Genomic Variation And Drought Stress Response In Different Drought-tolerant Maize Inbred Lines

Drought is one of the major abiotic stress factors limiting agricultural production all over the word,increasing research on drought tolerance of maize,grasping the mechanism of maize response drought stress and exploring the related drought-tolerance genes deeply,it has a far-reaching impact on maize drought-tolerant molecular breeding and food security.This research with 10 domestic backbone inbred lines as materials,comprehensive analysis of four types of genetic variation in the genome using WGS,including single nucleotide polymorphism(SNP),insertion deletion marker(InDel),structural variation(SV),and copy number variation(CNV).According to the result of drought tolerance of classification,genetic variation and the corresponding genes associated with drought tolerance.And combing with 10 inbred lines of RNA-seq under WW and WS condition,screening DEGs in drought stress response significantly,and statistical analysis of relationship between DEGs and SV/CNV variation.To reveal the genetic variation of different drought resistance of maize inbred lines and drought stress response mechanism of the interaction.The main results were as followings:1.Using WGS detected the genetic variation of 10 maize inbred lines,obtained 52,692,769 SNP sites,10,170,325 InDel sites,643,485 SV sites and 95,507 CNV sites in total.Through PCA of four genetic variants,explained the relationship between drought tolerance and genetic variation of inbred line.2.Comparing the drought-tolerance and drought-sensitivity groups in 10 maize inbred lines,obtained 648,552 genetic variants with differences between two groups,including 551,903 SNP sites,96,345 InDel sites and 304 SV sites respectively.SNP is the main type of genetic variation,including 6 types of mutations,the most of which is A-G,had 198,295,the least is C-G,had 31,040.SV contains four types of variation,including deletion,reversal,chromosomal heterotopic and complex structural variation,including 241,2,52 and 9 respectively.Further comments analysis showed that the SNP,InDel and SV are mainly distributed in intergenic.3.To analyze the variation between different drought-resistant materials,selected genetic variation with differences between the two groups of expressed genes as candidate genes.The RNA-seq performed on 10 maize inbred lines under WW and WS conditions,with the FC of gene expression between the two conditions,obtained 9,182 DEGs,including 3,082 up-regulated genes and 6,100 downregulated genes.The genes with significant differences between the two types of drought-resistant materials overlapped with the candidate genes found by genomic variation,had 19 and 34,respectively.4.A total of 14,935 genes were expressed for different genetic variations,comparing with control-set genes from random selection,the results showed that candidate genes expression was higher significantly.Analyzing the expression changes of candidate genes and control-set genes under drought stress,the results showed that the proportion of up-regulated genes in the inbred line was not different significantly(except the inbred line X178),and down-regulated expression genes were different significantly in the inbred lines Ji81162,B73,Chang7-2,Tie7922 and X178.The FC-standard deviation of gene expression was not significant.5.GO enrichment for the candidate genes of response significantly in drought stress,found that the function of the main enrichment had biological regulation,RNA biosynthetic process and response to abiotic stimulus.The genes involved in abiotic stimulation response may be important genes in drought stress response.A total of 2,492 candidate genes had known functional annotations,mainly including structural proteins,energy metabolism,material metabolism,signal transduction,redox reaction and transcriptional regulation.6.Analyzing the genetic variation of SV and CNV in the candidate genes respectively,there were 64,47,22 and 30 SV sites in upstream/downstream regions(within 2Kb)and intron/exon regions respectively.SV only exists in drought-sensitivity groups,after drought stress,the gene expression of drought-tolerance materials was higher.There were 21,291 CNV-related expression genes in the candidate genes,the expression ratio and FC-standard deviation were higher significantly than control-set genes from random selection.