Abstract
BackgroundMaize (Zea mays L. ssp. mays) was domesticated from teosinte (Zea mays ssp. parviglumis) about 9000 years ago in southwestern Mexico and adapted to a range of environments worldwide. Researchers have depicted the maize domestication and adaptation processes over the past two decades, but efforts have been limited either in sample size or genetic diversity. To better understand these processes, we conducted a genome-wide survey of 982 maize inbred lines and 190 teosinte accessions using over 40,000 single-nucleotide polymorphism markers.ResultsPopulation structure, principal component analysis, and phylogenetic trees all confirmed the evolutionary relationship between maize and teosinte, and determined the evolutionary lineage of all species within teosinte. Shared haplotype analysis showed similar levels of ancestral alleles from Zea mays ssp. parviglumis and Zea mays ssp. mexicana in maize. Scans for selection signatures identified 394 domestication sweeps by comparing wild and cultivated maize and 360 adaptation sweeps by comparing tropical and temperate maize. Permutation tests revealed that the public association signals for flowering time were highly enriched in the domestication and adaptation sweeps. Genome-wide association study identified 125 loci significantly associated with flowering-time traits, ten of which identified candidate genes that have undergone selection during maize adaptation.ConclusionsIn this study, we characterized the history of maize domestication and adaptation at the population genomic level and identified hundreds of domestication and adaptation sweeps. This study extends the molecular mechanism of maize domestication and adaptation, and provides resources for basic research and genetic improvement in maize.
Highlights
Maize (Zea mays L. ssp. mays) was domesticated from teosinte (Zea mays ssp. parviglumis) about 9000 years ago in southwestern Mexico and adapted to a range of environments worldwide
In addition to the population structure analysis, we carried out a principal component analysis (PCA) using the same Singlenucleotide polymorphism (SNP) data set, and found that the PCA results strongly supported the classification of species, subspecies, and races based on the population structure analysis of the genus Zea (Fig. S2)
We calculated the polymorphic information content (PIC) for each SNP, and found that the genetic diversity was quite similar between the results calculated from two different datasets (Fig. S3E). These results suggest that the ascertainment bias caused by Syngenta SNPs did not affect the global estimation of genetic relationship and genetic diversity in the genus Zea it affected the genetic distance of maize inbred lines
Summary
Maize (Zea mays L. ssp. mays) was domesticated from teosinte (Zea mays ssp. parviglumis) about 9000 years ago in southwestern Mexico and adapted to a range of environments worldwide. Researchers have depicted the maize domestication and adaptation processes over the past two decades, but efforts have been limited either in sample size or genetic diversity. To better understand these processes, we conducted a genome-wide survey of 982 maize inbred lines and 190 teosinte accessions using over 40,000 single-nucleotide polymorphism markers. Maize and teosinte make up the genus Zea, which consists of five species distributed from northern Mexico through Central America [2,3,4]. The annual species Zea mays consists of four subspecies, including the domesticated maize, the lowland adapted Zea mays ssp. A refined understanding of the genetic relationship within the genus Zea can help elucidate the trajectories of maize domestication and adaptation
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