White rice spread through single japonica gene

A new study strongly suggests that about98 percent of today's white rice evolved from red rice through natural selection and was spread through a gene that originated in the japonica variety.

The results are surprising as the two major types of rice, indica and japonica are infertile toward each other, while the study suggests that japonica must have crossed (introgressed) with indica t an early period.

Early studies have shown that the gene for non-shattering in rice also originated in japonica.

Apparently farmers selected the RC gene that gives the white pericarp because, among other things, the hull was easier to remove and it required less cooking time than red rice.

Since rice pollen rarely travels more than 10 meters, and the RC gene was able to transverse barriers like the Himalayas, added with the fact that there is obvious evidence of human selection, the researchers concluded the gene must have spread through human transport and migration.

Some time before the infertility barrier between japonica and indica arose, this gene along with sh4 non-shattering allele, both of which are believed to have a single origin, spread through almost all varieties of both japonica and indica.

While the authors don't speculate as to the time and which people would have spread these genes, I think one obvious candidate would be either early Austric or Austro-Asiatic speakers who migrated across broad areas on both sides of the Himalayas at a very early period.

The full article is available free at:

http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0030133

Abstract:

Global Dissemination of a Single Mutation Conferring White Pericarp in Rice

Megan T. Sweeney¹, Michael J. Thomson^2,3, Yong Gu Cho⁴, Yong Jin Park⁵, Scott H. Williamson⁶, Carlos D. Bustamante⁶, Susan R. McCouch^1*

1 Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America, 2 International Rice Research Institute, Los Baños, Philippines, 3 Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor, Indonesia, 4 Department of Agronomy, Chungbuk National University, Chongju, Republic of Korea, 5 National Institute of Agricultural Biotechnology, Suwon, Republic of Korea, 6 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America

Here we report that the change from the red seeds of wild rice to the white seeds of cultivated rice (Oryza sativa) resulted from the strong selective sweep of a single mutation, a frame-shift deletion within the Rc gene that is found in 97.9% of white rice varieties today. A second mutation, also within Rc, is present in less than 3% of white accessions surveyed. Haplotype analysis revealed that the predominant mutation originated in the japonica subspecies and crossed both geographic and sterility barriers to move into the indica subspecies. A little less than one Mb of japonica DNA hitchhiked with the rc allele into most indica varieties, suggesting that other linked domestication alleles may have been transferred from japonica to indica along with white pericarp color. Our finding provides evidence of active cultural exchange among ancient farmers over the course of rice domestication coupled with very strong, positive selection for a single white allele in both subspecies of O. sativa.