The Oryza officinalis complex is the largest species group in Oryza, with more than nine species ... more The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read...
The Oryza officinalis complex is the largest species group in Oryza, with more than nine species ... more The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read...
Crop domestications are long-term selection experiments that have greatly advanced human civiliza... more 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.
ABSTRACT Panicle branchiness is one of the key characters specifying rice yield. To understand th... more ABSTRACT Panicle branchiness is one of the key characters specifying rice yield. To understand the potential of panicle branchiness, the diversity of panicle branching patterns was investigated in 43 accessions of 19 wild Oryza species and 27 accessions of O. rufipogon, which is the wild ancestor of the Asian cultivated species O. sativa. All these accessions were selected from a core collection of wild relatives of rice maintained at the National Institute of Genetics (NIG), Mishima, Japan. We found that panicles of wild Oryza species closely related to O. sativa generated primary branches with homogeneously large numbers of secondary branching organs, resulting in a truncated conical type of branching pattern. In contrast, panicles of distantly related wild species had primary branches with acropetally declining numbers of secondary organs toward the distal end of panicles, resulting in a conical type of branching pattern. The main axis meristem, which was aborted in closely related species, was converted into a terminal spikelet in distantly related species. Our data suggested that the panicle branching pattern evolved from conical to truncated conical in the genus Oryza. The possible advantage of a truncated-conical type of branching pattern for rice yield will be discussed.
The Oryza officinalis complex is the largest species group in Oryza, with more than nine species ... more The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read...
The Oryza officinalis complex is the largest species group in Oryza, with more than nine species ... more The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read...
Crop domestications are long-term selection experiments that have greatly advanced human civiliza... more 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.
ABSTRACT Panicle branchiness is one of the key characters specifying rice yield. To understand th... more ABSTRACT Panicle branchiness is one of the key characters specifying rice yield. To understand the potential of panicle branchiness, the diversity of panicle branching patterns was investigated in 43 accessions of 19 wild Oryza species and 27 accessions of O. rufipogon, which is the wild ancestor of the Asian cultivated species O. sativa. All these accessions were selected from a core collection of wild relatives of rice maintained at the National Institute of Genetics (NIG), Mishima, Japan. We found that panicles of wild Oryza species closely related to O. sativa generated primary branches with homogeneously large numbers of secondary branching organs, resulting in a truncated conical type of branching pattern. In contrast, panicles of distantly related wild species had primary branches with acropetally declining numbers of secondary organs toward the distal end of panicles, resulting in a conical type of branching pattern. The main axis meristem, which was aborted in closely related species, was converted into a terminal spikelet in distantly related species. Our data suggested that the panicle branching pattern evolved from conical to truncated conical in the genus Oryza. The possible advantage of a truncated-conical type of branching pattern for rice yield will be discussed.
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Papers by Toshie Miyabayashi