ArticlePloS one2016
Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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Who cites it
45 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
- Impact of Drought Stress on Photosynthetic Electron Transport in Rice Seedlings.Plants (Basel, Switzerland) · 2026Article
- A Genome‑wide Association Study of the Grain Ionome in Rice Oryza Sativa Ssp. Japonica under Two Diverse Water Management Systems.Rice (New York, N.Y.) · 2025Article
- Biologically meaningful genome interpretation models to address data underdetermination for the leaf and seed ionome prediction in Arabidopsis thaliana.Scientific reports · 2024Article
- Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh.Plant direct · 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
- Association mapping in bambara groundnut [Vigna subterranea (L.) Verdc.] reveals loci associated with agro-morphological traits.BMC genomics · 2023Article
- Growth-defence trade-off in rice: fast-growing and acquisitive genotypes have lower expression of genes involved in immunity.Journal of experimental botany · 2023Article
- Article
- The Identification of a Yield-Related Gene Controlling Multiple Traits Using GWAS in Sorghum (Plants (Basel, Switzerland) · 2023Article
- Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome.Communications biology · 2023Article
- Marker-Assisted Pyramiding of Blast-Resistance Genes in aPlants (Basel, Switzerland) · 2023Article
- Genome-wide association, RNA-seq and iTRAQ analyses identify candidate genes controlling radicle length of wheat.Frontiers in plant science · 2022Article
- Exploring the Developmental Progression of Endosperm Cavity Formation in Maize Grain and the Underlying Molecular Basis Using X-Ray Tomography and Genome Wide Association Study.Frontiers in plant science · 2022Article
- Salinity tolerance mechanisms and their breeding implications.Journal, genetic engineering & biotechnology · 2021Review
- Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces.BMC plant biology · 2021Article
- Genome-wide association study for morphological, phenological, quality, and yield traits in einkorn (Triticum monococcum L. subsp. monococcum).G3 (Bethesda, Md.) · 2021Article
- Analysis of Cadmium Root Retention for Two Contrasting Rice Accessions Suggests an Important Role forPlants (Basel, Switzerland) · 2021Article
- Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach.Heredity · 2021Article
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions.
resultsIn total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10-7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10-7) and for plant height on chromosome 6 (FDR = 0.011).
conclusionsWe demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.
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