Integration of genomic tools to assist breeding in the japonica subspecies of rice

Negrão, Sónia; Oliveira, M. Margarida; Jena, Kshirod K.; Mackill, David J.

doi:10.1007/s11032-008-9177-3

Cited by 47 publications

(19 citation statements)

References 60 publications

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“…The long grain type belongs to tropical japonica and the medium (or short) to temperate japonica , two groups of a subspecies japonica in O. sativa (Mackill, 1995). Another subspecies, indica, has greater genetic diversity than japonica (Gao et al, 2005; Mackill, 1995; Ni et al, 2002; Negrao et al, 2008; Caicedo et al, 2007; Konishi et al, 2008), probably because indica is grown on about 80% of the world's total rice area and japonica on the remaining 20% (Mackill, 1995). Furthermore, intensive breeding efforts greatly reduce genetic diversity of U.S. cultivars (Dilday, 1990).…”

Section: Discussionmentioning

confidence: 99%

Geographic Description of Genetic Diversity and Relationships in the USDA Rice World Collection

Wang

Agrama²,

Jia

et al. 2010

Crop Science

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Knowledge of genetic diversity and relationships among global germplasms of rice collected by the USDA since 1866 is critical for utilization, conservation, and management of the collection. A core subset developed from this collection, including 1794 accessions obtained from 112 countries in 14 geographic regions, was genotyped with one indel and 71 simple sequence repeat (SSR) markers. Total alleles were 1005, averaging 14 alleles per locus. A great majority of genetic variance was due to within instead of among geographic regions and within instead of among countries. The regions and countries were highly and significantly differentiated using these markers. Germplasm accessions obtained from the southern Asia, Southeast Asia, and Africa were highly diversified, while those from North America and western and eastern Europe had the lowest diversity. Different measurements of genetic diversity, including average number of alleles per locus, polymorphism information content (PIC), Nei index, and average number of private alleles per locus uniformly reached this conclusion. Three main clusters were revealed by both analyses of principal coordinates and Nei genetic similarities for the 14 regions. Seventy‐eight countries, from which five or more accessions were collected in the core subset, were differentiated into five main clusters. Germplasm accessions obtained from Myanmar, Indonesia, Cambodia, Malaysia, and Nepal were highly diversified, while those from France, Spain, Romania, Italy, and the United States were poorly diversified. This study proves that the USDA global collection effectively supports the U.S. rice industry with vast genetic diversity responsive to biotic and abiotic stresses.

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Section: Discussionmentioning

confidence: 99%

Geographic Description of Genetic Diversity and Relationships in the USDA Rice World Collection

Wang

Agrama²,

Jia

et al. 2010

Crop Science

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“…Both hypotheses admit that the ancestor is an invaluable gene pool for the genetic improvement of modern rice cultivars (Cheng et al 2003;Londo et al 2006;Kovach et al 2007;Sang and Ge 2007;Yuan et al 1989;Jackson 1994Jackson , 1997Tanksley and McCouch 1997). Conservation of genetic diversity in the gene pool plays important role in security of food production worldwide because rice is the staple food for more than 50% of the world's population (Negrao et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon)

Xie

Agrama²,

Kong

et al. 2009

Genet Resour Crop Evol

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The wild progenitor species (Oryza rufipogon) of Asian cultivated rice (O. sativa L.) is located in Dongxiang county, China which is considered its the northernmost range worldwide. Nine ex situ and three in situ populations of the Dongxiang wild rice (DXWR) and four groups of modern cultivars were genotyped using 21 SSR markers for study of population structure, conservation efficiency and genetic relationship. We demonstrated that the ex situ conservation of the DXWR failed to maintain the genetic identity and reduced genetic diversity. Therefore, in situ conservation is absolutely necessary to maintain the genetic identity, diversity and heterozygosity. Also, in situ conservation is urgently needed because natural populations in DXWR have decreased from nine to three at present due to farming activity and urban expansion. In DXWR, the three surviving in situ populations had greater expected heterozygosity than any cultivated rice, and were genetically closer to japonica than either the male-sterile maintainer or restorer lines, or indica. Japonica has the lowest genetic diversity of cultivated rice. As a result, DXWR is a rich gene pool and is especially valuable for genetic improvement of japonica rice because these O. rufipogon accessions are most closely related to the japonica as compared to O. rufipogon collected anywhere else in the world.

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Section: Discussionmentioning

confidence: 99%

“…Japonica subspecies can be classified into temperate and tropical types. The former is predominantly cultivated across Northeast Asia, Europe, US and Australia; the latter is commonly grown in Southeast Asia, Southern China and the uplands of Latin America and Africa (Negra˜o et al 2008). Among the straighthead resistant cultivars, there were 26 indica cultivars classified in two groups, and two others were between the two groups (Table 3, Fig.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and relatedness of rice cultivars resistant to straighthead disorder

Agrama

Wang

2010

Plant Breeding

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Straighthead, a physiological disorder of rice (Oryza sativa L.), has been reported in numerous rice-growing countries for its severe impact on yield reduction. Genetic diversity, relatedness and structure of parental germplasm are important for breeders to design strategies in breeding programmes. We analysed 1002 rice accessions that were sampled from the USDA core collection, evaluated for straighthead and genotyped with 72 molecular markers. Forty-two accessions were resistant to straighthead with no yield reduction under severe infestation. The resistant cultivars originated from 15 countries in 10 geographic regions worldwide. The accessions had great diversification indicated by 15 phenotypic characteristics including all types of grain and cooking quality. The number of alleles averaged 5.9, and the 72 molecular markers were highly informative among the 42 resistant accessions. Thirty resistant accessions were identified as indica type and were clearly classified in two groups. Ten resistant cultivars were identified as temperate japonica and the other two were positioned between temperate and tropical japonica rice. Breeders worldwide could use these findings on phenotypic diversification and genetic relatedness among the straighthead resistant accessions in order to make germplasm choices for transferring straighthead resistance to their local cultivars, serving various needs on grain, cooking quality and genetic classification in their programmes.

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Integration of genomic tools to assist breeding in the japonica subspecies of rice

Cited by 47 publications

References 60 publications

Geographic Description of Genetic Diversity and Relationships in the USDA Rice World Collection

Geographic Description of Genetic Diversity and Relationships in the USDA Rice World Collection

Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon)

Genetic diversity and relatedness of rice cultivars resistant to straighthead disorder

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