Submitted to: The Plant Genome
Publication Type: Peer reviewed journal
Publication Acceptance Date: 1/15/2008
Publication Date: 5/22/2008
Citation: Yamasaki, M., Schroeder, S., Sanchez-Villeda, H., Gaut, B., Mcmullen, M.D. 2008. Empirical analysis of selection screens for domestication and improvement loci in maize by extended DNA sequencing. The Plant Genome. 1(1):33-43. Interpretive Summary: A major area of research is to identify genes that control agronomic trait expression. One novel approach is to use population genetic methods to identify genes that have nucleotide polymorphism patterns that are consistent with a history of artificial selection. We have recently screened 2000 corn genes and have identified 30 candidate genes by these approaches. However, as this screening was conducted on only a small region of each gene, a certain level of false positives are expected. In this publication we report on the use of extended sequencing to support the candidate status of the genes identified in prior studies. Our results indicate that about half of the genes identified in the initial screens show evidence of selection throughout the entire gene and therefore are strong candidates for controlling agronomic traits. This research is important to biologists and plant breeders because it identifies the best candidate genes for study and use in crop improvement programs.
Technical Abstract: Both domestication and crop improvement in maize (Zea mays ssp. mays) have involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. This difference in genetic diversity has led to the development of genomic screens for artificial selection in maize that have identified ~ 50 candidate agronomic genes. One limitation of these initial genome screens is that the short length of the alignment (average length: <300 bp) restricts the statistical power and may lead to false positives. Therefore, we performed extended sequencing throughout the available gene sequence of 27 previously identified selection candidates using maize inbred, maize landrace (for 12 genes) and teosinte (Zea mays ssp. parviglumis) accessions. The extended sequence alignments (average length: >2,000 bp) allowed clear separation of strong candidates for selection from those that cannot be distinguished from the tail of the diversity distribution of all maize genes. The extended alignments also allowed linkage disequilibrium to be considered in evaluating a candidate’s selection status. This proved particularly useful in distinguishing selection at domestication versus subsequent crop improvement.