Domesticated And Improved Genes For Seed Oil-related Traits In Soybean

Soybean(Glycine max L.Merr.,2n = 2× = 40)is an important oil crop in the world and the main source of edible oil for human beings.With the development of domestication and improvement in crops,their genetic bases have been becoming narrower and narrower.At this case,the use of elite genes in wild soybean in cultivated soybean can broaden its genetic basis and improve its important traits.Therefore,it necessitates a more in-depth study of soybean domestication and improvement to improve soybean yield,quality,resistance,and adaptability.In the process of domestication from wild to landrace soybeans and improvement from landrace to bred soybeans,the oil content of soybean seed increasingly increases.Although there have been many studies in the past decades,their results are almost derived from their own experimental materials.To address this issue,firstly,286 soybean accessions,along with the results in previous studies,were used to determine domestication and improvement regions.Secondly,genome-wide association studies(GWAS)in 286 soybean accessions,linkage analysis in 519 recombinant inbred lines(RILs)and bulked sergeant analysis(BSA)in 4 extreme pools from 519 RILs were carried out to identify quantitative trait loci(QTLs)for oil-related traits.These QTLs were integrated with the above-mentioned domestication and improvement regions to obtain domestication and improvement loci for seed oil-related traits.Next,transcriptome high expression analysis,allele frequency difference analysis across sub-populations in 302 soybean accessions,SNP annotation,and gene differential expression analysis were used to mine candidate domestication and improvement genes around the above-mentioned domestication and improvement loci.Finally,tissue-specific expression analysis,GO annotation,mi RNA and DNA methylation analysis,along with previously reported oil-related genes,were used to further identify candidate domestication and improvement genes;with 30 soybean genomes,sequence difference comparison and haplotype analysis would provide further evidences for candidate domestication and improvement genes.These genes were used to explain the difference of seed oil content between wild and landrace soybeans,and between landrace and bred soybeans.The main results are as follows.1.The XP-CLR method was used to calculate the genetic diversity for each SNP marker in 286 soybean accessions.As a result,534 domestication and 458 improvement regions were identified.Among these regions,300 domestication and 408 improvement regions were new,and 234(43.82%)domestication and 50(10.92%)improvement regions were identified to be consistent with those in previous studies.In summary,together with the results in previous results,there have been 952 domestication and 538 improvement regions.2.Seed oil-related traits measured at five environments and their BLUP values in 286 soybean accessions were associated multi-locus GWAS methods with 106,013 SNPs,these traits at three environments and their BLUP values in 519 RILs were linked by GCIM method with 11,846 SLAF markers,and four extreme pools in 519 RILs were analyzed by BRM method.As a result,555 loci for seed oil related traits were detected.Among these loci,111 were new,444 were found to be consistent with those in previous results,257 were domesticated,and 192 were improved.3.To obtain candadite domestication and improvement genes around the abovementioned domestication and improvement loci,several kinds of analyses were carried out.First,transcriptome datasets at 7 different seed development stages in soybean were used to detect high expression genes.Totally,2027 genes around domestication loci and 1662 genes around improvement loci were expressed highly at oil accumulation stages.Then,1530 potential candidate domestication genes(CDGs)and 552 potential candidate improvement genes(CIGs)were identified by SNP allele frequency difference significance,SNP annotation,and variation information and differential expression analysis of upstream regulatory region,UTR region and coding region of these genes.Next,a total of 118 potential CDGs and 60 potential CIGs were further obtained by specific expression in seed,GO annotation,previously reported oil-related genes and mi RNA binding with candidate genes.Finally,92 CDGs and 50 CIGs were found to have significant differences for both SNP variations in 30 soybean genomes and seed oil contents acorss various gene haplotypes in 172 soybean accessions.In 172 soybean accessions,the number of haplotypes decreased,and the frequencies of elite haplotypes with high oil content increased from wild to bred soybeans.The results confirmed that these candidate genes are responsive for seed oil-related traits.In addition,33 CDGs and 4 CIGs were found to be located on the differential methylation regions in one previous study.In conclusion,there have been 125 CDGs and 54 CIGs.4.The 125 CDGs and 54 CIGs were used to explain why seed oil content increases from wild to landrace soybean,and from landrace to bred soybeans.Firstly,the numbers of elite haplotypes of 66 CDGs and 38 CIGs from wild to landrace soybeans and from landrace to bred soybeans are gradually reduced,and the frequencies of elite haplotypes with high oil content are gradually increased.The results provide evidences for the increase of seed oil content in domestication and improvement processes.These CDGs include PKP3,KAS I,BCCP2,PLC2,LACS2,DES1.2,HCD1,DGK1,TT8,MYB94,CYP71B7,NF-YA7,and CYP97C1,and these CIGs include KAS III,LACS9,Gm MFT,MYB30,and LCB2.Secondly,some genes have changes in amino acid sequences and gene expression levels in domestication and improvement processes.The first case may be derived from base mutation in coding region,which leads to protein changes.This may affect seed oil related traits.These genes include 33 CDGs,such as PKp3,and 24 CIGs,such as MYB30.The second case may come from sequence variation of regulatory region(55 CDGs,such as,KASI,and 31 CIGs,such as,KAS III),mi RNA targeted regulation(3 CDGs,such as,UPL3,and 3 CIGs,such as,NRPB9A),and DNA methylation modification(33 CDGs,such as,FAS4 and 4 CIGs,such as,ARFA1F).Their expression levels were significantly different across wild,landrace,and bred soybeans.Although the functions of individual genes,with unknown encoding proteins,have not been found to be associated with oil metabolism,finally,these domesticated and improved genes are candidate genes for seed oil related traits,including 9 CDGs,such as Glyma02g16660,and 4 CIGs,shch as Glyma08g18400.5.Based on elite haplotypes and their proportions in subpopulations,53 CDGs and 36 CIGs would be valuable in future soybean breeding.In addition,9 CDGs and 4 CIGs with unknown gene function might be valuable in future soybean breeding.This study provides a new framework for domestication and improvement research,and new gene resources for soybean breeding and molecular biology research.