Genomic Variation And Evolution Of Elite Germplasm In The Spring Maize Zone In Northern China

Maize is an important cereal crop to ensure national food security,and the spring maize zone in Northern China is the dominant area of maize production in China.Next generation re-sequencing technology with 30 ×coverage was used in this study to analyze genomic variation and evolution of 364 parental lines of major maize single-cross hybrids in the past 50 years in Northern China.The main results are as follows:(1)A fine map of genomic variation of elite maize in Northern China was constructed.Genome-wide variation analysis suggested that different types of variations are dominantly distributed in intergenic and promoter regions in a highly similar pattern,and the variations are mainly related to long terminal repeat transposable elements.(2)The analysis of population genetic structure showed that 364 inbred lines could be divided into seven known subgroups SPT,LRC,Lan,PA,PB,BSSS and Iodent,and one mixed subgroup.Genetic diversities within and among populations vary to different extent.(3)Maps of genomic selection signals of elite maize in Northern China were constructed.A large number of known loci or genes for flowering time,plant architecture,and yield traits could be found in the selective sweeps.KEGG pathway analysis indicated that the overlapped selected genes among different eras of breeding are mainly involved in biological pathways such as spliceosome,plant hormone signal transduction,and protein processing in endoplasmic reticulum.The selected genes in the middle stage(1980&90s)are mainly involved in biological pathways such as carbon fixation in photosynthetic organisms and carbon metabolism,while those in the recent stage(2000&10s)are mainly involved in biological pathways such as flavonoid biosynthesis,plant-pathogen interaction,phenylpropanoid biosynthesis and biosynthesis of secondary metabolites.(4)Comprehensive analysis of phenotypic data collected from five locations in two consecutive years showed that,with the advance of breeding progress,the anthesis-silking interval of elite maize in Northern China gradually shortened,the relative ear height gradually decreased,the leaf angle gradually decreased,the tassel branch number gradually decreased,the grain length gradually increased,the hundred-kernel weight gradually increased,and the grain yield per plant gradually increased.(5)Through genome-wide association study,a total of 259 loci were identified to be significantly associated with agronomic traits,of which 30 were associated with flowering time,181 were associated with plant architecture,and 48 were associated with yield components.The analysis of five loci and candidate genes associated with improved traits suggested that the frequency of favorable alleles gradually increased with the advance of breeding progress.(6)ZmMADS69,an important locus for maize flowering time improvement in Northern China,was taken as an example to reveal the distribution and evolution of its favorable haplotype during modern maize breeding.Hap1,which was selected in the breeding progress,is mainly distributed in Iodent,Lan,and BSSS,while HapCNV,which was not selected,have a better effect on promoting flowering than Hap1,and is mainly distributed in SPT and Mixed.This study revealed the mechanism for formation and evolution of elite maize germplasm in Northern China on the whole genome level,and will provide basic support for the genetic improvement and molecular design breeding of maize in Northern China.