Study On The Genetic Basis Of Plant Height And Ear Height Of Maize In NAM Nested Population

Maize is an important food and economic crop,and an important source of animal feed and biological raw materials.Plant height（PH）and Ear height（EH）are two important traits of maize（Zea mays L.）,which are closely related to lodging resistance and planting density.In this study,the NAM nested population constructed by Ye107 as the common parent and seven inbred lines（Q11,Y32,D39,CML312,CML373,TML02,CML395）from different heterosis groups was used as the research material.Based on SNP molecular markers,8 parents and 1215 RILS(F_2:7)populations were genotyped by parent resequencing and simplified genome sequencing（GBS）,respectively.The plant height and ear height phenotypes of NAM nested population RILs were identified in Dehong and Baoshan.The genome-wide association study（GWAS）and high-density genetic linkage map（QTL mapping）were used to study the co-localization of genes or QTL loci controlling plant height and ear height in maize,and the heterosis between parents of NAM nested population was analyzed to achieve the following experimental purposes:（1）The mapping results of GWAS and QTL mapping were compared to find out the overlapping QTL intervals and explore the location distribution of these co-located QTLs on maize chromosomes.（2）Functional annotation,candidate gene prediction and haplotype effect analysis of co-located QTLs were carried out to find out the candidate genes most directly related to maize plant height and ear height,and their genetic regulation mechanism was analyzed to explore the application value of candidate genes in maize breeding.（3）It laid the foundation for further cloning and verification of related candidate genes,and also provided a theoretical basis for molecular marker-assisted breeding（MAS）of maize plant height and ear height.（4）The heterosis relationship between plant height,ear height and yield of maize was studied,and the utilization value of’triangular heterosis group’theory in reducing plant height and ear height to increase yield was further verified.The main results are as follows:1.A total of 264,694 high-quality SNPs were found by genotyping 1215 RILs in the NAM population using GBS technology.Combined with the phenotypic data of plant height and ear height in Dehong and Baoshan,a total of 125 SNP loci associated with traits were detected by GWAS analysis,of which 56 were associated with PH,49 were associated with EH,and 20 were associated with EP.These loci are distributed on 9 chromosomes of maize except chromosome 3.In order to further determine the SNP loci stably associated with the target traits in the two environments of Dehong and Baoshan,under the four conditions of EH＿BLUP,PH＿BLUP,EH＿DH and PH＿DH,around the GWAS-SNP signal peak（chr1＿210043412）before and after each 20 kb region,a major QTL locus（containing multiple significant SNPs）was located in the 207-210 Mb position region of chromosome 1,named Qtl-chr1-EP.2.A total of 13,936,14,450 and 13,683 polymorphic SNPs were screened in CML312-Ye107,D39-Ye107 and Y32-Ye107 RILs populations,respectively.Based on these SNPs,three high-density genetic linkage maps were constructed.The total genetic distances of the maps were 3473.92 c M,3017.52 c M and 3315.86 c M,respectively.QTL mapping of PH,EH and EP traits was performed using these three maps.A total of 19 QTLs closely linked to PH,EH and EP were identified,of which 4 QTLs were associated with PH.A total of 30.7%of phenotypic variation was explained,6 QTLs were associated with EH,64.92%of phenotypic variation was explained,9 QTLs were associated with EP,and 75.43%of phenotypic variation was explained.In order to identify QTLs significantly associated with PH,EH and EP traits from the three RILs genetic linkage maps,we compared the physical locations of the QTLs linked to PH traits in the D39-Ye107 RILs population and the QTLs linked to EP traits in the Y32-Ye107 RILs population.A QTL that simultaneously regulates plant height and ear height traits in maize was mapped in the 200-260 Mb region of chromosome 1.3.In order to further verify the accuracy of GWAS analysis results,so as to achieve a more accurate positioning effect on the target traits,we compared the positioning results of genetic linkage map（QTL mapping）and genome-wide association analysis（GWAS）.The results showed that the QTLs mapped by QTL mapping at 200-260 Mb on chromosome 1 overlapped with the QTL signal peaks mapped by genome-wide association analysis（GWAS）at 207-210 Mb on chromosome 1,and the positioning results of the two methods were mutually verified.Therefore,this study used GWAS and QTL mapping methods to co-locate an overlapping QTL interval（207-210 Mb）on chromosome 1,which was defined as the main QTL that simultaneously regulates maize plant height（PH）and ear height（EH）traits,namely Qtl-chr1-EP.4.A total of 105 candidate genes were obtained by gene function annotation of the significantly associated SNPs.Furthermore,through LD Block analysis and RNA-seq gene expression map analysis,it was finally determined that Zm00001d031938 was the candidate gene regulating plant height（PH）and ear height（EH）development in this study.It encodes UDP-N-acetylglucosamine peptide N-acetylglucosamine transferase,which is homologous to rice OS08G0559300 gene,and may regulate the development of plant height and ear height traits by regulating GA content in maize.Haplotype analysis showed that it had the specific regulatory function of reducing plant height and ear height of maize.The genetic regulation mechanism of candidate gene Zm00001d031938 on plant height and ear height of maize was preliminarily analyzed.5.The results of heterosis analysis of plant height,ear height and yield traits among parents of NAM nested population showed that when Reid germplasm represented by Ye107 was combined with Non-Reid germplasm and Suwan1 germplasm,the mid-parent heterosis value was higher,which could form better heterosis complementation,and the probability of strong heterosis combination was high.There is a certain positive correlation between the heterosis of maize plant height and ear height and yield.Under certain planting density,when the ear plant height ratio>0.45,the yield of maize tends to decrease with the increase of ear plant height ratio.Under the heterosis model of’Non-Reid×Reid’and’Suwan1×Reid’,TRL02×Ye107 has bred excellent variety Yunrui 88,D39×Ye107 has bred excellent variety Dedan 5,which further proves that it is feasible to use the theory of’triangular heterosis group’and’triangular heterosis model’to breed hybrid groups with high yield and low EH/PH（EP）value.