Toshie Miyabayashi

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. Whole-genome sequences of wild rice and cultivated rice varieties are used to produce a map of rice genome variation, and show that rice was probably first domesticated in southern China. Cultivated rice (Oryza sativa) is thought to have been domesticated from wild rice (Oryza rufipogon) thousands of years ago. This Chinese/Japanese collaboration reports whole-genome sequences from 446 wild rice isolates from across Asia and Oceana, and from more than 1,000 indica and japonica subspecies of cultivated rice. The resulting map of genome variation will be an important resource for rice breeding and for crop-domestication research.

The wild Oryza species are rich in genetic diversity and are good resources for modern breeding of rice varieties. The reliable ex situ conservation of various genetic resources supports both basic and applied rice research. For this purpose, we developed PCR-based and co-dominant insertion/deletion (INDEL) markers which enable the discrimination of the genome types or species in the genus Oryza. First, 12,107 INDEL candidate sequences were found in the BAC end sequences for 12 Oryza species available in public databases. Next, we designed PCR primers for INDEL-flanking sequences to match the characteristics of each INDEL, based on an assessment of their likelihood to give rise to a single or few PCR products in all 102 wild accessions, covering most Oryza genome types. Then, we selected 22 INDEL markers to discriminate all genome types in the genus Oryza. A phylogenetic tree of 102 wild accessions and two cultivars according to amplicon polymorphisms for the 22 INDEL markers corresponded well to those in previous studies, indicating that the INDEL markers developed in this study were a useful tool to improve the reliability of identification of wild Oryza species in the germplasm stocks.

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 O. officinalis, and draft genomes for two other C genome diploid species Oryza eichingeri and Oryza 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 Oryza sativa, mostly due to proliferation of Gypsy type long-terminal repeat 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, Oryza eichingeri and Oryza rhizomatis, and short-read resequencing of a series of other C genome species and accessions reveal that after the divergence of the C genome progenitor, there was still a substantial degree of variation within the C genome species through proliferation and loss of both DNA and long-terminal repeat transposable elements. We provide a detailed phylogeny and evolutionary history of the Oryza C genomes and a genomic resource for the exploitation of the Oryza tertiary gene pool.

The National Institute of Genetics (NIG), Mishima, Japan, maintains 1,725 accessions of 20 wild species of the genus Oryza, which have been collected from tropical and subtropical areas all over the world and covering all species in the genus except for O. schlechteri Pilger. A core collection of 282 accessions was chosen to represent the genetic spectrum of the whole NIG collection. The genome sizes of 39 accessions of Oryza core collection, covering all 20 species and 9 genome types, were measured based on both flow cytometry and microscopic observation. Most accessions showed good correspondence with respect to genome size within the same species and genome type, but showed significant differences between different genome types. In contrast to other species, however, CC, CCDD and HHJJ species showed significant variation within the same genome type. The total somatic chromosome length and ploidy level were also investigated for several accessions, and they correlated well with the DNA content. In this study, a simple flow cytometric analysis provided reliable results for genome size evaluation, and in addition, the genome size of five species was newly determined. Thus the DNA content, which is the simplest reliable indicator of genome variability, should be a good means of monitoring for evaluation and identification of Oryza germplasm.

The destruction of natural habitats of wild plant species is accelerating due to environmental changes and various human activities. This situation requires sustained and extensive efforts to preserve and safeguard wild species. The National Institute of Genetics (NIG), Mishima, Japan, maintains 1,701 accessions of 20 wild species of the genus Oryza, which have been collected from tropical and subtropical areas all over the world. This paper reviews the history, biodiversity, ex-situ conservation, and utility of the NIG wild Oryza collection. In addition, we describe our recent activities to improve the reliability of the collection and our contributions as part of the National BioResource Project (NBRP) of Japan. This project aims to provide reliable and high-quality rice materials for researchers worldwide. As part of the NBRP, we have evaluated wild Oryza accessions for eighteen morphological or physiological traits of vegetative and reproductive organs and for resistance to bacterial blight disease, developed molecular markers to distinguish species and/or genome-species in the genus, and published the information on the Oryzabase database.