| Maize yield is one of the most complex quantitative traits, influenced by many factors. There exists a rich functional genetic variation for grain yield in maize germplasm. Identification of these functionally favorable alleles contributes not only to understand molecular mechanism of grain-yield related traits but also to develope functional markers and thus facilitates the development of new germplasm and genetic improvement by marker-assisted selection. Quantitative trait loci (QTL) mapping is an important tool for studying complex traits. However, because of its limitations, QTL mapping is used only in certain cases. Association analysis, a new approach for dissecting complex traits based on linkage disequilibrium, can overcome the limitations of QTL mapping for use in plant genetic studies. Association analysis is an approach to identify the relationship of molecular markers or candidate genes with traits in a given population based on linkage disequilibrium (LD) that complements QTLs analysis in the development of tools for molecular plant breeding. As a high resolution QTL mining techniques, Association analysis can regard diversity of target traits and gene analyses, direct identification of closely related with phenotypic variation functional alleles, and has become a techniques about complex quantitative traits excellent allele mining effectively.In this study, excellent maize inbred populations of Abundant variation were selected from the maize germplasm resources, based on the target sequence capture platform technology of NimbleGen, the target sequences of gene LEAFY, RTCS and dbfl were re-sequenced and identified haplotypes and nucleotide polymorphism loci in our maize elite inbred lines, explain the frequency of these genetic variations in elite maize inbred lines. At the same time, identification and evaluation of grain-yield related traits of these materials, and mining production related functional alleles based on the analysis of candidate gene association. The major results are as follows:Post-domestication selection refers to the artificial selection on the loci controlling important agronomic traits during the process of genetic improvement in a population. The maize genes ZFL1and ZFL2, duplicate orthologs of Arabidopsis LEAFY, are key regulators in plant branching, inflorescence, flower development and reproduction. In this study, the full sequences of the genes ZFL1and ZFL2from62China elite inbred lines were amplified to evaluate their nucleotide polymorphisms and haplotype diversities. A total of118and110variants, including SNP and InDel, were identified from the full sequences of ZFL1and ZFL2, respectively. Although most of the variants were found to be located in the non-coding regions, the polymorhpisms of CDS sequences classified these two genes into16and18haplotypes, encoding16and8deferring ZFL1and ZFL2proteins, respectively. The population of Huangzaosi and its derived lines showed statistically significant signal of post-domestication selection in ZFL1CDS sequences, in addition to the lower nucleotide polymorphism and haplotype diversity than others. However, the locus ZFL2was only found to have been selected in the heterotic group Reid. Further evidence revealed that at least17and16recombination events contributed to the genetic and haplotype diversities of the loci ZFL1and ZFL2, respectively. Association analysis of ZFL1and ZFL2gene of coding sequence polymorphism and phenotypes of yield related traits showed that the encoding regions of the gene ZFL1and ZFL2had high nucleotide diversity and lowlevel LD. Additionally, four and three significant associations between coding sequence polymorphism of ZFL1and ZFL2with some phenotypic traits were identified, respectively.The maize RTCS gene, encoding a LOB domain proten, plays important roles in the initiation of embryonic seminal and postembryonic shoot-borne root. In this study, the genomic sequences of this gene in73China elite inbred lines, including63lines from5temperate heteroric groups and10tropic germplasm group, were obtained, and the nucleotide polymorphisms and haplotype diversity were detected. A total of63sequence variants, including44SNP and19InDel, were identified at this locus, and most of them were found to be located in the regions of UTR and intron. The coding region of this gene in all tested inbred lines carried14haplotypes, which encoding7deferring RTCS proteins. Analysis of the polymorphism sites revealed that at least6recombination events have occurred. Candidate-gene association analysis between genotypes and phenotypes of yield related traits were:two SNP and one InDel sites in RTCS gene of coding sequence were identified significantly to be associated with three traits (P<0.05), cob diameter, branch number of tassel and the rate of seed. Of them, InDel was significantly associated with trait cob diameter with contribution of10.91%; Tow SNP significantly associated with trait branch number of tassel and the rate of seed with contribution of6.132%and7.259%, respectively. Among all6groups tested, only the P heterotic group had a much lower nucleotide diversity than the whole set, and selection analysis also revealed that only this group was under strong negative selection. However, the set of Huangzaosi and its derived lines possessed high nucleotide diversity than the whole set, and no selection signal were identified.The protein product encoded by maize dbfl gene will combine with DIP1protein to regulate ABA responsive gene rabl7expression under drought stress, resulting in improvement of drought tolerance. In order to illustrate the sequence polymorphism of maize gene dbfl, we sequenced the dbf1gene in104maize inbred lines, using the genomic sequence of B73as the reference. A total of48SNP and12InDel were identified among2118bp nucleotide sequences at this locus. Although most of these polymorphic sites were found to be located in non-coding regions,1InDel and3nonsynonymous mutations in coding regions may change the amino acid sequences. The polymorphic sites in the genomic sequences and the coding sequences of maize dbfl classified all the tested inbreds into33and11haplotypes, respectively, In addition, we noticed that7deferring DBF1proteins were encoded by these inbred lines. Analysis of the polymorphism sites revealed that at least9recombination events have occurred in dbfl locus. Furthermore, the evolution of maize dbfl gene in the tested lines fit the neutral theory model. One InDel in dbfl gene coding sequence was identified significantly to be associated with kernel number of ear (p<0.05), and with phenotypic contributions of7.159%. The results provide basic information for analyzing the key candidate genes of dbfl. |
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