Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice

Abstract

Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation.

Consilience of genetics and archaeobotany in the entangled history of rice

“…Recent genetic classifications (e.g. Garris et al 2005;Caicedo et al 2007;McNally et al 2009) suggest that there are five analytically useful groups which can be recognised: indica, aus, temperate japonica, tropical japonica (including javanica) and fragrant, although most discussions of origins have focussed on whether the indica (including aus) and japonica groups derived from a single or multiple domestications. There is a now a wide range of genetic studies, using markers from the chloroplast genome, neutral variation in the nuclear genome and variation within functional alleles that have been used to examine this issue.…”

“…Whole genome comparisons of representative accessions for the nuclear genome suggest a similarly deep divergence on the orders of 100,000 s of years (Vitte et al 2004;Ma and Bennetzen 2004), whilst various genes or gene systems also point to differences such as pSINEs (Ohtsubo et al 2004), SSR and STS datasets (Garris et al 2005;Caicedo et al 2007), SAM and vTPASE sequence variation (Londo et al 2006) and ∼3,000 single nucleotide polymorphisms assayed across 20 representative landraces (McNally et al 2009). Whilst all of these studies agree on the deep divergence of indica and japonica, they also suggest that there are some indicators of possible multiple derivations in both indica and japonica.…”

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

“…In view of direct correlation between degree of polymorphism and genetic diversity level present among germplasm accessions, the difficulty in selecting such polymorphic informative genome-wide SSR markers increases manifold while dealing with closely related germplasm lines having low level of genetic diversity. The studies pertaining to phylogenetics and domestication of rice have resolved its cultivated accessions belonging to Oryza sativa primarily into five different population groups, namely indica , tropical and temperate japonica, aus , and aromatics, while accessions representing the two wild progenitors ( O. rufipogon and O. nivara ) of cultivated species are classified as wild population group (Garris et al, 2005; Caicedo et al, 2007; Parida et al, 2009, 2012; Zhang et al, 2011). Remarkably, these marker-based evolutionary and population genetic structure studies have documented the existence of a very low level of molecular (allelic) diversity among the accessions representing an individual cultivated O. sativa population group.…”

Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

“…Recent population genomics studies suggest that domestication affects the entire genome and that selection acts on a large number of loci Caicedo et al 2007), so a multilocus approach is appropriate to study the effects of domestication and selection. Similar results were obtained by Papa et al (2007) on P. vulgaris using 2509 AFLPs.…”