As one of the earliest domesticated crops by human being, rice has undergone significant phenotypic and physiological changes during the process of transformation from wild rice to cultivated rice that contains two major subspecies “indica and japonica”. However, the genome-wide variation patterns involved in the process remains a puzzle.

In order to clarify the issue, the Kunming Institute of Zoology, Chinese Academy of Sciences (CAS) resequenced the genomes of 40 Asian cultivated rice accessions and 10 wild rice accessions in collaboration with worldwide research bodies including CAS Institute of Botany, Berkley University and Cornell University.

Using a strict pipeline, they identified around 15 million candidate single nucleotide polymorphisms (SNPs) in all 50 accessions and obtained 6.5 million high-quality SNPs after excluding sites with missing data in any accession, representing the largest high-quality SNP data set ever obtained in rice. Among the 6.5 million high-quality SNPs, 4,124,470 were found in cultivars. A large proportion (2,953,712; 71.6%) of these SNPs were also found in wild rice accessions, indicating that most genetic variation in cultivated rice is derived from the variation in wild rice.

Millions of SNPs in representative wild and cultivated rice strains provided an unprecedented opportunity to finely resolve the domestication history of cultivated rice. The analysis of the SNPs not only gave support to the hypothesis that japonica and indica were independently domesticated, but also further suggested japonica was domesticated from the Chinese strain of O. rufipogon. Besides, they also identified thousands of candidate genes that may have been artificially selected during the domestication of one or both of the two cultivated subspecies.

The data generated in the research provide valuable dense molecular markers for rice breeding and for identifying agronomically important genes in rice. The paper entitled “Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes” has been published online in Nature Biotechnology on Dec. 11. (www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2050.html)