Genetic Basis Of Important Agronomic Traits In Maize Breeding Population

Maize(Zea mays ssp.mays)is one of the most important staple crops around the world which also plays a fundamental role in protecting the food security in China.Maize was domesticated from teosintes about 10,000 years ago around the Balsas River Basin of southern Mexico.Since its cultivation,tremendous efforts have been taken to improve the yield and quality,predominated by the effective utilization of heterosis and molecular markers in recent decades' scientific breeding.Along with this process,abundant genetic variations accumulated in maize,mainly through inheriting from the pre-existing variations in wild relatives and keeping the new mutations during breeding.Dissecting the genetic variants and population structure within modern maize cultivars will help us to understand the genetic basis of agronomic traits and hybrid vigor.In this study,we resequenced 777 individuals in a maize breeding population combined with 102 published resequencing data to construct a high density SNP map.We analyzed the population structure and further dissected the genetic architecture of important agronomic traits by GWAS analysis.We also estimated the proportion of phenotypic variance that can be explained by genetic variance.Below are the main conclusions:1.-65 million SNPs were identified based on the resequencing data of 879 accessions.We inferred that crops experienced strong purifying selection during breeding by analyzing the non-syn/syn ratio.Maize experienced two rounds of genetic bottleneck during domestication and improvement.We also divided the 879 accessions into 12 subpopulations with significant phenotypic differentiation among them;2.We detected the selective sweeps and genes during maize domestication,improvement and modern breeding process by using genetic bottleneck and CLR method.We found that three rounds of selection focused on different sets of genes.Selective sweeps with no protein coding genes show evidence of non-coding transcripts and active histone marks for open chromatin;3.We performed GWAS analysis for important agronomic traits and identified 16 significant loci for 9 traits.We identified candidate genes for 6 newly identified loci and found an interesting loci located between 123.0 Mb and 123.5 Mb on chromosome 8 significantly associated with DTA,DTS,PH EH and De2-Del.Evolution analysis further narrowed down the functional loci into a smaller region(100 Kb)and we identified ZCN8 as the candidate gene;4.Whole genome SNP variation can explain as more as 80%phenotypic variance,while the SNPs that were weakly associated with phenotypes(-logP?6)only explain-13%of the phenotypic variance on average.It implied that the heritability for agronomic traits was not missing.The stringent threshold used to control false positives during GWAS reduced the power to detect loci with small effects.Also,we analyzed the ribosome profiling data in maize seedlings.The mapping efficiency of ribosome profiling data was-12%,with the peak of RPF length located around 30 bp.We found enriched RPF abundance and significant 3 nt periodicity around the start and stop codon.We have set up a pipeline to analyze the ribosome profiling data in maize.Overall,we analyzed the genetic basis of important agronomic traits in maize breeding population.We also identified the selective genes during domestication,improvement and modern breeding of maize and dissected the population structure in modern inbred lines.The results above may be beneficial for the efficient and scientific maize breeding in the future.