New Study Constructs a Map of Rice Genome Variation and Origin of Cultivated Rice

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.

Recently, through in-depth analyses of the domestication sweeps and genome-wide patterns, researchers revealed 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.

In the study, researchers generated 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, researchers identified 55 selective sweeps that have occurred during domestication. The domestication-associated traits are analyzed through high-resolution genetic mapping.

The study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.

This work was conducted by researchers led by Prof. HAN Bin from the National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, CAS, in cooperation with scientists from the National Institute of Genetics of Japan, the China National Rice Research Institute, the Institute of Genetics and Developmental Biology, CAS and etc.

The study entitled “A map of rice genome variation reveals the origin of cultivated rice”（http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11532.html#/affil-auth）was published online in Nature on Oct. 4, 2012.