Empirical Analysis of Selection Screens for Domestication and Improvement Loci in Maize by Extended DNA Sequencing

Abstract

Both domestication and crop improvement in maize ( Zea mays ssp. mays ) have involved selection of specific alleles at genes controlling key morphologic 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. The major objective of this research was to provide an empirical determination of the false positive rate of genomic screens for artificial selection in maize. 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 > 2000 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.