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. 2015 Jun 11:5:11303.
doi: 10.1038/srep11303.

Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index

Pasupathi Rathinasabapathi  1 , Natarajan Purushothaman  1 , V L Ramprasad  2 , Madasamy Parani  1
Affiliations

Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index

Pasupathi Rathinasabapathi et al. Sci Rep. .

Abstract

Swarna is a popular cultivated indica rice variety with low glycemic index (GI) but its genetic basis is not known. The whole genome of Swarna was sequenced using Illumina's paired-end technology, and the reads were mapped to the Nipponbare reference genome. Overall, 65,984 non-synonymous SNPs were identified in 20,350 genes, and in silico analysis predicted that 4,847 of them in 2,214 genes may have deleterious effect on protein functions. Polymorphisms were found in all the starch biosynthesis genes, except the gene for branching enzyme IIa. It was found that T/G SNP at position 246, 'A' at position 2,386, and 'C' at position 3,378 in the granule bound starch synthase I gene, and C/T SNP at position 1,188 in the glucose-6-phosphate translocator gene may contribute to the low GI phenotype in Swarna. All these variants were also found in the genome of another low GI indica rice variety from Columbia, Fedearroz 50. The whole genome analysis of Swarna helped to understand the genetic basis of GI in rice, which is a complex trait involving multiple factors.

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Figures

Figure 1
Figure 1. Classification of the Swarna reads mapped on to the Nipponbare reference genome.
The total number reads in the center circle. Number of mapped reads on the nuclear genome and unmapped reads in the middle circle. The outer circle represents the uniquely mapped reads, and the reads mapped to multiple locations.
Figure 2
Figure 2. Annotation of SNPs and InDels that were identified in Swarna.
Annotated SNPs and InDels were classified based on their locations.
Figure 3
Figure 3. Distribution and skewness of the number of non-synonymous SNPs per kb in the 20,350 genes of Swarna.
The outlier value calculation indicated that 6,589 genes had >1.37 non-synonymous SNPs per kb (orange bars).
Figure 4
Figure 4. Functional categorization of the contigs assembled from the unmapped reads into gene ontology (GO) terms: biological processes, cellular components, molecular functions.
See this image and copyright information in PMC

References

    1. Kaushik S. et al. Glycemic Index, Retinal Vascular Caliber, and Stroke Mortality. Stroke 40, 206–212 (2009). - PubMed
    1. Sheu W.H.H. et al. Addressing the burden of type 2 diabetes and cardiovascular disease through the management of postprandial hyperglycaemia: An Asian-Pacific perspective and expert recommendations. Diabetes Res. Clin. Pr. 92, 312–321 (2011). - PubMed
    1. Hu P., Zhao H., Duan Z., Linlin Z. & Wu D. Starch digestibility and the estimated glycemic score of different types of rice differing in amylose contents. J. Cereal Sci. 40, 231–237 (2004).
    1. Fitzgerald M.A. et al. Identification of a Major Genetic Determinant of Glycaemic Index in Rice. Rice 4, 66–74 (2011).
    1. Kharabian-Masouleh A., Waters D.L.E., Reinke R.F., Ward R. & Henry R.J. SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci. Rep. 2, 557: 10.1038/srep00557 (2012). - PMC - PubMed

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