Analysis Of Selected Genomic Regions And Related Genes Mining During Domestication And Improvement In Maize

Maize is an important food crop and economic crop in China,and plays an important role in ensuring food security and promoting national economic development.Maize is evolved from teosinte that was distributed in southern Mexico about 10,000 years ago and has been domesticated and genetically improved.The domestication and improvement of maize is a complex evolutionary process,regulated by a large number of sites.During domestication and improvement,traits such as yield,plant type and adaptability were strongly selected.Mining the key regions of maize domestication and improvement at the genomic level,identifying key gene loci and candidate genes can help to deeply understand the evolutionary rules of maize and have important theoretical guiding significance for our morden breeding.In this study,348 maize inbred lines,68 landraces and 32 teosinters were used as test materials.Population genetic analysis of the test population through simplified genome sequencing and targeted sequence capture.Identify key regions selected during domestication and improvement;GWAS of 21 yield and plant type-related traits in 3 environments of 348 inbred lines,excavation of genetic loci that are significantly associated with agronomic traits;further selection signal analysis and association analysis to determine Key domestication regions and candidate genes that affect agronomic traits.The main findings are as follows:1.A total of 970,844 high-quality SNPs were obtained from simplified genome sequencing and targeted sequence capture of 448 test materials.The population structure and phylogenetic tree analysis divided the test population into three main subgroups,namely inbred lines,landraces and teosinters.The linkage disequilibrium analysis found the attenuation distance of three types of materials:inbred lines>landraces>teosinters.There are significant differences in the minimum allele frequency among the three groups.2.A total of 1,191 improvement regions were detected by selective response analysis at the genome-wide level,with a total length of 43.82Mb and 1,076 genes.There are 971 domestication regions with a total length of 37.03Mb and 775 genes.There are 461 overlapping sections in the domesticated and improved regions.Chromosome 4 exists the most and chromosome 6 the least.3.Whole genome association analysis found a total of 520 loci,with an average of 1.59 associated loci per 1 Mb,of which 37 loci were significantly associated with multiple traits.There are a maximum of 122 loci found on chromosome 2.There are at least 19 loci found on chromosome 10.The SL can be positioned up to 120 at most.The KW and STS both can be found 9 loci at least.There are 1,194 related genes in the vicinity of the association site.There are a total of 448 significant sites in the three types of materials.Examination of the gene frequency revealed that the gene allele frequency of 43 sites changed significantly during the domestication.Among them,6 sites were located in the domestication regions;97 The gene allele frequency of loci changed significantly during the improvement,of which 28 sites were located in the improvement regions,the gene allele frequency of 4 loci changed significantly during domestication and improvement.of which SNP₁0₁38496527 was located both in the improvement and in the domestication.A total of 16 candidate genes were found near the 35 sites mentioned above.These genes mainly exist in the pathways of plant hormone signal transduction,amino acid biosynthesis,and zeatin biosynthesis.4.The scanning of the selection signal and the precise test of the significant associated SNP are both located to the re-sequencing candidate gene GRMZM2G109354,which was analyzed by nucleotide polymorphism analysis and neutral evolution analysis.Subject to choice during domestication/improvement.Nucleotide polymorphism of this gene:Inbred lines<landraces<teosinters,the Indel of the AT base of indel-1444 upstream of it reduced the ear weight and ear grain weight.