Allelic Diversification at the C (OsC1) Locus of Wild and Cultivated Rice

Saitoh, Kumi; Onishi, Kazumitsu; Mikami, Ichiho; Thidar, Khin; Sano, Yoshio

doi:10.1534/genetics.103.018390

Cited by 145 publications

(137 citation statements)

References 48 publications

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“…The loss of genetic diversity in Japonica rice appears to result from a genetic bottleneck effect rather than a selective sweep since the OsC1 and Wx genes on a different chromosome (Chr. 6) show a similar trend (Saitoh et al 2004;Olsen and Purugganan 2002).…”

Section: Resultssupporting

confidence: 64%

Genealogy of the "Green Revolution" gene in rice

Nagano¹,

Onishi²,

Ogasawara³

et al. 2005

Genes Genet. Syst.

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During the "Green Revolution" of rice, high-yielding varieties (HYVs) were developed using a semi-dwarf gene ( sd1 or OsGA20ox2 ). The presence or absence of the two mutant alleles (DGWG type in Dee-geo-woo-gen and JKK type in Jikkoku) were surveyed by PCR using 256 accessions of eight wild and two cultivate rice species. The DGWG allele was detected in a landrace ( Oryza sativa ) and two accessions of wild rice ( O. rufipogon ), all of which are from China, showing their limited distribution. Genealogical studies of the OsGA20ox2 gene showed that the 62 sequences of O. sativa and O. rufipogon included 20 distinct haplotypes, indicating that the species complex contained OsGA20ox2 genes from two different lineages. The silent site nucleotide diversities ( π and θ w ) were extremely low in Japonica rice, suggesting a genetic bottleneck. The haplotype network showed that the DGWG and JKK alleles were derived in different lineages. The DGWG carrier (W1944) had unique polymorphisms in the surrounding region of the locus, suggesting that the DGWG allele has been preserved in the wild progenitor, rather than that the DGWG allele has been introgressed from HYVs to W1944. Although a semi-dwarfing plant is a weak competitor under saturated fields, the crossing experiment revealed that the DGWG variant might have been preserved as a hidden variation in the genetic background of wild rice, without expressing a short-stature.

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Section: Resultssupporting

confidence: 64%

Genealogy of the "Green Revolution" gene in rice

Nagano¹,

Onishi²,

Ogasawara³

et al. 2005

Genes Genet. Syst.

Self Cite

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“…To perform GWAS in O. rufipogon, we used the k-nearest neighbour algorithm for data imputation (Supplementary Table 6), and phenotyped the O. rufipogon population for two traits, leaf sheath colour and tiller angle. The strongest associations for sheath colour and tiller angle were found to be just around the known loci OsC1, for colouration 32 , and PROG1, for prostrate growth 7,8 (Fig. 1d and Supplementary Figs 7-9).…”

Section: Analysis Of Wild Rice Populationsmentioning

confidence: 95%

A map of rice genome variation reveals the origin of cultivated rice

Huang

Kurata

Wei

et al. 2012

Nature

1,379

109

1,518

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Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.Cultivated rice (Oryza sativa L.), which is grown worldwide and is one of the most important cereals for human nutrition, is considered to have been domesticated from wild rice (Oryza rufipogon) thousands of years ago 1-4 . The differences between O. sativa and O. rufipogon are reflected in a wide range of morphological and physiological traits [5][6][7][8][9] . Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated. The puzzles about rice domestication include: (1) where the geographic origin of cultivated rice was, (2) which types of O. rufipogon served as its direct wild progenitor, and (3) whether the two subspecies of cultivated rice, indica and japonica, are derived from a single or multiple domestications.A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 . However, the well-characterized domestication genes in rice were found to be fixed in both subspecies with the same alleles, thus supporting a single domestication origin [6][7][8][9]16 . Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 . Meanwhile, population genetics analyses of genome-wide data of cultivated and wild rice have tended to suggest that indica and japonica genomes generally appear to be of independent origin 1...

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“…The Rd locus may be a biosynthetic gene that, when nonfunctional, results in the accumulation of a brown proanthocyanidin precursor. The rice gene OsC1, with similarity to the maize Myb gene C1, has been cloned on rice chromosome 6 (Saitoh et al, 2004). This locus is acknowledged to have a role in purple (anthocyanin) rice pigmentation but has not been shown to play a role in red (proanthocyanidin) rice pigmentation.…”

Section: Functional Parallelsmentioning

confidence: 99%

Caught Red-Handed:RcEncodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice

et al. 2006

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Rc is a domestication-related gene required for red pericarp in rice (Oryza sativa). The red grain color is ubiquitous among the wild ancestors of O. sativa, in which it is closely associated with seed shattering and dormancy. Rc encodes a basic helix-loop-helix (bHLH) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between Oryza rufipogon (red pericarp) and O. sativa cv Jefferson (white pericarp). Sequencing of the alleles from both mapping parents as well as from two independent genetic stocks of Rc revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 that knocked out the bHLH domain of the protein. A premature stop codon was identified in the second mutant stock that had a light red pericarp. RT-PCR experiments confirmed that the Rc gene was expressed in both red-and white-grained rice but that a shortened transcript was present in white varieties. Phylogenetic analysis, supported by comparative mapping in rice and maize (Zea mays), showed that Rc, a positive regulator of proanthocyanidin, is orthologous with INTENSIFIER1, a negative regulator of anthocyanin production in maize, and is not in the same clade as rice bHLH anthocyanin regulators.

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Allelic Diversification at the C (OsC1) Locus of Wild and Cultivated Rice

Cited by 145 publications

References 48 publications

Genealogy of the "Green Revolution" gene in rice

Genealogy of the "Green Revolution" gene in rice

A map of rice genome variation reveals the origin of cultivated rice

Caught Red-Handed:RcEncodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice

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