Maize Population Variation Mining And Genetic Dissection Of Complex Quantitative Traits Based On Omics Data

Maize(Zea mays)is one of the most diverse crop species containing tremendous variation,making it a perfect model organism for both genetic and genomic studies in plants.In present study,a maize Complete-diallel design plus Unbalanced Breeding-like Inter-Cross(CUBIC)population,a waxy maize population and a regular maize population was used for population-level genomic studies and analysis of genetic architecture of complex traits.The main results are summarized as follows:1.High density variation map of maize CUBIC population and construction of Maize-CUBIC database We provided an integrated strategy in variant calling and imputation for a newly developed multi-parent synthetic maize CUBIC population at ~1x sequencing coverage.Over 14 M SNPs,430 K In Dels,660 K SVs,600 M PAV sequences were finally obtained,which representing a comprehensive high-density variant map for CUBIC population.The SNPs set was found >97% consistency compared with genotypes derived from arrayand assembly-based methods,while the percent of validated large structural variants was considered as ~60%.A database named Maize-CUBIC was constructed for maize CUBIC population,which includes above genomic variations,gene expression,phenotypes of CUBIC population.Based on genomic variations,the database demonstrate the mosaic structure for each progeny,reflecting a high-resolution reshuffle across parental genomes.And two different methods of GWAS results were provided for dissecting genetic mechanisms of 23 agronomic traits.Additionally,BLAST and Primer Design tools are developed to help follow-up analysis and experimental verification.All these original data and related analysis results can be accessed through some user friendly online queries and web interface dynamic visualization tools,as well as downloadable documents.These data and tools provide valuable information on genetic and genomic studies of maize and other species.2.The genetic architecture dissection of flowering time traits in maize The high density variation map of maize CUBIC population was further shown to be excellent in association mapping of flowering time traits in maize.Two different mapping methods,single variant GWAS and haplotype based GWAS were applied for QTL mapping of flowering time related traits in maize CUBIC population.A total of 28,29 and 34 QTLs were detected for three flowering time related traits DTT,DTA and DTS.We selected and verified the candidate genes in small QTL regions with high mapping accuracy,and analyzed function patterns of some typical QTL regions.Meanwhile,flowering time is a major reason that maize can adapt to temperature climate.Whole genome selective sweep analysis was applied to tropical and temperate subgroups in a regular maize population to reveal the genetic architecture of maize flowering time related traits adaptation from tropical to temperate climate.In total,33 selection candidates among 33.13 Mb selection regions were found to be involved in the flowering time pathways based on the studies of their orthologous genes in rice and Arabidopsis thaliana,including the strongest selection signal Tunicate1.Among them,Zm COL9,in photoperiod pathway and Zm PRR7 in circadian clock pathway,were further conducted experimental verification by CRISPR/Cas9-based gene editing techniques.3.Analysis of genetic architecture and metabolic basis of waxy maize flavor Through integration omics analysis and comparative genetic analysis of 318 waxy maize with 507 regular maize inbred lines,we found that not only the famous gene waxy1 and starch pathway have been selected during its breeding history,other genes and pathways,such as benzoxazinoid and brassinosteroid pathway,are also involved in the selection of waxy maize both on genomic and transcriptional level,which shape the dramatic differences between waxy and regular maize.Further we found that the divergence of these metabolic pathways is probably due to artificial selection of flavor-associated traits of waxy maize.In order to deeply explore the metabolic basis of waxy maize flavor related traits,over 1600 metabolites are qualified in the waxy population.And totally 84 metabolites were identified as the important contributions to flavor and consumer liking by large scale tasting experiences.These metabolites can be categorized into sugar and sugar derivatives,amino acid-related and some secondary metabolites.The genome-wide association study permitted the identification of genetic loci that affect most of the flavor-associated metabolites and 458 candidate genes were identified.Our findings not only shed lights on the selection of waxy maize,but also provides useful resources and knowledge for high nutritional maize breeding.