Combined Environment Gwas And Transcriptome Analysis To Reveal The Regulatory Network Of Maize Drought Tolerance

Plants,especially crops,are extremely sensitive to stress which leads to growth and development defects and reduced yield.Therefore,it is important to analysis this mechanism to clarify the response of plants to stress.Northeast area is a major grain production area in our country,where maize as an important food and forage crop is one of the most widely grown crop.Due to geographical and climatic conditions and other factors,maize production is threatened by various biotic and abiotic stresses.Drought is one of the most common abiotic stresses,resulting in a large reduction in maize harvest or even no yield.Therefore,it is particularly urgent to study the adaptability of maize to stress,detect the genes related to stress tolerance and analyze the stress tolerance network in maize.This thesis has three parts.First,the association between genomic variation with local temperature and precipitation in Arabidopsis among a set of natural population was analyzed by environment GWAS,and a number of genes required for stress tolerance were identified.Second,transcriptome analysis of two maize inbred lines with opposite phenotypes under drought treatment was performed to analyze the differences in water response,and to reveal drought tolerance mechanism and identify drought tolerance genes of maize.Third,GWAS analysis of water environmental factors and drought tolerance transcriptome analysis was used in combination to identify drought-related genes,which revealed drought tolerance gene network,which laid a groundwork for breeding drought tolerant maize varieties.Research contents and conclusions are as follows:1.Analysis on the correlation between the genetic variation and environment factors to assess the feasibility to identify the stress tolerance genes from environment GWAS.1)This is the first study to our knowledge that tests the function of a relatively large number of genes associated with local environment parameters.This study analyzed environment GWAS related to local temperature and precipitation in 1129 atural populations of Arabidopsis thaliana,and identified 29 temperature-related genes and a large number of temperature-drought-related SNP data.In addition,the growth,development and stress tolerance of these 29 loss-of-function mutants were evaluated at 5 temperatures.Twenty of these genes were found to affect the mutant’s growth and development or tolerance to stress at one or more of the temperatures.Significantly,genes associated with the highest temperature were more likely to function at higher temperatures,while genes associated with the lowest temperature were more likely to function at lower temperatures.In addition,five genes were identified in this study,whose geographical distribution was significantly different between the reference group and the variant group according to the genomic variation.Moreover,in these geographical locations,the five tested genes significantly improved the growth and development of plants and enhanced the tolerance of plants to stress,indicating that there is a strong correlation between genomic variation and environmental adaptation.2)The precipitation GWAS was conducted on the Arabidopsis natural accessions too.Candidate precipitation associated genes are involved in water response,plant hormone signal transduction and metabolic related biological processes.Among these genes,ten have been functionally characterized as drought tolerance genes,suggesting many others might also contribute to drought tolerance.In addition,the analysis of eight genes revealed an association of genetic variation and the drought adaptation.2.Transcriptome analysis of drought-tolerant and drough susceptible maize inbred lines to identify pathways related to drought tolerance response.The transcriptome differences between drought tolerant and sensitive maize lines are still unknown,even though several studies have focused on selecting drought tolerant maize lines and analyzing drought response mechanisms in maize.A total of3147 differentially expressed genes(DEGs)were identified by RNA-seq analysis on the leaves of drought sensitive line B73 and drought tolerant lins W9706 under drought treatment.The up-regulated DEGs in W9706 gene were enriched in ABA signal response,wax biosynthesis,CHO metabolism,signal transduction and brassinolide biosynthesis,while the down-regulated DEGs were enriched in stomatal movement and other specific processes.Therefore,drought tolerance was related to the differential expression of genes,and drought tolerance in W9706 likely results from a faster response to stimuli under water shortage,the stronger ability to retain water and the more stable cellular environment.This provides a mechanistic basis for breeding drought-resistant maize lines.3.Combined analysis of precipitation GWAS and maize drought transcriptome to identify drought tolerance related genes and analyze maize drought tolerance regulatory network.This study uses environment GWAS to idneitify genomic variation that are associated with local drought stress.In addition,transcriptome analysis can reveal the drought response genes.As each analysis yields many(in thousands)candidate genes associated with drought tolerance,combined environment GWAS and drought transcriptomics was used to further select candidate genes for drought tolerance.There was a total of 8 precipitation environmental factors,among which GWAS related to precipitation in the driest month and the driest quarter have a high correlation with transcriptome analysis.GO analysis results showed that genes associated with these two dry environment factors were involved in environmental stimulus response,brassinosteroid synthesis and other biological processes.In contrast,the GWAS associated with precipitation in the wettest month and wettest quarter have a lower correlation with differential expressed genes from transcriptome analysis which likely was due to low gene numbers.Analysis of the candidate genes from combined analysis indicate that drought resistance in maize may involve biological processes such as response to environmental stimuli and brassinosteroid synthesis.Eight candiate genes were selected for functional study in Arabidopsis.Therefore,the combination analysis of the GWAS and transcriptome could be used to reveal the regulatory network for drought tolerance in maize.In conclusion,this study revealed the feasibility of using environmental GWAS to identify stress tolerance related genes.It analyzed drought tolerance mechanism in maize through the combined analysis of environmental GWAS and transcriptomics,and it built a foundation for future research on drought tolerance mechanism and breeding drought-tolerance maize lines.