ArticlePloS one2013
Genome-wide association mapping of root traits in a japonica rice panel.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers, 1 of them a synthesis that pooled it.
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Who cites it
132 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Pooled it
- Application of NGS Technology, Association Mapping, and Physical Mapping Technologies to Identify Candidate Genes Associated with Maize (International journal of molecular sciences · 2026Article
- Characterization of spelt wheat (Triticum spelta L.) genotypes using DArTseq technology.Journal of applied genetics · 2026Article
- Using Genome-Wide Association Studies to Reveal DArTseq and SNP Loci Associated with Agronomic Traits and Yield in Maize.Current issues in molecular biology · 2025Article
- DArTseq-Based, High-Throughput Identification of Novel Molecular Markers for the Detection of Fusarium Resistance in Maize.International journal of molecular sciences · 2025Article
- Genetic Diversity of Indigenous Rice Varieties Cultivated by Mon-Khmer-Speaking Ethnic Communities in Thailand.Rice (New York, N.Y.) · 2025Article
- Genome-Wide Identification and Functional Characterization of Brown Spot Resistance Genes in Rice (Journal of agricultural and food chemistry · 2025Article
- Identification of SNP and SilicoDArT Markers and Characterization of Their Linked Candidate Genes Associated with Maize Smut Resistance.International journal of molecular sciences · 2024Article
- Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach.Rice (New York, N.Y.) · 2024Article
- Genome-wide association study and genotypic variation for the major tocopherol content in rice grain.Frontiers in plant science · 2024Article
- Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice.Rice (New York, N.Y.) · 2023Article
- Dissecting the genetic architecture of root-related traits in a grafted wild Vitis berlandieri population for grapevine rootstock breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Haplotype-Based Genome-Wide Association Analysis Using Exome Capture Assay and Digital Phenotyping Identifies Genetic Loci Underlying Salt Tolerance Mechanisms in Wheat.Plants (Basel, Switzerland) · 2023Article
- Utilizing Genomics to Characterize the Common Oat Gene Pool-The Story of More Than a Century of Polish Breeding.International journal of molecular sciences · 2023Article
- Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Frontiers in plant science · 2023Article
- Genome-wide association study as a powerful tool for dissecting competitive traits in legumes.Frontiers in plant science · 2023Review
- Genome-wide association study reveals that GhTRL1 and GhPIN8 affect cotton root development.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Root system architecture in rice: impacts of genes, phytohormones and root microbiota.3 Biotech · 2022Review
- Identification of quantitative trait loci for tillering, root, and shoot biomass at the maximum tillering stage in rice.Scientific reports · 2022Article
- Quantitative trait loci (QTL) for low temperature tolerance at the young microspore stage in rice (Breeding science · 2022Article
72 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r(2)>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.
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