A First-Generation Haplotype Map of Maize

TLDR

Maize is a highly genetically diverse crop species. The study aims to create a foundation for global breeding collaboration and enable genome‑wide association studies of complex traits. The analysis of 27 diverse inbred lines uncovered millions of polymorphisms, highly divergent haplotypes, 10‑ to 30‑fold recombination variation, pericentromeric suppression influencing selection and heterosis, and hundreds of selective sweeps tied to geographic adaptation.

Abstract

Maize is an important crop species of high genetic diversity. We identified and genotyped several million sequence polymorphisms among 27 diverse maize inbred lines and discovered that the genome was characterized by highly divergent haplotypes and showed 10- to 30-fold variation in recombination rates. Most chromosomes have pericentromeric regions with highly suppressed recombination that appear to have influenced the effectiveness of selection during maize inbred development and may be a major component of heterosis. We found hundreds of selective sweeps and highly differentiated regions that probably contain loci that are key to geographic adaptation. This survey of genetic diversity provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through genome-wide association studies.