Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice

Department of Genetics, North Carolina State University, Raleigh, North Carolina, USA.
PLoS Genetics (Impact Factor: 7.53). 10/2007; 3(9):1745-56. DOI: 10.1371/journal.pgen.0030163
Source: PubMed


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.

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    • "Due to the remarkable adaptability to various environments, rice varieties with diverse flowering times have been domesticated or improved from their ancestry. For example, the two major rice subspecies, indica and japonica, were domesticated to adapt to different ecological and geographical environments (Chou 1948; Caicedo et al. 2007). Some elite rice cultivars flower extremely early with weak photoperiod sensitivity in order to adapt to short summer growing seasons (Fujino and Sekiguchi 2005; Wei et al. 2008; Li et al. 2013). "
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    ABSTRACT: Due to the remarkable adaptability to various environments, rice varieties with diverse flowering times have been domesticated or improved from Oryza rufipogon. Detailed knowledge of the genetic factors controlling flowering time will facilitate understanding the adaptation mechanism in cultivated rice and enable breeders to design appropriate genotypes for distinct preferences. In this study, four genes (Hd1, DTH8, Ghd7 and OsPRR37) in a rice long-day suppression pathway were collected and sequenced in 154, 74, 69 and 62 varieties of cultivated rice (Oryza sativa) respectively. Under long-day conditions, varieties with nonfunctional alleles flowered significantly earlier than those with functional alleles. However, the four genes have different genetic effects in the regulation of flowering time: Hd1 and OsPRR37 are major genes that generally regulate rice flowering time for all varieties, while DTH8 and Ghd7 only regulate regional rice varieties. Geographic analysis and network studies suggested that the nonfunctional alleles of these suppression loci with regional adaptability were derived recently and independently. Alleles with regional adaptability should be taken into consideration for genetic improvement. The rich genetic variations in these four genes, which adapt rice to different environments, provide the flexibility needed for breeding rice varieties with diverse flowering times. This article is protected by copyright. All rights reserved.
    Preview · Article · Jul 2015 · Journal of Integrative Plant Biology
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    • "domesticated around 8200 to 13,000 years ago although the precise date of the first domestication is still unknown (Caicedo et al. 2007; Molina et al. 2011). The differences are due to estimates of the haploid effective population size N e for various species. "
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    ABSTRACT: The resistance gene Pi-ta has been effectively used to control rice blast disease, but some populations of cultivated and wild rice have evolved resistance. Insights into the evolutionary processes that led to this resistance during crop domestication may be inferred from the population history of domesticated and wild rice strains. In this study, we applied a recently developed statistical method, time-dependent Poisson random field model, to examine the evolution of the Pi-ta gene in cultivated and weedy rice. Our study suggests that the Pi-ta gene may have more recently introgressed into cultivated rice, indica and japonica, and U.S. weedy rice from the wild species, Oryza rufipogon. In addition, the Pi-ta gene is under positive selection in japonica, tropical japonica, U.S. cultivars and U.S. weedy rice. We also found that sequences of two domains of the Pi-ta gene, the nucleotide binding site (NBS) and leucine-rich repeat (LRR) domain, are highly conserved among all rice accessions examined. Our results provide a valuable analytical tool for understanding the evolution of disease resistance genes in crop plants.
    Full-text · Article · Oct 2014 · G3-Genes Genomes Genetics
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    • "For the generation of these four subpopulations, a burn-in length of 50,000 and run length of 100,000 iterations seemed to be sufficient for giving reasonably consistent values of maximum log likelihood across ten replicates. This observation was comparable to that documented earlier based on population structure analysis using microsatellite and SNP markers (Ni et al. 2002; Garris et al. 2003, 2005; Caicedo et al. 2007; Agrama et al. 2007). The level of diversity was comparable to that reported previously (Garris et al. 2005; Agrama et al. 2007) with microsatellite and SNP markers, but lower than (0.047–0.760 with an average of 0.470) that estimated with the microsatellite markers using a larger set of rice genotypes (Jin et al. 2010). "
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    ABSTRACT: Development and large-scale genotyping of single-nucleotide polymorphism (SNP) is required to use identified sequence variation in the alleles of different genes to determine their functional relevance to the candidate gene(s). In the present study, Illumina GoldenGate assay was used to validate and genotype SNPs in a set of six major rice blast resistance genes, viz. Pi-ta, Piz(t), Pi54, Pi9, Pi5(1) and Pib, distributed over five chromosomes, to understand their functional relevance and study the population structure in rice. All the selected SNPs loci (96) of six blast (Magna-porthe oryzae) resistance genes were genotyped successfully in 92 rice lines with an overall genotype call rate of 92.0 % and minimum GenTrain cutoff score of C0.448. The highest genotyped SNPs were found in japonica type (97.1 %) rice lines, followed by indica (92.12 %), indica basmati (91.84 %) and minimum in case of wild species (82.0 %). Among the genotyped loci, the highest score (98.68 %) was observed in case of Piz(t), followed by Pi-ta, Pi5(1), Pib, Pi54 and Pi9. Polymorphism was obtained in 87.5 % SNPs loci producing 7,728 genotype calls. Minor allele frequency ranged from 0.01 to 0.49 and Electronic supplementary material The online version of this article (doi:10.1007/s11032-014-0129-9) contains supple-mentary material, which is available to authorized users.
    Full-text · Article · Jun 2014 · Molecular Breeding
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