ArticlePloS one2013
Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula.
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 70 papers.
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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.
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70 citing papers in PubMed, 186 citations in OpenAlex.
- Quantitative trait loci and genome-wide association study identifies novel loci for plant height in pepper (Frontiers in plant science · 2026Article
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- Gene Family Expansions Provide Molecular Flexibility Required for Context-Dependent Species Interactions.Ecology letters · 2025Article
- Genome-Wide Association Study for Nodule Traits in Guar.Current issues in molecular biology · 2025Article
- Medicago truncatula genotype drives the plant nutritional strategy and its associated rhizosphere bacterial communities.The New phytologist · 2025Article
- Genotypic variation in resource exchange, use, and production traits in the legume-rhizobia mutualism.Ecology and evolution · 2024Article
- Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance.BMC genomics · 2024Article
- Novel SNP markers for flowering and seed quality traits in faba bean (Frontiers in plant science · 2024Article
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- Genetic architecture of the response ofFrontiers in plant science · 2023Article
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- Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions.Scientific reports · 2022Article
- Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype.Applied and environmental microbiology · 2022Article
- Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont.Proceedings. Biological sciences · 2022Article
- Negotiating mutualism: A locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts.Journal of evolutionary biology · 2022Article
- Genome-Wide Identification of Histone Modification Gene Families in the Model LegumePlants (Basel, Switzerland) · 2022Article
- Flavonoid Accumulation Varies inFrontiers in plant science · 2022Article
- Root rot a silent alfalfa killer in China: Distribution, fungal, and oomycete pathogens, impact of climatic factors and its management.Frontiers in microbiology · 2022Review
- Salt Stress Enhances Early Symbiotic Gene Expression inMolecular plant-microbe interactions : MPMI · 2021Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide association study (GWAS) has revolutionized the search for the genetic basis of complex traits. To date, GWAS have generally relied on relatively sparse sampling of nucleotide diversity, which is likely to bias results by preferentially sampling high-frequency SNPs not in complete linkage disequilibrium (LD) with causative SNPs. To avoid these limitations we conducted GWAS with >6 million SNPs identified by sequencing the genomes of 226 accessions of the model legume Medicago truncatula. We used these data to identify candidate genes and the genetic architecture underlying phenotypic variation in plant height, trichome density, flowering time, and nodulation. The characteristics of candidate SNPs differed among traits, with candidates for flowering time and trichome density in distinct clusters of high linkage disequilibrium (LD) and the minor allele frequencies (MAF) of candidates underlying variation in flowering time and height significantly greater than MAF of candidates underlying variation in other traits. Candidate SNPs tagged several characterized genes including nodulation related genes SERK2, MtnodGRP3, MtMMPL1, NFP, CaML3, MtnodGRP3A and flowering time gene MtFD as well as uncharacterized genes that become candidates for further molecular characterization. By comparing sequence-based candidates to candidates identified by in silico 250K SNP arrays, we provide an empirical example of how reliance on even high-density reduced representation genomic makers can bias GWAS results. Depending on the trait, only 30-70% of the top 20 in silico array candidates were within 1 kb of sequence-based candidates. Moreover, the sequence-based candidates tagged by array candidates were heavily biased towards common variants; these comparisons underscore the need for caution when interpreting results from GWAS conducted with sparsely covered genomes.
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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.