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. 2017 Nov 30;12(11):e0188920.
doi: 10.1371/journal.pone.0188920. eCollection 2017.

Whole genome sequencing of Oryza sativa L. cv. Seeragasamba identifies a new fragrance allele in rice

Ganigara Bindusree  1 , Purushothaman Natarajan  1 , Sukesh Kalva  1 , Parani Madasamy  1
Affiliations

Whole genome sequencing of Oryza sativa L. cv. Seeragasamba identifies a new fragrance allele in rice

Ganigara Bindusree et al. PLoS One. .

Abstract

Fragrance of rice is an important trait that confers a large economic benefit to the farmers who cultivate aromatic rice varieties. Several aromatic rice varieties have limited geographic distribution, and are endowed with variety-specific unique fragrances. BADH2 was identified as a fragrance gene in 2005, and it is essential to identify the fragrance alleles from diverse geographical locations and genetic backgrounds. Seeragasamba is a short-grain aromatic rice variety of the indica type, which is cultivated in a limited area in India. Whole genome sequencing of this variety identified a new badh2 allele (badh2-p) with an 8 bp insertion in the promoter region of the BADH2 gene. When the whole genome sequences of 76 aromatic varieties in the 3000 rice genome project were analyzed, the badh2-p allele was present in 13 varieties (approximately 17%) of both indica and japonica types. In addition, the badh2-p allele was present in 17 varieties that already had the loss-of-function allele, badh2-E7. Taken together, the frequency of badh2-p allele (approximately 40%) was found to be greater than that of the badh2-E7 allele (approximately 34%) among the aromatic rice varieties. Therefore, it is suggested to include badh2-p as a predominant allele when screening for fragrance alleles in aromatic rice varieties.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Biosynthetic pathway of 2-acetyl-1-pyrroline (2AP) in rice.
Functional BADH2 converts γ-aminobutyraldehyde (GABald) to γ-aminobutyric acid (GABA). When BADH2 is partly or fully non-functional, GABald is diverted to the production of Δ1pyrroline and 2AP (responsible for fragrance).
Fig 2
Fig 2. The dendrogram showing the relationship between Seeragasamba and 39 aromatic rice varieties based on whole genome SNPs.
The SNP data for the 39 aromatic rice varieties were extracted from the Rice SNP-Seek Database. Name of the aromatic rice variety followed by its type in bracket, and its geographical origin are given for each entry.
See this image and copyright information in PMC

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