Mining Of Key Genetic Loci For Plant Architecture Of Nitrogen Response In Maize Based On Genome-wide Association Analysis And Linkage Analysis

Nitrogen is a crucial nutrient element in plant growth and development.Rational use of nitrogen fertilizer will significantly increase crop yield,while insufficient nitrogen nutrient supply will reduced crop yield.However,excessive application of chemical fertilizer would lead to easily environmental pollution.Therefore,how to improve the nitrogen utilization efficiency,which is one of the most important issues in maize breeding at present.It has become one of the important directions by screening high-efficiency nitrogen varieties,which can reduce the application of nitrogen fertilizer in the field.As one of the most direct evaluation indexes of maize growth,plant architecture architecture is a key factor in affecting maize planting density,photosynthesis and grain yield.So it is necessary to identify key QTL about plant-architecture related traits under nitrogen architecture treatment.In this study,an natural diverse population(AS)containing 226 maize inbred lines and a single segment substitution population(SSSLs)containing 145 lines were used as materials.Combining with linkage analysis and genome-wide analysis strategy,nine maize plant architecture traits in six environments were evaluated under low nitrogen(N0),medium nitrogen(N1)and high nitrogen(N2),respectively.The purpose of this study was to identify the genetic loci controlling ideal plant architecture of maize under different nitrogen treatments,and to excavate QTL(or candidate genes)related to plant architecture traits and nitrogen response in large-scale,so as to provide scientific support for revealing the physiological mechanism of maize plant architecture and nitrogen efficient utilization.The main results were listed as follows:(1)The plant height(PH),ear height(EH),total leaf number(LN),the tassel spike length of spindle(TL),the tassel primary branch number(TPBN),leaf length(EL),leaf width(LW),chlorophyll content and leaf angle were investigated in six environments for three levels of nitrogen treatment.Phenotypic data analysis showed that phenotypic value of the nine plant architecture related traits varied widely,and the nitrogen response for different traits was also diversity.These results indicated that the population was suitable for genome-wide association analysis.Under the three nitrogen treatments,the genotypic effects of the 9 plant architecture traits were extremely significant(P < 0.01).In addition,in the SSSLs population,9 plant architecture related traits showed quasi-normal distribution under different nitrogen treatments,each trait had bidirectional super parent separation and showed continuous variation.These results indicated that the nitrogen response of different corn plant architecture related traits belonged to quantitative traits,and were controlled by multiple genotypes.(2)Based on the genotype microarray containing 60,000 SNPs markers,genotype identification of the associated populations was carried out.According to the screening criteria of high-quality SNP marker,8,905 SNPs evenly distributed throughout the whole genome,with rich diversity and low deletion rate were selected for further population structure,principal component analysis(PCA)and association analysis.The Farm CPU model was used to analyze the genome-wide association of plant-type related traits in 6 environments with three nitrogen levels.A total of 41,47 and 41 SNP sites were significantly correlated with plant architecture under the three nitrogen treatments,respectively.Bioinformatics analysis showed that there were 73 candidate genes in the target QTNs linkage region,including 64 genes with known functional annotation.Under the treatment of N0-N1,one SNP marker of PZE-108074276,which controlled spike length,branch number of male spike and plant height simultaneously,which was detected on chromosome 8.The SNP markers of PZE-101175276 and PZE-103054355,which controlled the spike height and the spindle length of male flowers,were located on chromosome 1 and chromosome 3respectively.Under the treatment of N1-N2,a SNP marker of PZE-10504973,which controlled chlorophyll content,male flower branch number and leaf length,simultaneously,was detected on chromosome 5.Two SNP markers of PZE-108079256 and PUT-163A-74240952-3655,which controlled spike height and male spike spindle length,were located on chromosome 8 and chromosome 2,respectively.The SNP marker of PZE-108052544,which controlled plant height and spike height,was located on chromosome 8.(3)Based on the SSSLs population,QTL mapping of plant architecture related traits under three nitrogen treatments were performed.A total of 83 QTL controlling plant architecture related traits were detected,including 24 under N0 treatment,29 under N1 treatment and 30 under N2 treatment.A total of 481 candidate genes were identified by bioinformatics analysis,including 430 genes with known functional annotation.There were no common QTL among three nitrogen treatments,which indicated that the plant architecture characters were greatly influenced by nitrogen fertilizer and the number of gene expression was different at different N levels.However,under the treatment of N0-N2,one leaf length QTL q LL5(q LLLN5,q LLHN5)was detected,which could explain 27.39% and 23.57% of leaf length phenotypic variation,and all allele with synergistic effect were derived from the parent of Zong3.These genetic loci would not only provided some candidate sites for the MAS in maize breeding,but also provide some new candidate region for gene cloning in future work.(4)Based on the reference physical map of B73,the enrichment analysis was performed.Results showed that there were 3 co-localizing sections(S62229237-S63525343,S167607737-S168626993 and S879531-S89101165)between the genome-wide association analysis and linkage analysis.These loci were located on chromosome 3,5 and 10 of maize,respectively.Bioinformatics analysis showed that there were 18 candidate genes with known functional annotation in these regions,including chloroplast protease,protein phosphorylation,transcriptional regulation,transmembrane transport and stress response.Their functions involved nitrogen energy metabolism,photosynthesis,biological regulation,signal transduction and stress response.