Genome-wide Evolution Of R Genes In Setaria Italica And Closely Related Grass Species

Foxtail millet is challenged by a variety of diseases during the growth process,and the cultivat ion of disease-resistant varieties is the most effective measure for disease control.As one of the largest gene families in plants,disease-resistant genes with NBS domain,also called R gene,are widespread and abundant in plants playing an important role in disease-resistant and defensive responses.The whole genome sequencing data of S.italica was published in 2012,and the resequencing data of its populat ion was reported in 2013,which provide valuable resources for the study of millet R genes at the genome level.In this study,the genome-wide R genes of S.italica and other grass species were systematically ident ified.By constructing a physical comparison map of multiple genom es of grass species with S.italica as the core,the evolutionary characteristics of R genes in multiple grass species were analyzed.At the same time,using the resequencing data of millet genome,the rule of variation and selection pressure of R gene in S.italica population were discussed.Besides,some functional ident ified R genes were selected to verify their characteristics of evolution and variat ion among the grass species and within the S.italica populations.The purpose of this study is to reveal the evolut ionary relat ionship and the route of R genes in grass species.It can also provide clues for the research of disease resistanc e in S.italica,as well as the selection of disease-resistant cultivation.The main results obtained are as follows:(1)The systematic identif ication of R genes in 11 grass species was completed by searching of the domains in genomes.According to the different distribution patterns in the genome,these genes can be divided into two parts,including tandem duplicat ions(TDs)and singletons.A total of 535 R genes,including 303 R TDs and 232 R singletons were detected in millet.In addition,it was found t hat polyploidy species could increase the number of R genes by whole genome amplif ication,while for species without genome amplification,tandem duplication were used to increase the number of R genes,which is an important way for the rapid evolution of R genes.(2)A set of physical comparative map of 10 grass species is obtained,including 45,748 syntenic orthologous gene families,which serves as an important resource for the evolutionary study of other genes.Through the identif ication and comparison of the syntenic orthologous genes among different grass species,it is found that the R TDs and R singletons adopt different evolutionacry strategies.Based on Ka/Ks analysis between syntenic loci pairs of TDs or singletons,we conclude that R singletons are conserved under stronger purifying selection among different grass species than R TDs,while R genes located at TD arrays have evolved much faster through diversifying selection.It suggests that in grass species the TD sites can provide sequence sources for new disease-resistant functions of R genes in response to different pathogens. Once obtained the sustained and stable resistance functions,the R genes would be retained in the form of singletons to prevent the loss of resistance functions caused by sequence variation.(3)We determined the variome datasets of SNPs and In Dels from the S.italica population after mapping the resequencing data to the reference genome.The functional variat ion rate of the all genes,R genes,TD R genes and singleton R genes is increasing,which suggests that R genes can accumulate a large amount of variat ion to evolve rapidly,with TD locus owing more variants than the singletons.In addition,two indicators named π and Tajima’s D were used to evaluate the genetic diversity and selection pressure of R genes in the populat ion of S.italica.The results showed that the R genes from TD sites are under balancing selection and evolve fast.While the singleton R genes with lower diversity are under purifying selection.This result is consistent with the functional variability analysis.(4)Addit ionally,we checked the synteny relationships of reported R genes in grass species and found that the functionally mapped R genes for novel resistance traits are prone to appear in TD arrays and are heavily divergent from their syntenic orthologs in other grass species,such as Rxo1,the black streak R gene in Z.mays,and Pi37,the blast R gene in O.sativus.These findings indicate that the R TDs evolve faster and accumulate more mutations to facilitate functional innovat ion and cope with variable threats from a fluctuating environment,while R singletons provide a way for R genes to maintain sequence stability and retain conservation of function.