The origin of fragrant rice

Basmati means many things to many people. Some translate it as the prosaic “full of aroma”. Others as the more fanciful “Mother of all Aroma” or “Queen of Fragrance”. But no matter how you render the word, which is Hindi, it is inseparably associated with India. India, however, is not the original source of fragrance in rice. And Basmati is not an Indica variety. A recently published study of The origin and evolution of fragrance in rice ^[1] suggests that this highly valuable trait arose first in the Japonica group of rice, characterized by short, sticky grains, and later apparently found its way into the Indica group, with their longer, fluffier grains.

The origin of rice itself is still in dispute. Vavilov believed that its home lay in India, in the foothills of the Himalayas. For a while the fashion was for a dual, independent origin, Japonica in China or Japan, Indica in India. More recent studies, of archaeobotany and molecular evidence, suggest a single origin of the shattering gene — the crucial mutation that keeps the ripe grains attached to the stalk — in Japonica types in southeast China, passing into the Indica types as a result of pollen flow.

A few words first about rice types (see pic above). Japonica and Indica (conventionally given an initial capital) are the two major varietal groups. Within them, five sub-groups have been identified on the basis of various measures; indica and aus, members of the Indica group, and then in the Japonica group tropical japonica, temperate japonica and the enigmatic Group V, which despite being a member of the Japonica group often has long, fluffy grains. Basmati types belong in Group V.

Fragrance itself had been linked to one of the rice chromosomes back in 1938, and more recently to mutations at a locus called BADH2. The mutant allele, known as bdh2.1 (lower case, because it is recessive) has an abnormally short BDH2 protein that doesn’t work properly; putting a working copy of the BDH2 allele (upper case, because it is dominant) into fragrant rice abolishes its fragrance.

Scientists from Cornell University and the International Rice Research Institute looked for the bdh2.1 allele in 176 samples of all types of cultivated rice that were genetically and geographically a very mixed bag. It was most common in Group V varieties (60% are aromatic), then in tropical japonica (15%) and then in indica (6%). No aus or temperate japonica varieties were aromatic. The researchers then sequenced the DNA of an even larger panel of 242 samples. They were looking for patterns called haplotypes. In the process of sexual reproduction, DNA from the two parents is swapped around, and the block that is exchanged can encompass several genes and DNA markers. If two varieties, for example, share a common haplotype around a gene of interest, then it is likely that they inherited the gene from a common ancestor fairly recently, because the haplotype has not been broken up in the meantime.

Looking at the DNA immediately on either side of the BDH2 locus, there were two types of haplotype pattern. Three patterns were characteristic of all Japonica varieties. Five others were characteristic of Indica varieties. But, every single fragrant variety had one of the Japonica haplotypes, regardless of which sub-group it came from. That suggests “a single origin of the badh2.1 allele in a Japonica-like genetic background”. It also creates a conflict between the mass of data, which place fragrant Jasmine varieties in the Indica group, and the BDH2 haplotypes, which say it is a Japonica. The team widened their area of interest to include a larger stretch of DNA on either side of the BDH2 locus. The same pattern emerged. In all fragrant varieties the bdh2.1 allele was surrounded by Japonica DNA.

The likeliest explanation is that the fragrant allele arose in a Japonica ancestor some time after the split between temperate japonica (no fragrant types) and tropical japonica and Group V, and then as a result of pollen flow made its way into some indica types, where it was strongly selected because it was so desirable. Possibly the mutation arose in a Group V ancestor and then spread in the same way to tropical japonica and indica types. Group V and Indica varieties overlap geographically across South Asia to a considerable extent, which would have provided the conditions needed for the Japonica DNA flanking the BDH2 locus to make its way into Indica rice.

There is a great deal more of interest in the paper, including other BDH2 alleles besides bdh2.1 that confer fragrance, and a couple of samples that are fragrant but that do not have a bdh2 allele. And there’s a paradox that the authors clearly identify as important:

It is noteworthy that despite the apparent importance of hybridization and gene flow during rice evolution, opposing forces have maintained the genetic divergence among the subpopulations of O. sativa. Solving this paradox will require future research to identify the key factors that contribute to subpopulation isolation, as well as to provide insight into the dynamics of genetic exchange among these groups.

I wonder whether any of the rice accessions collected by Vavilov on his journeys through Asia will contribute to our future understanding of rice domestication and evolution.

Notes:

1. Kovach, M., Calingacion, M., Fitzgerald, M., & McCouch, S. (2009). The origin and evolution of fragrance in rice (Oryza sativa L.) Proceedings of the National Academy of Sciences, 106 (34), 14444-14449 DOI: 10.1073/pnas.0904077106 [↩]

Tagged as: Domestication, Evolution, Rice