Genome-wide Association Analysis For Chilling Tolerance Indices At The Stage In Maize

Maize(Zea mays L.)is one of the main food crops in the world.It has high yield and high nutritional value.It is widely used as raw materials in food,feed and fuel industries.As a thermophilic plant,the seedlings are vulnerable to low cold stress during growth,especially in early growth stage.Low temperature chilling injury reduces the life process of crops,astricts of the distribution range of plants and reduces the total yield.Improvement of cold tolerance has always been one of the goals of breeders.In addition,with the maturity and innovation of GWAS technology,more and more scientists apply GWAS technology to cold tolerance research of plant-related traits,which can accurately screen regulatory genes.Therefore,in this study,genome-wide association analysis(GWAS)was used to map five cold-tolerant traits in 205 maize inbred lines.SNP loci affecting cold-tolerant traits at seedling stage were screened and candidate genes were obtained,which provided a theoretical basis for the future breeding of maize seed resources with high stress-resistance.Main findings are as follows:(1)Five indices related to cold tolerance were measured and analyzed in 205 maize inbred lines under low temperature stress.There was a significant positive correlation between fresh weight of maize seedlings and root length,plant height and dry weight,with Pearson correlation coefficients of 0.27,0.29 and 0.55,respectively.There was a significant negative correlation between fresh weight and ion permeability,with Pearson correlation coefficient of-0.25.In addition,the correlation between plant height and root length,ion permeability is not significant.The experimental results may indicate that there is no direct relationship between plant height and root length,ion permeability.(2)Through the analysis of five phenotypic measurements among different subsets,it was found that the data distribution range of temperate inbred lines was significantly better than that of tropical or subtropical regions,indicating that the cold tolerance of temperate inbred lines was better than that of tropical or subtropical inbred lines.In addition,the actual measurements of five cold tolerance traits also existed in the four subsets.There are differences.The above results indicate that the population structure of the subpopulation has some influence on cold tolerance,and the difference of cold tolerance in the population materials may be mainly due to the difference of geographical distribution.(3)In this experiment,45 independent significant SNP loci related to cold tolerance at seedling stage were identified based on the measured data of five cold tolerance traits.113 candidate genes were screened and classified into eight categories: 23 genes in signal transduction pathway,35 genes in metabolic regulation pathway,16 genes in transcriptional regulation pathway,8 genes in cell transduction pathway,6 genes in DNA edition,2 genes in secretion pathway,1 gene in RNA edition,and 25 genes whose functions are unknown.(4)Twenty-five candidate genes were identified at the significantly associated SNP loci in this study.By analyzing the homologous genes in Arabidopsis thaliana and rice and previous research results,we found that GRMZM2G157177,GRMZM2G022242,GRMZM2G311059,GRMZM2G080516,GRMZM2G093744,GRMZM2G145756,GRMZM2G174673,GRMZM2G093858,GRMZM2G028054,GRMZM5G875502 and GRMZM2G29135,respectiely.Because of its function annotation in the homologous genes of Arabidopsis thaliana and rice,genes can play genetic and physiological roles in cold response process,and can be used as important candidate genes in future research.(5)Sequence alignment of five representative cold tolerance related genes(GRMZM2G080516,GRMZM2G157177,GRMZM2G028054,GRMZM2G022242,GRMZM2G093744)with homologous genes in different species showed that the homology was over 80%.Conservative domains related to cold tolerance were found in the sequences:AP2/EREBPF domain,b ZIP domain,MYB domain,UGTs domain and b HLH domain,The expression of five cold-tolerant genes in maize was analyzed by q RT-PCR.It was found that after low temperature induction,the expression of five cold-tolerant genes increased first and decreased gradually,which indicated that these five representative cold-tolerant genes were related to plant stress resistance.