The evolving story of rice evolution

Vaughan, Duncan A.; Lu, Bao‐Rong; Tomooka, Norihiko

doi:10.1016/j.plantsci.2008.01.016

Cited by 354 publications

(339 citation statements)

References 88 publications

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“…The rayada cultivars comprise a very particular rice sown in November-December and harvested as much as 12 months later. This group is able to tolerate cold and flooding, is photoperiod sensitive and lacks secondary dormancy (Glaszmann, 1987;Vaughan et al, 2008). Having these unusual characteristics and being genetically distinct, rayada rice should be considered as a new (the sixth) major group of rice germplasm.…”

Section: Six Distinct and Major Groups Within O Sativamentioning

confidence: 99%

“…Rice not only serves as a primary food source for more than half of the world's population (Khush, 1997), but also provides an excellent model system for studying a wide range of biological questions (Shimamoto and Kyozuka, 2002;Wing et al, 2005;Zhang et al, 2008). As a result of both natural and artificial selection, rice has evolved into a crop containing high levels of morphological, physiological and genetic diversity, with 41 20 000 distinct rice varieties recognized worldwide (Oka, 1988;Khush, 1997;Sang and Ge, 2007;Vaughan et al, 2008). An assessment and classification of this diversity is important for effective utilization of the germplasm and will provide a powerful evolutionary framework for many future biological studies using rice as a model.…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

et al. 2013

Heredity

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Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of modelbased grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments.

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Section: Six Distinct and Major Groups Within O Sativamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

et al. 2013

Heredity

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“…The history of O. sativa itself has been thoroughly reviewed elsewhere (Vaughan et al 2008a, b), and will only be summarized here. Oryza sativa is comprised of two subspecies, indica and japonica, both of which are domesticated from a wild ancestor similar to O. rufipogon.…”

Section: The Species O Sativamentioning

confidence: 99%

“…In the presence of gene flow and selection, both of which are occurring, the two patterns in fact cannot be distinguished. (See also discussions in Vaughan et al (2008a, b)) For a few types of domesticated rice, the history appears easier to assess. For example, fragrant rice is a result of a mutation at the Badh2 locus (Chen et al 2008), which encodes the gene for betain aldehyde dehydrogenase.…”

Section: The Species O Sativamentioning

confidence: 99%

The Evolutionary History of Ehrhartoideae, Oryzeae, and Oryza

Kellogg

2009

Rice

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Rice is a member of the genus Oryza, which has a history extending back into the Miocene. Oryza is in turn a member of the tribe Oryzeae, which along with the tribe Ehrharteae is included in the subfamily Ehrhartoideae. This paper reviews current knowledge of the genus, tribe and subfamily, and places rice in the larger evolutionary context of the entire grass family. The morphological characteristics of rice are an amalgam of characters that have originated at different times in its long evolutionary history. Increasingly, genomic characteristics are also being placed in a broad evolutionary context and it is becoming possible see which are characteristic of all grasses and which are more restricted to the genus Oryza or even to rice itself.

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“…Wild rice was first domesticated in the Yangtze region of China to 2 cultivated subspecies, indica and japonica [1]. Phylogeographic investigations have suggested that cultivated rice has experienced at least two independent domestications: indica rice was domesticated within a region south of the Himalaya mountains whereas japonica was domesticated from wild rice in southern China [2].…”

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confidence: 99%

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

et al. 2011

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Rice (Oryza sativa) was first domesticated in the lower and middle Yangtze regions of China, and rice remains have been found in many Chinese archaeological sites. Until now, only phenotypic archeobotanical evidence, such as the spikelet bases of ancient grains, has been used to speculate on the domestication process and domestication rate of rice. In this study, we sequenced 4 genomic segments from rice remains in Tianluoshan, a site of the local Hemudu Neolithic culture in the low Yangtze and two other archaeological sites (~2400 and 1200 BC, respectively). We compared our sequences with those of the current domesticated and wild rice (O. rufipogon) populations. At least two genotypes were found in the remains from each site, suggesting a heterozygotic state of the rice seeds. One ancient genotype was not found in the current domesticated population and might have been lost. The rice remains belonged to the japonica group, and most if not all were japonica-type, suggesting that the remains might be at an early stage of indica-japonica divergence or an indica-japonica mixture. We also identified sequences with significant similarity to those from species of Sapindales, Zygophyllales, and Brassicales, which is consistent with the identification of other plant remains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.

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The evolving story of rice evolution

Cited by 354 publications

References 88 publications

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

The Evolutionary History of Ehrhartoideae, Oryzeae, and Oryza

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

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