ArticleMolecular genetics and genomics : MGG2020
Genome-wide association studies using 50 K rice genic SNP chip unveil genetic architecture for anaerobic germination of deep-water rice population of Assam, India.
Article in Molecular genetics and genomics : MGG, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 48 citations in OpenAlex.
- The Cost of Bad Timing: How Phenology and Frequency Determine Agricultural Flood Risk.Water resources management (Dordrecht, Netherlands) · 2026Article
- Study on Rice Submergence Germination Through the Combination of RNA-Seq and Genome Resequencing Strategies.Plants (Basel, Switzerland) · 2025Article
- Identification of submergence tolerance QTLs/genes during seed germination in 432 rice varieties by GWAS.BMC plant biology · 2025Article
- Genetic dissection of total protein content, phenolic content and seed quality traits in pigeonpea (Cajanus cajan) using 62K pigeonpea genic SNP chip.Molecular genetics and genomics : MGG · 2025Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Association mapping of important agronomic traits in Mucuna pruriens (L.) DC.Botanical studies · 2024Article
- Article
- Plant Adaptation to Flooding Stress under Changing Climate Conditions: Ongoing Breakthroughs and Future Challenges.Plants (Basel, Switzerland) · 2023Review
- Genetic potential of grain-related traits in rice landraces: phenomics and multi-locus association analyses.Molecular biology reports · 2023Article
- GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination.Rice (New York, N.Y.) · 2023Article
- Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome.Communications biology · 2023Article
- Flooding tolerance in Rice: adaptive mechanism and marker-assisted selection breeding approaches.Molecular biology reports · 2023Review
- Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes.Frontiers in plant science · 2023Article
- Genome-wide association analysis for emergence of deeply sown rice (Frontiers in plant science · 2023Article
- Genome-wide association study of agronomical and root-related traits in spring barley collection grown under field conditions.Frontiers in plant science · 2023Article
- Genome-Wide Association Mapping Reveals Novel Putative Gene Candidates Governing Reproductive Stage Heat Stress Tolerance in Rice.Frontiers in genetics · 2022Article
- The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean - An review.Frontiers in plant science · 2022Review
- Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS.BMC plant biology · 2021Article
- Population structure and genome-wide association studies in bread wheat for phosphorus efficiency traits using 35 K Wheat Breeder's Affymetrix array.Scientific reports · 2021Article
- Genome-Wide Association Study Reveals Marker-Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice.Plants (Basel, Switzerland) · 2021Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
North Eastern part of India such as Assam is inundated by flood every year where the farmers are forced to grow the traditional tall deep-water rice. Genetic improvement of this type of rice is slow because of insufficient knowledge about their genetic architecture and population structure. In the present investigation, the genetic diversity architecture of 94 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPs and genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition. The anaerobic germination (AG) related trait-associated genes identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNP chip across 94 deep-water rice genotypes collected from different flood-prone districts/villages of Assam. Population structure and diversity analysis revealed that these genotypes were stratified into four sub-populations. Using GWAS approach, 20 significant genes were identified and found to be associated with AG-related traits. Of them, two most relevant genes (OsXDH1and SSXT) have been identified which explain phenotypic variability (R
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