Construction Of Quantitative Trait Loci Database And Genetic Dissection Of Tassel Traits In Maize

Maize(Zea mays L.)is an important grain crop.Dissecting the genetic basis of important agronomic traits and coordinating the improvement of high yield,high quality,disease resistance and stress resistance are important ways to breed breakthrough maize varieties.Optimizing male traits not only increases the photosynthetic efficiency of the maize canopy but also facilitates energy redistribution,thus contributing to yield increase.In addition,maize is one of the most successful crops in utilizing heterosis,among which male sterile line is essential to maize hybrid seed production.Therefore,mining of male sterile gene resources is also useful for yield improvement in maize.In this study,we firstly summarized the progress of genome-wide association analysis(GWAS)and constructed a database of quantitative trait loci in maize.The tassel traits were examined through 15 environments in the association panel containing 1223 maize inbred lines.Whole genome resequencing was performed,and GWAS was used to evaluate the genetic loci related to maize tassel traits.Meanwhile,the phenotype of a male sterile mutant(ms20)was studied by cytological observation,and the genic male sterile gene ZmMs20 was cloned by positional mapping.At the same time,transcriptomics,genomic microcollinearity and its application in breeding were further studied.The main results were as follows:1.By analyzing GWAS researcharticles on maize GWAS,a total of 48,339 quantitative trait nucleotide(QTN)related to 183 quantitative traits blonging three categories of main traits were collected,then a consensus physical map was constructed and QTN hotspot region(QH)for different levels of traits was identified,which will be valuable for subsequent genetic mapping and cloning of functional genes,and provides basic data for maize breeding.2.Tassel branch number(TBN),tassel branch length(TBL)and tassel main branch length(TL)were investigated in 1223 maize inbred lines under 15 environments.The phenotypic variation coefficients ranged from 14.52%to 56.12%,indicating that the tassel phenotype of the associated panel had wide diversity.Correlation analysis showed that the correlation coefficient between TBN and TBL significantly positively correlated,while TL showed no correlation with TBN and weakly correlated with TBL.3.The genome of 1223 maize inbred lines was resequenced with an average depth of 14.3×,and a total of 35.5 million variation sites(including SNP and Indel)were obtained.There were 7.48 million polymorphic loci with missing rate<10%and minimum allele frequency(MAF)>5%,among which 116,973 polymorphic loci were located in the gene region.Such results indicated that the population in this study had rich genetic variations.4.Based on population structure,principal component analysis(PCA)and evolutionary analysis,the inbred lines were divided into four subgroups,which contained 286(C1),242(C2),208(C3)and 494(C4)materials,respectively.Combined with phenotypic analysis and material information,it is speculated that the differentiation of subpopulations may be corelated with breeding selection.5.Combining with 6.48 million high-quality SNP markers and phenotypic data of the three tassel traits derived from 37 environmental in total,GWAS was performed,and a total of 645 significant regions were detected.Transcriptome analysis revealed that 1595 candidate genes were expressed at different developmental stages of maize tassel.By summarizing the SNPs significently associated with tassel traits form the published GWAS papers,67 hot spots(HSIs)for TBN and 29 HSIs for TL were identified.Interestly,the associated SNPs in this study were located in 22 TBN and four TL HSIs respectively.6.Through population selection analysis,it was found that there are some differences in π and Tajima’D values among subpopulations.Both Fst and TBN analysis showed that the average differentiation rate between C1 and C3 subgroups was the largest.328 genome-wide selected regions with Fst(C1-C3)>0.25 were identified,and 13 regions overlaped with the significant SNPs of tassel traits,indicating genetic divergence of C1 and C3 could partially explained the genetic variation of TBN traits.Combined with LD block and haplotype analysis,gene Zm00001eb180330 was identified in the overlapping region chr4:92.9～93.1Mb.7.Inbred lines B345 and B704 with similar genetic backgrounds were selected to construct the bi-parental genetic population.A QTL regulating TBN was detected in chr4:12.2-15.3 Mb by linkage analysis,and the value of phenotypic variation explained was 13.48%and the additive effect was 1.42.interestingly,several significant SNPs detected by GWAS were located in this region,indicating linkage analysis and association analysis can be mutually confirmed.8.LG2 was a candidate gene revealed by GWAS,thus knockout lines were developed using the CRISPR/Cas9 technology,and found that TBN of lines lg2208 and lg2-209 showed quantitive changes,suggesting allelic variation of LG 2 has application potential in breeding by modifying tassel traits.9.The ms20 mutant showed typical male sterility,and developmental defects were observed on the epidermis and tapetum of the anthers.Gene cloning by mapbased cloning showed that ms20 was a novel allele of ipe1.Phylogenetic analysis showed that ZmMs20 and its homologues may differentialy evolved between monocotyledon and dicotyledon plants.Similar with other GMS genes,ZmMs20 expressed at specific stages during anther development in maize.Furthermore,phenotype of ms20 mutation is stable under different genetic backgrounds,indicating that it has application potential in hybrid seed production of maize.