ArticlePlant biotechnology journal2019
Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice.
Article in Plant biotechnology journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it, 83 citations in OpenAlex.
- Multi-omics revolution to promote plant breeding efficiency.Frontiers in plant science · 2022Pooled it
- Molecular mechanisms underlying low glycemic index in rice: Insights from Indian landrace diversity.Molecular biology reports · 2026Review
- Unlocking Low-glycemic Potential in Rice: Genetic Insights and Breeding Strategies.Plant foods for human nutrition (Dordrecht, Netherlands) · 2026Review
- Clinical study and the diagnosis of lumpy skin disease in cattle using genomic, immunological, and pathological indicators.Frontiers in veterinary science · 2026Article
- Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Food chemistry. Molecular sciences · 2025Article
- Unlocking the potential of wild rice to bring missing nutrition to elite grains.Plant communications · 2025Review
- Integrative transcriptogenomic analyses reveal the regulatory network underlying rice eating and cooking quality and identify a role for alpha-globulin in modulating starch and sucrose metabolism.Plant communications · 2025Article
- Creating a SuperiorFoods (Basel, Switzerland) · 2025Article
- TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean.Plant communications · 2024Article
- Genome-Wide Association Study of Starch Properties in Local Thai Rice.Plants (Basel, Switzerland) · 2023Article
- A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat.NAR genomics and bioinformatics · 2023Article
- 5M approach to decipher starch-lipid interaction in minor millets.Plant cell reports · 2023Article
- GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals.Nucleic acids research · 2023Article
- Polyploidization and genomic selection integration for grapevine breeding: a perspective.Frontiers in plant science · 2023Review
- Potential of underutilized crops to introduce the nutritional diversity and achieve zero hunger.Functional & integrative genomics · 2022Article
- Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2.Journal of advanced research · 2022Article
- DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate.Plant methods · 2022Article
- Resistant starch formation in rice: Genetic regulation and beyond.Plant communications · 2022Review
- Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century.Plant communications · 2022Review
- Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reliably generating rice varieties with low glycaemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wx
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.