Monday, April 30, 2018

Evidence Continues To Support Multiple Rice Domestications

The number of times that rice was domesticated in Eurasia has been a long standing question, but once again, this time in an article published in Nature based upon genetic analysis, the answer is more than once.
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence–absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.
From the Introduction:
For over 2,000 years, two major types of O. sativaO. sativa Xian group (here referred to as Xian/Indica (XI) and also known as Hsien or Indica) and O. sativa Geng Group (here referred to as Geng/Japonica (GJ) and also known as Keng or Japonica)
have historically been recognized. Varied degrees of post-reproductive barriers exist between XI and GJ rice accessions; this differentiation between XI and GJ rice types and the presence of different varietal groups are well-documented at isozyme and DNA levels. Two other distinct groups have also been recognized using molecular markers; one of these encompasses the Aus, Boro and Rayada ecotypes from Bangladesh and India (which we term the circum-Aus group (cA)) and the other comprises the famous Basmati and Sadri aromatic varieties (which we term the circum-Basmati group (cB)).
From the Discussion:
3K-RG population structure analyses based on SNPs and SVs were consistent with the five major groups that were previously known, additional subpopulations in the XI and GJ groups were identified and were suggestive of nine subpopulations that are correlated with geographic origin. Large numbers of SNPs, genes and gene families, and SVs were found to be unique to or predominant in single subpopulations. Varying patterns of diversity reduction across different rice subpopulations were observed in and around about 1,000 well-characterized genes. A closer look at patterns of haplotype sharing at domestication genes suggests that not all ‘domestication’ alleles came to XI from GJ. Taken together, our results—combined with archaeological evidence of XI cultivation for >9,000 years in both India and China.
I would include a figure or two from the paper, but none of them were all that compelling in explaining the paper's finding, and honestly the discussion was not particularly articulate either. I would have liked one superimposed on a map comparing the results geographically, or on images of the various types of rice or rice plants discussed. There was also no effort made to link the various domestication events to historical times or places despite the fact that the paper contains the data necessary to do so with a modicum of interdisciplinary effort.

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