Mining Of Genetic Loci For Nitrogen Use Efficiency In Maize Based On Genome-Wide Association Study

Nitrogen is an essential mineral nutrient for plant growth and development.However,there are problems from the excessive application of nitrogen fertilizer in agricultural production.A large number of nitrogen fertilizers did not substantially increase yield,but caused great waste of resources and serious environmental pollution,it is not conducive to the sustainable development of agriculture.Maize is not only an important grain,feed and cash crop,but also one of the world's most widely planted,crop with the largest area and the highest yield,it has important social and economic value.Therefore,dissecting genetic basis of nitrogen use efficiency,mining the genes of nitrogen use efficiency,is of great significance to increase the yield of maize,reduce the usage of nitrogen fertilizers and control agricultural pollution.In this study,139 maize inbred lines were grown in nitrogen input?+N?treatment and without nitrogen input?N?treatment in field condition.Firstly,the effects of different nitrogen treatments on nitrogen use efficiency related?NUE-related?traits were studied.Next,the population structure of association panel was calculated based on 56 K SNP chip markers of 139 maize inbred lines.Further,genome-wide association study?GWAS?was conducted to mine the genetic loci for NUE-related traits by combining genotypic and phenotypic data.Finally,candidate genes were predicted for NUE-related traits based on the LD intervel of significant SNP loci.The main results are as follow:1.Whether under+N or N condition,all NUE-related traits have shown wide variation and high heritability?range from 71.5%to 85.7%?in the population.Except for NHI,the remaining NUE-related traits have shown significant differences in two nitrogen levels.Whether under+N or N condition,the partial correlation coefficient?0.76-0.88?and path coefficient?0.63-0.66?between NutE and NUE were higher than the partial correlation coefficient?0.52-0.80?and path coefficient?0.13-0.40?between NupE and NUE.Based on the cluster analysis of phenotypic value??N-+N?of NUE-related traits,139 inbred lines were divided into 4 groups.2.Based on genetic component>60%,139 inbred lines were classified into 7subpopulations and a mixed population.In which,the genetic distance between P3,P4 and P6are far away from each other.The relationship coefficient of among most accessions were less than 0.1,there was no obvious relationship in the population.When r²=0.1,LD decay distance of whole genome is²00 kb,fastest LD decay in chromosome 1 and 2?¹00 kb at r²=0.1?,followed by chromosome 5?¹50 kb at r²=0.1?.However,the slowest LD decay were seen on chromosome 4 and 9?³30 kb at r²=0.1?.In addition,the LD decay?r²=0.1?of other chromosomes were similar to that of the genome.3.Using FarmCPU method,GWAS was carried out for NUE-related traits,total of 50SNP loci associated with NUE-related traits were detected under different nitrogen treatments and across all 10 maize chromosomes.The most SNPs were identified distributed on the chromosomes 10,number is 11,and the least distributed on the chromosomes 5 and 8,number is 3,respectively.Among them,27 significant SNP loci were detected under+N conditions,and 23 significant SNP loci were detected under N conditions.These SNP loci P values ranged from 8.73×10^-0505 to 3.93×10^-13.4.Based on 50 significant genetic loci,32 possible candidate genes for NUE-related traits were predicted within LD?r²=0.1?interval of peak locus.Among them,20 candidate genes were detected under+N conditions,and 12 candidate genes were detected under N conditions.Gene annotation and GO analysis revealed that functions of these genes including nucleic acid metabolism,amino acid metabolism,protein metabolism,hydrolase activity,transmembrane transport and transcriptional regulation,and so on.Of which,29 genes were involved in nitrogen compound?nucleic acid,protein and amino acid et al.?metabolism process,5 genes were involved in transcriptional regulation process and 2 genes were involved in transport process.