Specific patterns of genetic diversity among aromatic rice varieties in Myanmar

Abstract

Background: After observing peculiar rice varieties in Myanmar, in terms of classification in varietal groups and of grain quality, we focused on Myanmar varieties and analyzed variations at 19 microsatellite loci as well as sequences of the aroma gene BADH2.

Results: Microsatellites were able to retrieve the well-established classification into Indica (isozyme group 1), Japonica (group 6, comprising temperate and tropical forms) and specific groups from the Himalayan foothills including some Aus varieties (group 2) and some aromatic varieties (group 5). They revealed a new cluster of accessions close to, but distinct from, non-Myanmar varieties in group 5. With reference to earlier terminology, we propose to distinguish a group "5A" including group 5 varieties from the Indian subcontinent (South and West Asia) and a group "5B" including most group 5 varieties from Myanmar. In Myanmar varieties, aroma was distributed in group 1 (Indica) and in group 5B. New BADH2 variants were found. Some accessions carried a 43 bp deletion in the 3' UTR that was not completely associated with aroma. Other accessions, all of group 5B, displayed a particular BADH2 allele with a 3 bp insertion and 100% association with aroma.

Conclusion: With the new group and the new alleles found in Myanmar varieties, our study shows that the Himalayan foothills contain series of non-Indica and non-Japonica varietal types with novel variations for useful traits.

Keywords: Aroma; BADH2; Genetic diversity; Oryza sativa; SSR.

Figure 1

Graph of estimated membership fraction for K = 5 (run with the highest likelihood). The first part of the graph represents the reference set with a vertical black bar separating the enzymatic groups.The first part of the graph represents the reference set with a vertical bar separating the enzymatic groups. The second part of the graph includes the Myanmar accessions. The five different colors correspond to the five Structure groups. Enzymatic groups: 1 = indica, 2 = aus/boro, 5 = sadri/basmati; 6 = japonica ([Glaszmann, 1987]).

Figure 2

Haplotype network for the gene BADH2 Each node represents a haplotype, its size being proportional to its frequency. 2A. Distribution according to the aromatic nature of the accessions Green: aromatic; blue: non-aromatic; gray: unknown 2B. Distribution according to Structure groups Red: 1 (indica); blue: 6 (japonica); light green = 5A; dark green = 5B; violet: admixed.