| Maize(Zea mays L.),is one of the widely cultivated crops with considerable high yield all over the world.Due to its abundant diversity,maize is also a classical model organism for cytological,genetics and genomics.However,to date,it’s obvious that the traditional mapping strategiesare unable to efficiently address the problems in maize breeding,including adaptation,yield increase and quality improvement.In recent years,the flourishment of Next-generation Sequencing(NGS)technologies and the advancements of statistic methodologies provide an alternative amazing approach for studying the genotype-phenotype association and the corresponding regulatory mechanisms;under which,tremendous progresses have been achieved especially since the release of maize reference genome,bringing up the promising landscape of maize functional genomics.Based on the existing natural population and newly developed multi-parent synthetic population,the present study attempted to:(1)study the regulatory mechanism on maize kernel;(2)explore the genomic and transcriptomic variations contributing to maize temperate adaptation;(3)dissect the genetic architecture of important agronomic traits.The main results are summarized as follows:Ⅰ.By integrating several sets of genomic variant derived from multiple genotyping platforms,a high-resolution variant map(with 2.65 M SNPs)of maize was created and applied to investigate the transcriptional regulation of maize kernel.In total,18,000 genes were identified by analyzing expression quantitative trait loci(e QTL)and it was found that the distant e QTLs and non-coding regions play a critical role in gene expression regulation.Ⅱ.Genomic,transcriptomic as well as phenomic variations were assembled to provide an insight into the molecular mechanism of modern maize temperate adaptation.Taking advantage of population structure in positive selection analysis,it is redeemed that the deficiency of genome-wide association study in analyzing structured traits.The findings of this study suggested the transcriptome regulation is of great importance in maize adaptation in a flexible and dynamic way,resulting to adapt to the varying environments on the global in a short evolutionary period.Ⅲ.With more balanced allele frequencies and larger sample size,the novel genetic design of MAGIC population was proved to be powerful in uncovering the genetic causative factors for 26 kinds of complex agronomic traits.Moreover,due to the prevalence of genetic heterogeneity within the whole genome,a new GWAS method based on heterogeneity was proposed in this study,which was used to detect much more genetic loci(increasing 1～2 times than that of regular method)and to redeem the missing heritability of important maize agronomic traits.Ⅳ.Originated from above synthetic population,the genetic responses to artificial selection in the modern breeding routine were studied in depth by means of proposed multi-scale selection analyses in this research.In addition to the traditional diagnosis,the selection on genetic heterogeneity and epistatic interactions were the critical concern during the breeding process.It was revealed that the selection among different sub-populations was inclined to be against to distinct QTLs,rather than to the alleles at the same locus.The combination of selection analysis and association mapping would probably identify more potential functional loci and provide the sound theories and potential materials for further breeding.Together,this study dug the association between genomic variation and phenotypic diversity,provided valuable clues for the subsequent gene cloning,and accelerated the understanding of maize functional genomics. |
PDF Full Text Request