| Wild rice varieties are considered as natural treasure house of genes that can be utilized for plant improvement.In face of the challenge of deteriorating global environment and growing population,utilizing these excellent sources of genes of wild rice to provide a crucial new source of desirable traits for introgression into the less diverse cultivated rice is an effective strategy to cultivate new rice varieties with high yield,stable yield and stress resistance.Therefore,it is of great significance to explore the genetic mechanism of Oryza sativa domestication and reveal the history of rice domestication to mine new resistance genes and achieve safe production of rice.The main contents and results of this study are presented as the follows:1.Evolution of cultivated riceBased on the 245 resequencing data of O.sativa,O.barthii,O.meridionalis,O.glumipatula,O.longistaminata,O.rufipogon and CCDD genome wild rice and Nipponbare as the reference,we detected 546,380 high quality SNPs in these 7 rice populations.Subsequently,based on these SNP data,the phylogenetic relationship,population structure,gene flow and genetic diversity between wild and cultivated rice were analyzed.The results showed that O.sativa evolved from O.rufipogon,and O.longistaminata was the ancestor of O.rufipogon.It was observed that the evolutionary gene flow of cultivated rice from O.longistaminata to O.rufipogon and then to O.sativa.There was frequent gene exchange in both O.rufipogon and two O.sativa subspecies(Japonica and Indica).O.rufipogon showed the highest genetic diversity.The number of selected regions/selected genes identified in the process of evolution from O.longistaminata to O.rufipogon,O.rufipogon to O.sativa,O.longistaminata to O.sativa and the process of evolutionary gene flow of O.sativa were 49/190,354/1139,22/64 and 5/9 respectively.Further analysis showed that the genes in the selected regions were mainly related to various desirable traits such as resistant to biotic and abiotic stresses and rice yield,which indicated that the genes related to various good traits were directionally selected in the evolution of O.sativa.2.Variation analysis of wild rice pan-genomesUsing the pangenome iterative assembly strategy,the pan-genomes of 5 AA genome wild rice and 1 CCDD genome wild rice were constructed.Abundant variants were identified in wild rice pan-genomes,including 7.24x10~6-2.60x10~7SNPs,2.01x10~6-7.24x10~6In Dels,68335-177680 SVs and 4457-19347 PAV genes.Further analysis of the variation in the selected regions during the evolution from O.rufipogon to O.sativa showed that the SNP density in the selected region of chromosome 12 was the highest,and the SNP density of chromosome 4 was the highest in the process of evolution from O.longistaminata to O.sativa.The results of the ns SNPs analysis of the selected genes in O.sativa gene flow showed that the ns SNPs in the selected genes had the same position and genotype in O.longistaminata and O.rufipogon,and the ns SNPs of these selected genes may be retained by directional selection,which is very likely to affect the function of the selected genes.The results of repeat sequence analysis of the pan-genomes of 6 wild and cultivated rice showed that the repeat sequences in rice were mainly composed of transposons(TRs).The Single-locus TRs and Muti-locus TRs were evenly distributed in the tandem repeat sequences.TE-derieved TRs accounted for half of all TRs,and LTR/Gypsy,LTR/Copia and SINE/t RNA were the highest transposable activity in TRs-related TEs.Through the analysis of the transposons in the selected gene,it was found that frequent transposon insertion events occurred in cultivated rice during the evolution of wild to cultivated rice.The homology analysis of genes between wild and cultivated rice pan-genome showed that a large number of genes were lost during the evolution of wild to cultivated rice.More than 40%of the genes were lost in the five AA wild rice genome,and nearly two-thirds of the genes in CCDD genome wild rice were lost in the process of evolution.Identification of RGAs and WRKY Transcriptional factor in the pan-genomes of 6 wild and cultivated rice result showed that a lot of RGAs and WRKY Transcriptional factor existed in the unplaced contigs.Most of the RGAs identified in O.longistaminata and O.rufipogon in the evolutionary gene flow of cultivated rice are PAV genes,and these RGAs belonged to PAV genes are more likely to be lost.3.Screening of candidate genes for salt stress toleranceBy combining the result of the differentially expressed gene set of O.rufipogon and Nipponbare under salt stress and the evolutionary analysis of the cultivated rice,we identified 74 genes in the selected and lost regions during the evolution of cultivated rice.42 of these candidate genes of salt tolerance were identified in the selected regions including 19 differentially expressed RGAs and 1 WRKY transcription factor.Among these genes,9 RGAs had ns SNPs that might affect protein function.In the lost regions of the cultivated rice,32 genes related to salt stress were identified,among which 11 were differentially expressed RGAs and and 1was WRKY transcription factor.The salt stress tolerance gene WRKY67 in rice was preliminarily confirmed using q PCR.In summary,in this study we analysed the evolutionary relationship between wild and cultivated rice and obtained the selected gene sets of cultivated rice during the evolution of wild to cultivated rice.By assembling the pan-genome of wild rice,the lost gene set of cultivated rice during the evolution of wild to cultivated rice was identified.Based on these two gene sets,and combined approach with the results of transcriptome data analysis showed that,a total of 42 candidate genes of salt stress tolerance were screened in the selected regions,and 32 candidate genes of salt stress tolerance were screened in the lost regions.The function of WRKY67 is confirmed through q PCR.This study not only broadens the gene resource pool for the resistance improvement of cultivated rice,but also provides the basis and theoretical guidance for the subsequent cloning of resistance genes. |
