ArticlePlant biotechnology journal2019
Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains.
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 63 papers, 1 of them a synthesis that pooled it.
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Who cites it
63 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-QTL s and haplotypes for efficient zinc biofortification of rice.The plant genome · 2023Pooled it
- Heat stress responses of plants during adaptation to high temperature environments: A review of recent advances and insights.Plant signaling & behavior · 2026Review
- Mining rare haplotypes to accelerate precision breeding in rice.The plant genome · 2026Article
- Genome-wide association mapping and haplotype analysis reveal the genetic architecture of sodicity tolerance in bread wheat (Triticum aestivum L.).Scientific reports · 2026Article
- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- Subspecies-specific haplotype signatures for customizing blanchability in groundnut (Arachis hypogaea L.) via haplotype-based breeding.Communications biology · 2026Article
- Dissecting multi-rust resistance in wheat through genome-wide association study, haplotype analysis, and marker validation.The plant genome · 2026Article
- Genome-wide detection of superior haplotypes for seed oil and protein content in Northeast China soybean (Frontiers in plant science · 2026Article
- Genome-wide association study (GWAS) and transcription analysis of candidate genes for rice grain eating and cooking quality (ECQ) traits.BMC genomics · 2025Article
- Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Food chemistry. Molecular sciences · 2025Article
- Superior haplotypes of genes associated with higher grain yield under reproductive stage drought stress in rice.Journal of experimental botany · 2025Article
- Allelic value in gene regulation-implications for gene editing.Annals of botany · 2025Article
- Haplotype characterization of phosphorus homeostasis gene,3 Biotech · 2025Article
- Drought's physiological footprint: implications for crop improvement in rice.Molecular biology reports · 2025Review
- Genome-wide association study revealed candidate genes associated with leaf size in alfalfa (Medicago sativa L.).BMC plant biology · 2025Article
- Review
- Identification of superior haplotypes and candidate gene for seed size-related traits in soybean (Molecular breeding : new strategies in plant improvement · 2025Article
- Candidate gene analysis of rice grain shape based on genome-wide association study.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genomic-wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.).The plant genome · 2024Article
- Genome-wide association study and transcriptome analysis reveal natural variation of key genes regulation flowering time in rapeseed.Molecular breeding : new strategies in plant improvement · 2024Article
3 more citing papers are in PubMed but not listed here.
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10 authors.
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Abstract
Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quality (33 genes) revealed significant variations in the 3K rice genome (RG) panel. For selected genes, meta-expression analysis using already available datasets along with co-expression network provided insights at systems level. Also, we conducted candidate gene based association study for the 120 genes and identified 21 strongly associated genes governing 10-grain yield and quality traits. We report superior haplotypes upon phenotyping the subset of 3K RG panel, SD1-H8 with haplotype frequency (HF) of 30.13% in 3K RG panel, MOC1-H9 (HF: 23.08%), IPA1-H14 (HF: 6.64%), DEP3-H2 (HF: 5.59%), DEP1-H2 (HF: 37.53%), SP1-H3 (HF: 5.05%), LAX1-H5 (HF: 1.56%), LP-H13 (3.64%), OSH1-H4 (5.52%), PHD1-H14 (HF: 15.21%), AGO7-H15 (HF: 3.33%), ROC5-H2 (31.42%), RSR1-H8 (HF: 4.20%) and OsNAS3-H2 (HF: 1.00%). For heading date, Ghd7-H8 (HF: 3.08%), TOB1-H10 (HF: 4.60%) flowered early, Ghd7-H14 (HF: 42.60%), TRX1-H9 (HF: 27.97%), OsVIL3-H14 (HF: 1.72%) for medium duration flowering, while Ghd7-H6 (HF: 1.65%), SNB-H9 (HF: 9.35%) were late flowering. GS5-H4 (HF: 65.84%) attributed slender, GS5-H5 (HF: 29.00%), GW2-H2 (HF: 4.13%) were medium slender and GS5-H9 (HF: 2.15%) for bold grains. Furthermore, haplotype analysis explained possible genetic basis for superiority of selected mega-varieties. Overall, this study suggests the possibility for developing next-generation tailor-made rice with superior haplotype combinations of target genes suiting future food and nutritional demands via haplotype-based breeding.
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