Asian wild rice, Oryza rufipogon is believed to represent the wild ancestor that gave rise to Asian domesticated rice, O. sativa, ~8,000 years ago. It is also one of the most important components of the primary gene pool on which modern rice breeding relies. Wild rice contributed the critical cytoplasmic male sterility gene underlying one of the most widely exploited ‘three-line’ hybrid rice system, Wild Abortive. In rice breeding practice, breeders frequently turn to wild rice for disease-resistant genes. And they have successfully fished out many effective resistant genes for an array of noxious rice diseases, including grassy stunt and Tungro from the wild rice gene pool. Thus, wild rice represents an invaluable genetic resource for breeding rice varieties of both high and steady production.

 

However, a recent study has shown that wild rice may not be so wild anymore, its genetic variation has been heavily eroded by extensive gene flow from domesticated rice. The researchers from CHU Chengcai’s group at Institute of Genetics and Developmental Biology, Chinese Academy of Sciences together with scientists from University of Copenhagen, Denmark and University of Berkeley, USA assembled a rice panel containing 203 domesticated and 435 wild rice accessions. Through the whole-genome analysis on these samples, they discovered extensive domesticated rice component in wild rice population. Interestingly, they also found out that many presumed wild rice varieties show signature of artificial selection in previously identified domestication genes, this directly points to the scenario of gene flow from domesticated rice into wild rice. Because the domesticated versions of these genes are presumed to be disadvantageous in wild conditions, they should be selected against rather than selected for in wild rice.

 

By genome analysis of rice chloroplasts which can only be transmitted through seeds, they show that modern wild rice admix with domesticated rice through both pollen- and seed-mediated gene flow. Also, different subgroups of domesticated rice have a distinct geographic pattern in gene flow, and the pattern can readily be explained by the overlapping area of these rice subgroups and wild rice.

 

“Asian wild rice is a hybrid swarm, co-evolves and is connected to domesticated rice by continuous and extensive gene flow”, the first author of this paper, Dr. WANG Hongru said, “the insight that most Asian wild rice is heavily admixed and some may even be feral rice has great impact on rice domestication research”. It is common practice to use the geographic distribution and genetic variation of wild relatives to pinpoint origin of domestication for crops. Many previous rice domestication studies also rely on the assumption that Asian wild rice is ‘pure’ descendants of ancestral population that gave rise to domesticated rice. “We should be cautious when evaluating the results of these studies”, says Dr. WANG.

 

This study entitled “Asian Wild Rice is a Hybrid Swarm with Extensive Gene Flow and Feralization from Domesticated Rice” was online published in Genome Research (DOI:10.1101/gr.204800.116).

 

This study was supported by grants from the Chinese Academy of Sciences and National Natural Science Foundation of China.