Analysis On Genetic Basis For Yield Difference Between Wild And Cultivated Soybeans Based On Proteome, Transcriptome And Genome

Soybean is one of the important economic and food crops in China,and molecular breeding is an effective method to improve its yield.The process of domestication and breeding is a microevolution,and the synergistic change of polygene makes soybean phenotype have a complicated change,resulting inits production significantly higher than its wild ancestor.In this study,we have screened genes related to soybean yield through analyzing populations of wild soybean,landraceand improved cultivar at proteomic,transcriptomic and genomic levels.And thenthe genetic basis of yield difference between wild and cultivated soybeans was investigated.Our main results are as following:1.We selected 120 samples including 40 wild soybean accessions,40 landraces and 40 improved cultivars depend on geographical distributions and ecotypes.And then proteomes of young pod,germ,terminal bud and other organs were compared among these three populations through applying two-dimensional electrophoresis.We have identified 56,25 and 35 proteins with significant differentially expression levels at young pods,germs and terminal buds,respectively.Moreover 37,22 and 34 of them were characterized by mass spectrometry from young pods,germs and top buds,respectively.Most of these differentially expressed proteins were associated with photosynthesis,sugar metabolism,protein synthesis and protein space structure folding.217 genes were identified through using BLASTP of Phytozome website as encoding differentially expressed proteins from different soybean tissues.2.Based on geographic distribution and flowering period,we chose seven wild soybean accessions and six cultivars from 120 samples,and then seeds of them were harvested thirteen days after fertilization for RNA sequencing on the Illumina Hi Seq 2500 platform.Nearly 400 million 151 nucleotides long paired-end reads were generated from thirteen samples with sequencing depth ranging from 75 to 137-fold for all genic regions in the soybean genome.360 and 160 significantly up-and downregulated genes were identified when comparing the six cultivated soybeans to the seven wild soybeans.3.We chose 60 samples including 20 wild soybean accessions,20 landraces and 20 improved cultivars from above 120 samples based on our previous studies and geographical distributions.2774 single nucleotide polymorphism(SNP)were found from 356100 bp DNA sequences through performing DNA sequencing on 624 soybean genes containing 217 differentially expressed protein-coding genes mentioned above.Our results shown that the genetic diversity continued to decline during soybean domestication and breeding,and the extent of decrease in domestication was significantly higher than that of breeding.Using the neutral test of Tajima's D,Fu and Li 's D *,Fu and Li' s F *,78 of 624 genes were significantly deviated from the neutral model.4.Combined with soybean yield quantitative trait loci(QTLs)information from the Soybase website,we found that,of 777 genes identified from our analyses of proteome(217),transcriptome(520)and genome(78 harbouring 38 differentially expressed protein-coding genes),269 correlated with these QTLs.The percentage is 34.6%,29.5% for proteome,36.5% for transcriptome and 35.9% for genome.In our study,777 genes with significant differences were found between wild and cultivated soybeansat proteomic,transcriptomic and genomic levels.Among them,269 were associated with QTLs of soybean yield.Our results show that omics technology can effectively identify genes related to soybean yield.It is not useful for further understanding of the molecular mechanisms of soybean domestication and breeding,but also helpful for revealing the genetic basis of the difference between wild and cultivated soybeans.