ArticleScientific reports2017
Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
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Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of GWAS in canola blackleg (Leptosphaeria maculans) disease traits demonstrates increased power from imputed whole-genome sequence.Scientific reports · 2020Pooled it
- Applications of omics in deciphering the unique traits of durian, the king of fruits.Plant molecular biology · 2026Review
- Soluble starch synthase IVa determines cooked rice elongation in waxy and non-waxy rices (Frontiers in plant science · 2026Article
- Ensemble AnalySis with Interpretable Genomic Prediction (EasiGP): Computational tool for interpreting ensembles of genomic prediction models.The plant genome · 2025Article
- Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass.Plant physiology · 2025Article
- Identification of novel candidate genes for regulating oil composition in soybean seeds under environmental stresses.Frontiers in plant science · 2025Article
- A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice.National science review · 2024Article
- Unraveling the genetics underlying micronutrient signatures of diversity panel present in brown rice through genome-ionome linkages.The Plant journal : for cell and molecular biology · 2023Article
- Genome-wide association study of cooking-caused grain expansion in rice (Frontiers in plant science · 2023Article
- Integrated multi-locus genome-wide association studies and transcriptome analysis for seed yield and yield-related traits inFrontiers in plant science · 2023Article
- MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.).DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Unveiling the genetic architecture for lodging resistance in rice (Frontiers in genetics · 2022Article
- Genome-wide association studies of five free amino acid levels in rice.Frontiers in plant science · 2022Article
- Genome-wide association study for resistance toFrontiers in plant science · 2022Article
- Genome-wide association study reveals novel genomic regions governing agronomic and grain quality traits and superior allelic combinations for Basmati rice improvement.Frontiers in plant science · 2022Article
- Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed.Biomolecules · 2021Review
- Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality.Scientific reports · 2021Article
- Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness.Plant biotechnology journal · 2021Article
- Article
- Genomic interventions for sustainable agriculture.Plant biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study, we used 2.9 million single nucleotide polymorphisms (SNP) and 393,429 indels derived from whole genome sequences of 591 rice landraces to determine the genetic basis of cooked and raw grain length, width and shape using genome-wide association study (GWAS). We identified a unique fine-mapped genetic region GWi7.1 significantly associated with cooked and raw grain width. Additionally, GWi7.2 that harbors GL7/GW7 a cloned gene for grain dimension was found. Novel regions in chromosomes 10 and 11 were also found to be associated with cooked grain shape and raw grain width, respectively. The indel-based GWAS identified fine-mapped genetic regions GL3.1 and GWi5.1 that matched synteny breakpoints between indica and japonica. GL3.1 was positioned a few kilobases away from GS3, a cloned gene for cooked and raw grain lengths in indica. GWi5.1 found to be significantly associated with cooked and raw grain width. It anchors upstream of cloned gene GW5, which varied between indica and japonica accessions. GWi11.1 is present inside the 3'-UTR of a functional gene in indica that corresponds to a syntenic break in chromosome 11 of japonica. Our results identified novel allelic structural variants and haplotypes confirmed using single locus and multilocus SNP and indel-based GWAS.
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