Multilocus Analysis of Nucleotide Variation of Oryza sativa and Its Wild Relatives: Severe Bottleneck during Domestication of Rice

Abstract

Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of O. sativa and its close relatives (Oryza rufipogon and Oryza nivara), we investigated nucleotide diversity data from 10 unlinked nuclear loci in species-wide samples of these species. The results indicated that O. rufipogon and O. nivara possessed comparable levels of nucleotide variation ((sil) = 0.0077 approximately 0.0095) compared with the relatives of other crops. In contrast, nucleotide diversity of O. sativa was as low as (sil) = 0.0024 and even lower ((sil) = 0.0021 for indica and 0.0011 for japonica), if we consider the 2 subspecies separately. Overall, only 20-10% of the diversity in the wild species was retained in 2 subspecies of the cultivated rice (indica and japonica), respectively. Because statistic tests did not reject the assumption of neutrality for all 10 loci, we further used coalescent to simulate bottlenecks under various lengths and population sizes to better understand the domestication process. Consistent with the dramatic reduction in nucleotide diversity, we detected a severe domestication bottleneck and demonstrated that the sequence diversity currently found in the rice genome could be explained by a founding population of 1,500 individuals if the initial domestication event occurred over a 3,000-year period. Phylogenetic analyses revealed close genetic relationships and ambiguous species boundary of O. rufipogon and O. nivara, providing additional evidence to treat them as 2 ecotypes of a single species. Lowest linkage disequilibrium (LD) was found in the perennial O. rufipogon where the r(2) value dropped to a negligible level within 400 bp, and the highest in the japonica rice where LD extended to the entirely sequenced region ( approximately 900 bp), implying that LD mapping by genome scans may not be feasible in wild rice due to the high density of markers needed.

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

“…Further studies are required, whether of empirical or simulation nature, to investigate the sensitivity of LD estimates to these factors. Within the same species, wild populations usually harbor lower LD compared with their domesticated counterparts, as shown in barley (Caldwell et al, 2006), soybean (Lam et al, 2010), rice (Zhu et al, 2007), tomato (Arunyawat et al, 2007;Labate et al, 2009) and common bean (Rossi et al, 2009), reflecting changes in effective population size (Mather et al, 2007). In cultivated maize, for which LD was estimated based on large sequence data sets, the mean r 2 was 0.24 over a distance of 100 nucleotides and remained above 0.20 within 2 kb (Yan et al, 2009).…”

Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence

“…(ii) Further investigation of more cultivated strains, particular japonica, is needed to confirm this. Crops, including rice, have experienced strong artificial selection during domestication and their genetic diversity has significantly decreased -the so-called bottleneck effect [17,18]. [19,20].…”

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

“…A recent investigation on domestication bottlenecks based on 10 neutral loci in rice indicated that domesticated rice maintains about 52.1% (p) of the variability found in its progenitor O. rufipogon [41]. In the MIR156b/c locus, however, only 8.9% diversity was maintained in the cultivated rice.…”