ArticleFrontiers in plant science2023
Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice.
Article in Frontiers in plant science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Integrative genomics resolves rice loci associated with acidic soil-related aluminum, cadmium, and manganese stress responses.Plant cell reports · 2026Article
- Haplotype Analysis of the Wx and SSIIa Genes and Their Association with Starch Physicochemical Properties in Diverse Rice Germplasm.Molecular biotechnology · 2026Review
- Split Potassium Fertilization Modulates Endogenous Hormone Homeostasis to Optimize the Grain-Filling Process and Mitigate High-Temperature Damage in Rice.Plants (Basel, Switzerland) · 2026Article
- Genomic dissection of iron toxicity tolerance in rice identifies key loci, candidate genes, and associated haplotypes.Scientific reports · 2026Article
- Genome-wide identification of QTNs and candidate genes in Ethiopian sorghum (Sorghum bicolor (L.) moench) landraces using SNP-based approaches.BMC genomic data · 2025Article
- Identifying Heat Adaptability QTLs and Candidate Genes for Grain Appearance Quality at the Flowering Stage in Rice.Rice (New York, N.Y.) · 2025Article
- Review
- Meta-QTL and ortho analysis unravels the genetic architecture and key candidate genes for cold tolerance at seedling stage in rice.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Exploring the genetic architecture of powdery mildew resistance in wheat through QTL meta-analysis.Frontiers in plant science · 2024Article
- Unravelling the genetic framework associated with grain quality and yield-related traits in maize (Frontiers in genetics · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
18 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes,
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