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

Abstract

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...

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

“…The LD extent in wild soybean was ~27 kb, similar to that of wild rice (Oryza. rufipogon, 20 kb) 17 and wild maize (Z. mays ssp. parviglumis, 22 kb) 5 .…”

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

“…Therefore, the alleles of the QTLs that increased cold tolerance were mainly from japonica. The possible reason might be that indica rice was developed from crosses between japonica rice and local wild rice (Huang et al 2012a); therefore, indica varieties may retain some characters of japonica, such as minor QTLs for cold tolerance.…”

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

“…The distinctness of the indica and japonica genomes suggests separate origins for most of each genome (Wei et al ., 2012). However, the presence of many shared domestication‐related alleles has led to suggestions that some level of introgression between the two genomes has also been a feature of their domestication history (Civáň et al ., 2015; Fuller et al ., 2010; Huang et al ., 2012a,b; Molina et al ., 2011). Geographic separation may have allowed early populations to diverge resulting in distinct O. rufipogon ‐like populations in Asia and Australia.…”