Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/21/2005
Publication Date: 10/14/2005
Citation: Yamasaki, M., Tenaillon, M., Vroh, I., Schroeder, S., Sanchez-Villeda, H., Doebley, J., Gaut, B., Mcmullen, M.D. 2005. A large scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. The Plant Cell. 17:2859-2872. Interpretive Summary: One major bottleneck in using transformation technology for crop improvement is our lack of understanding of which genes control agronomic traits. In this manuscript we have developed a novel approach for identifying these key genes. Our approach is to develop genomic screens to identify genes exhibiting signatures of selection at domestication or crop improvement by contrasting the genetic diversity remaining in genes in inbred lines of maize (improved maize) to the diversity present in accessions of the wild relative teosinte and exotic maize landraces. We sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero genetic diversity as potential targets of selection. From these 35 genes, four domestication and four improvement genes were identified as significant for selection by two separate statistical tests. The 'selected' genes we have identified become candidate genes for crop improvement by maize plant breeders. In addition, as a proof of concept our approach can be adapted and used by geneticists and plant breeders of other crops to identify candidate genes for crop improvement.
Technical Abstract: Maize (Zea mays ssp. mays) was domesticated from teosinte (Zea mays ssp. parviglumis) through a single domestication event in southern Mexico between 6,000 and 9,000 years ago. This domestication event resulted in the original maize landrace varieties that were spread throughout the Americas by Native Americans, leading to adaptation 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. The loss of genetic diversity in maize varieties involves not only directional selection, but also population bottlenecks and hitchhiking effects. Here we sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero single nucleotide polymorphism (SNP) diversity as potential targets of selection. These 35 genes were then sequenced in a sample of diverse maize landraces and teosintes. Hudson-Kreitman-Aguadé (HKA) tests and coalescent simulations of domestication (CS) were performed to test for selection. Four domestication and four improvement genes were identified as significant for selection by both analyses. Genomic screens for evidence of selection identified genes of potential agronomic importance even when gene function and the phenotype of interest are unknown.