These days, we enjoy four main varieties of domesticated rice (Oryza sativa): short-grained japonica which becomes sticky after cooking, long-grained indica common in south and southeast Asia, drought-tolerant aus, and aromatic rice like basmati and sadri. According to new work published in Nature Plants this week, rather than one domestication event in China, rice may have been tamed three separate times across the Asian continent.
The earliest archaeological evidence for human exploitation of rice dates back to 9,000 to 10,000 years ago, in the Ganges Plain of India and China’s middle and lower Yangtze Valley. One estimate puts the divergence of Oryza sativa subspecies indica and japonica at 200,000 to 440,000 years ago – much earlier than the beginning of agriculture in southeast Asia. And while genome sequences for indica and japonica have been available for more than a decade, exactly when or where the cultivated groups originated remains unclear. Archaeological and genetic evidence have resulted in diverse and even contradictory scenarios, though the most recent genetic analysis suggested that all cultivated Asian rice comes from a single domestication.
To investigate, University of Manchester’s Terence Brown and colleagues analyzed sequence data from 1,083 Oryza sativa varieties and 446 wild rice samples. By examining the footprints of selection in the genomes of different cultivated rice types, they found three independent domestications in different parts of Asia.
Wild populations in southern China and Poyang Lake near the Yangtze River are the source of the japonica gene pool; modern tropical and temperate versions of japonica are later adaptations of the same crop. Populations in southern Indochina and the Brahmaputra Valley in the Himalayas are the source of the indica gene pool. And the aus variety originated from a broad region from central India to Bangladesh. Aromatic rice is simply the hybrid of japonica and aus types.
Image in the text from P. Civáň et al., Nature Plants 2015