Mining And Analysis Genome Heat Resistance Genes In Rice(Oryza Sativa L.)

Rice(Oryza sativa L.)is one of the most important food crops for over half of the world's population,while China is the world's largest rice producer and consumer.Rice plant grows under a suitable temperature,and high temperature will affect the growth and yield of rice plant.Because of the increasing temperature induced by greenhouse,development of new rice cultivars with heat-susceptible ability should be the right way for future rice produce.With the completion of the rice 3K genome re-sequencing project,it is possible to mine and analyze heat-resistant genes in rice from the whole genomic sequencing data.In this study,genome re-sequencing data of 22 rice cultivars with different ability to avoid heat stress was downloaded from rice 3K genome project and NCBI databases.Among them,Azucena(CX151)is a heat-susceptible rice variety,and the others 21 varieties have heat-tolerant ability.Transcriptome data of Azucena under heat stress and differentially expressed genes of CO39 under heat stress were downloaded from the GEO databases of NCBI.The Nipponbare genome downloaded from the website of The Rice Annotation Project(RAP)in the United States was used as the reference genome.The comparative genomics and comparative transcriptome were used to mine heat-resistant genes and analyze their expression patterns in rice.All the results were list below.1.Mining potential genes with the ability to avoid heat stress in riceUsing the Nipponbare genome as the reference genome,the genome re-sequencing data of 21 heat-tolerant varieties and heat-susceptible variety Azucena were mapping to the reference genome.Single-nucleotide polymorphisms(SNPs)were detected in heat-tolerant rice varieties and heat-sensitive rice,respectively.Among them,920,481 high quality SNPs were detected in heat-susceptible rice variety,while 4457430 high quality SNPs were detected in heat-tolerant rice varieties.Non-synonymous SNPs(nsSNPs)and non-sense SNPs(nonsense SNPs)were screened and analyzed from all the above SNPs,which will induce the change of the amino acid sequence encoded by the target gene.Finally,525 common SNPs in 21 heat-tolerant rice varieties were achieved,20 of which were nsSNPs and mapped to 15 genes.These genes are Os11g0587000,Os04g0244400,Os07g0614100,Os10g0168751,Os11g0233000,Os12g0225700,Os01g0153800,Os12g0438100,Os01g0150800,Os12g0631800,Os11g0229700,Os08g0254600,Os10g0133800,Os09g0349700,Os10g0141300.The direction for the next step in the functional verification test of potential heat-tolerant genes in rice was pointed out.2.Mining the up-regulated genes in rice under heat stressAfter downloaded from NCBI's GEO databases,the differentially expressed genes of Azucena under heat stress were obtained by analysis of RNA-seq data.Azucena heat stress treatment for 15 minutes is the most intense.A total of 2486 differentially expressed genes were detected in Azucena under 15 min heat stresses,of which 1480 were up-regulated and 1006 were down-regulated genes.Whilst,3487 differentially expressed genes of CO39 under high temperature stress were detected,among which 1370 were up-regulated genes and 2117 were down-regulated genes.GO analysis of the common differential expressing genes between CO39 and Azucena showed that these common genes were involved in cell homeostasis and protein folding.3.Identifying up-regulated genes with heat-tolerant nsSNPs in riceThree heat up-regulated genes with heat-tolerant SNPs,including Os09g0349700,Os11g0229700 and Os12g0631800,were found in the test 21 heat-tolerant rice varieties.The nsSNP in Os09g0349700 with known ability to improve water usage induce the change of aspartate at site 96 by threonine,which might change the gene function.Os11g0229700 is a NBS-LRR gene with resistant ability.The expressing abundance of Os12g0631800 in CO39 under heat stress was up-regulated to 5.06 fold,and the nsSNP in this gene change methionine at site 143 by threonine,indicating that it might participate in immue reaction of rice.Summary,in this study,genomic re-sequencing and transcriptome sequencing technology were used to mine heat-tolerance genes and heat up-regulated genes in rice.Finally,15 genes with potential ability to avoid heat stress and 3 heat up-regulated genes with heat tolerant SNPs were achieved,providing evidence for functional identification of these genes in future research work.