| Drought is one of important abiotic factors limiting the rice growth and production.In this study,an Affymetrix array covering 48,564 transcripts(japonica)and 1,260transcripts(indica)was used to profile the change of genome-wide gene expression and co-expression analysis,try to elucidate the difference of drought introgression lines(ILs)with diverse OTLs and select gene modules with the similar function,which provides the theoretical basis to discover the drought related genes,gene interaction and networks,understanding the molecular mechanism of drought-tolerance(DT)and eventually for the rice molecular breeding.Various varation and new genes would be detected by re-sequencing for the species with reference genome,which is very important for its geneticvariation and breeding.In this study,recurrent parent IR64 and donor BR24(local varieties)&Binam(Iranian cultivars)were selected to build an eight pyramiding lines represent four group genotypes(GG),deeply analysing the five QTL association group(AG)impacted the DT and GY of pyramiding lines by the phenotypic,geneexpression,genome and transcriptome variation and identifying a large of candidate genes within the QTLs related with DT and their pathways,exploring the numbers of structural variation(SV)and new genes in 8 ILs and discusses their effect for the DT mechanism based on the blast from the SVs,pan-genome of PLs and the results from re-sequencing data of 3000 rice lines,discussingthese SVs and newgenes in PLs effecting the DT mechanism.The main results were summarized as follows:1)The grain yield of ILs was signifcantly higher than IR64 under drought stress,while lower or the same with IR64 under normal condition except the GG1;The ILs within same genotype groups had similar phenotypes,thephenotypes of the ILs in different genotype groups were strikingly different,such as GG1(more effective DT mechanism presumedly)with higer grain yield in severe drought stress than that in light stress.2)The five association groups for DT: AG1 and AG2 are the upper reaches of regulatory networks which are present in all ILs,mainly with the DNA-binding funcation and response to stimulus and transcriptional regulation process,enriched in the pathways of protein processing in endoplasmic reticulum,plant-pathogen interaction and thiamine metabolism,such as heat shock protein family,calmodulin-like genes,etc;The AG3 and AG5 mainly play a part in GG1,which are related with photosynthesis,ABA,JA/Auxin,cytokinin and serine/threonine phosphorylation pathway,fatty acid synthesis,thiamine synthesis.The AG4 most in GG2 and GG3 with heat shock protein,spliceosome and Glutathione transferase.3)The pathway osa04141(Protein processing in endoplasmic reticulum)is present in most ILs;Under drought stress,the osa04712(circadian rhythm of plant)only expressed in GG1 which might be relevant to the heading date and flowering time;osa00940(Phenylpropanoid biosynthesis)is present in GG1 and GG3,which contains lignin synthesiselement,is presumed tobe one of the factors impacting the plant height under drought stress.4)Many function-similar modules were got with gene co-expression analysis and selecting some core module of genes of high correlation with the phenotype,which is consistent with DEGs analysis.5)A large of SVs were detected in eight ILs and two donors compared with IR64,most of which are deletion and translocation,the inversion and duplication are fewer but longer.The SVs present in all donors and ILs include RAGs,protein binding and transcriptionfactor.The SVs specially in GGs are related to lectin,germins,cytochromeprotein kinase,etc.Many unknown genes affected by SVs,which are homologous in sorghum,maize and wheat,are highly conservative.The reason is presumably that homologous gene structure and gene variants originate from the ancestor species and replication occurs when new species evolve.6)Nearly 10000 new genes were predicted by the pan-genome analysis in ILs and IR64.The new genes in ILs much more than those in IR64 and mainly consist of core/ Indica-dominant genes in rice germplasm resources.The new genes in GG3 are much more than the others and,the minimum is GG2.Those Nipponbare/new genes specially expressed in ILs is the major source of DT/GY difference wich need to functional verification further.7)Buliding anR package for rice annotation-“org.Osativa.eg db”,which is suit for the Micoaray analysis using R,the version is 0.1. |
