Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

Xianfa Xie,Andy Reynolds,Michael D Purugganan,Adam R Boyko,Carlos D Bustamante,Jeanmaire Molina,Ryan Hernandez

doi:10.1371/journal.pone.0020670

Xianfa Xie, Andy Reynolds + Show 5 more

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https://doi.org/10.1371/journal.pone.0020670

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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.

Highlights

Crop domestication is the adaptive divergence of a plant species as a result of selection and the initial evolutionary transition from wild to human-associated cultivated environments [1,2]
Using re-sequencing data for gene fragments across these three putative domestication Quantitative trait locus (QTL) regions in rice, we examine whether the levels and patterns of polymorphism in these three regions are consistent with the possibility that they have experienced recent positive selection accompanying the evolution of this cultivated grass species
Neither indica rice nor the wild ancestor O. rufipogon shows any significant departure of nucleotide diversity distribution at all three domestication QTLs compared to the genomewide data

Summary

Introduction

Crop domestication is the adaptive divergence of a plant species as a result of selection and the initial evolutionary transition from wild to human-associated cultivated environments [1,2]. Phenotypic comparisons identify numerous traits that differ between domesticated species and their wild ancestors. Three classes of traits that differentiate domesticated and wild ancestral species can be defined [1]. First are domestication traits, which evolve during the initial movement of species from natural to cultivated environments. A second class is crop improvement traits, which are further phenotypic changes that have occurred after the initial domestication to human-associated cultivated environments [3]. There are crop diversification traits, which are associated with different crop varieties or cultivars adapted to different cultures or agro-ecological environments

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