A Large-Scale Screen for Artificial Selection in Maize Identifies Candidate Agronomic Loci for Domestication and Crop Improvement

TLDR

Maize was domesticated from teosinte in southern Mexico 6000–9000 years ago, spread across the Americas, and later refined by breeders selecting inbred lines for hybrid production. The authors sequenced 1095 genes from 14 inbred lines, selected 35 with no diversity, resequenced them in landraces and teosintes, and applied two statistical tests to pinpoint eight candidate genes under selection. Eight candidate loci were identified, six showing selection across the gene and two in the 3′ region, with functions linked to nutritional quality, maturity, and productivity, demonstrating that large‑scale screens can uncover agronomically important genes even without known phenotypes.

Abstract

Maize (Zea mays subsp mays) was domesticated from teosinte (Z. mays subsp parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties, which were spread throughout the Americas by Native Americans and adapted to a wide range of environmental conditions. Starting with landraces, 20th century plant breeders selected inbred lines of maize for use in hybrid maize production. Both domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. Here, we sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero sequence diversity as potential targets of selection. These 35 genes were then sequenced in a sample of diverse maize landraces and teosintes and tested for selection. Using two statistical tests, we identified eight candidate genes. Extended gene sequencing of these eight candidate loci confirmed that six were selected throughout the gene, and the remaining two exhibited evidence of selection in the 3' portion of each gene. The selected genes have functions consistent with agronomic selection for nutritional quality, maturity, and productivity. Our large-scale screen for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown.