elements related to growth and development,stress response,and hormone regulation were identified in the promoter regions of RCI 2genes in soybean and the other four species.The study results provide a reference for further research on the biological functions of the soybean RCI 2 gene family,soybean stress breeding,and genetic improvement.(4)In this study,10 BBR / BPC family genes were identified in the soybean genome,which are distributed on six chromosomes and contain gene copies,and are rich in basic amino acids.Phylogenetic analysis indicated that BPC proteins from soybean and four other species could be divided into three distinct branches.Most BBR genes contain 1-2 exons and 1-2 introns,with the majority being zero-phase introns.Many cis-regulatory elements related to development,stress,and hormones were discovered in the promoter regions of BBR genes in soybean and the four other species,but further experimental evidence is needed to support these findings.