title: Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.
abstract: Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America. Xianfa.Xie@gmail.com
authors.forename: Xianfa
authors.initials: X
authors.lastname: Xie
authors.forename: Jeanmaire
authors.initials: J
authors.lastname: Molina
authors.forename: Ryan
authors.initials: R
authors.lastname: Hernandez
authors.forename: Andy
authors.initials: A
authors.lastname: Reynolds
authors.forename: Adam R
authors.initials: AR
authors.lastname: Boyko
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
authors.forename: Michael D
authors.initials: MD
authors.lastname: Purugganan
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D018556:Crops, Agricultural / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D015810:Linkage Disequilibrium / Q000235:genetics; D008957:Models, Genetic; D009711:Nucleotides / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D040641:Quantitative Trait Loci / Q000235:genetics*; D012641:Selection, Genetic; D013045:Species Specificity
chemical_list: D009711:Nucleotides