The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species

Wing, Rod A.; Ammiraju, Jetty S.S.; Luo, Meizhong; Kim, Hye Ran; Yu, Yeisoo; Kudrna, Dave; Goicoechea, José Luis; Wang, Wenming; Nelson, Will; Rao, K. Srinivasa; Brar, D. S.; Mackill, David J.; Han, Bin; Soderlund, Cari; Stein, Lincoln; SanMiguel, Phillip; Jackson, Scott A.

doi:10.1007/s11103-004-6237-x

Cited by 143 publications

(100 citation statements)

References 29 publications

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“…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).…”

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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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: Introductionmentioning

confidence: 99%

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

et al. 2013

Heredity

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“…It is known that many populations of Asian wild rice have introgressed genes from cultivated rice [7,34,65,86]. Among wild rice accessions for which bacterial artificial chromosome libraries are available [82], at least one accession appears to have introgressed genes from cultivated rice. This accession [International Rice Research Institute (IRRI) 105491] from Malaysia has been studied in detail, and among its characteristics are upright habit and bold grains that point to introgression from cultivated rice [44].…”

Section: Hybridisation-introgression and Its Probable Role In Rice Domentioning

confidence: 99%

Was Asian Rice (Oryza sativa) Domesticated More Than Once?

Vaughan

Tomooka

2008

Rice

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Recently, a dual or multiple origin of domesticated rice has been the prevailing opinion among rice scientists because rice is clearly differentiated into two major varietal groups, indica and japonica, and several minor groups. Molecular clock studies that suggested that divergence in the A-genome wild rice genepool occurred prior to domestication gave further weight to the opinion that rice had a dual origin. However, recent analysis of the major gene that is responsible for the difference in degree of shattering between rice and wild rice has revealed that it is the same mutation in indica and japonica rice, which is not compatible with a dual origin of domesticated rice. Here, we discuss the geographic and genetic reasons why a single origin for domesticated rice is compatible with current data regarding the evolution of rice. The apparently conflicting data regarding the origin of rice can be resolved by the role hybridisation-introgression has played during rice evolution since domestication.

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“…The long-term objective of this program is to create a genome-level closed experimental system for the genus Oryza by developing comparative BAC-based physical maps of all 10 genome types of the genus to study evolution, genome organization, domestication, gene regulatory networks, and crop improvement (Wing et al 2005).…”

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confidence: 99%

The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza

Ammiraju¹,

Luo²,

Goicoechea³

et al. 2005

Genome Res.

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201

224

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Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the rice genome by a variety of methods, including comparative genomic analysis between cereal species and within the genus Oryza. Oryza contains two cultivated and 22 wild species that represent 10 distinct genome types. The wild species contain an essentially untapped reservoir of agriculturally important genes that must be harnessed if we are to maintain a safe and secure food supply for the 21st century. As a first step to functionally characterize the rice genome from a comparative standpoint, we report the construction and analysis of a comprehensive set of 12 BAC libraries that represent the 10 genome types of Oryza. To estimate the number of clones required to generate 10 genome equivalent BAC libraries we determined the genome sizes of nine of the 12 species using flow cytometry. Each library represents a minimum of 10 genome equivalents, has an average insert size range between 123 and 161 kb, an average organellar content of 0.4%–4.1% and nonrecombinant content between 0% and 5%. Genome coverage was estimated mathematically and empirically by hybridization and extensive contig and BAC end sequence analysis. A preliminary analysis of BAC end sequences of clones from these libraries indicated that LTR retrotransposons are the predominant class of repeat elements in Oryza and a roughly linear relationship of these elements with genome size was observed.

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The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species

Abstract: The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima.

Cited by 143 publications

References 29 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

Was Asian Rice (Oryza sativa) Domesticated More Than Once?

The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza

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