ArticleScientific reports2015
Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 34 citations in OpenAlex.
- Functional nutritional rice: current progresses and future prospects.Frontiers in plant science · 2024Review
- Endosperm structure and Glycemic Index of Japonica Italian rice varieties.Frontiers in plant science · 2023Article
- Whole-Genome Sequencing of KMR3 andFrontiers in plant science · 2022Article
- Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing.Molecular genetics and genomics : MGG · 2022Article
- Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing.Molecular biology reports · 2020Article
- Article
- Gene Expression Dynamics in Rice Peduncles at the Heading Stage.Frontiers in genetics · 2020Article
- Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties.International journal of genomics · 2019Article
- Rice Genomics: over the Past Two Decades and into the Future.Genomics, proteomics & bioinformatics · 2018Review
- Assembly of an early-matured japonica (Geng) rice genome, Suijing18, based on PacBio and Illumina sequencing.Scientific data · 2017Article
- Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection.International journal of genomics · 2017Article
- Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India.Rice (New York, N.Y.) · 2016Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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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