ArticleBMC plant biology2016
Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam.
Article in BMC plant biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 67 citations in OpenAlex.
- 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
- Exploring Hormonal Pathways and Gene Networks in Crown Root Formation Under Stress Conditions: An Update.Plants (Basel, Switzerland) · 2025Review
- Quantitative trait loci for grain mineral element accumulation in Vietnamese rice landraces.PloS one · 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
- CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice.The Plant journal : for cell and molecular biology · 2022Article
- Genomic regions and candidate genes selected during the breeding of rice in Vietnam.Evolutionary applications · 2022Article
- Effects of irrigation on root growth and development of soybean: A 3-year sandy field experiment.Frontiers in plant science · 2022Article
- Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress.Frontiers in plant science · 2022Article
- Genome-Wide Association Analyses to Identify SNPs Related to Drought Tolerance.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Identification of Markers for Root Traits Related to Drought Tolerance Using Traditional Rice Germplasm.Molecular biotechnology · 2021Article
- Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces.BMC plant biology · 2021Article
- Nitrate Regulates Maize Root Transcriptome through Nitric Oxide Dependent and Independent Mechanisms.International journal of molecular sciences · 2021Article
- Genetic basis and network underlying synergistic roots and shoots biomass accumulation revealed by genome-wide association studies in rice.Scientific reports · 2021Article
- Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.Rice (New York, N.Y.) · 2021Article
- Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice.Plants (Basel, Switzerland) · 2021Article
- Assessment of root phenotypes in mungbean mini-core collection (MMC) from the World Vegetable Center (AVRDC) Taiwan.PloS one · 2021Article
- Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought?Rice (New York, N.Y.) · 2020Article
- The physiological mechanism underlying root elongation in response to nitrogen deficiency in crop plants.Planta · 2020Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDespite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them.
resultsThe panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed.
conclusionsSome of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.