ArticleNature genetics2020
Identifying genetic variants underlying phenotypic variation in plants without complete genomes.
Article in Nature genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers, 1 of them a synthesis that pooled it.
What it found
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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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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.
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Who cites it
108 citing papers in PubMed, 1 synthesis or guideline pooled it, 181 citations in OpenAlex.
- Advancing crop improvement through GWAS and beyond in mung bean.Frontiers in plant science · 2024Pooled it
- CRISPR editing of TERMINAL FLOWER 1 recapitulates perpetual flowering in strawberry, mimicking repression by the PERPETUAL FLOWERING locus.Plant physiology · 2026Article
- Converging GWAS and Genome Editing Decrypts MsCBF8-MsGolS2 Regulatory Module for Drought Tolerance Without Yield Penalty in Medicago sativa.Plant biotechnology journal · 2026Article
- Review
- Article
- Same Sex Chromosomes With Independent Origins in Haplochromine Cichlids.Genome biology and evolution · 2026Article
- Scalable medium-density genotyping platforms for cultivar identification, pedigree authentication, marker-assisted and genomic selection, and other applications in strawberry.G3 (Bethesda, Md.) · 2026Article
- A Cis-Regulatory Duplication in a Hox Hotspot Implicated in Mimetic Convergence in the Bumble Bee Bombus flavifrons.Molecular ecology · 2026Article
- The control of prickle formation in Rubus.Plant physiology · 2026Article
- BiTUGA: scalable prevalence-based unitig association testing for binary traits.G3 (Bethesda, Md.) · 2026Article
- A VIM2/4 deletion, and premature truncations of CMT2 and FBX5, drive DNA methylation changes after colonization of a novel habitat.Nature plants · 2026Article
- Wild genes to the rescue: high-throughput genomics reveals the wild source of broomrape resistance in sunflower.Journal of experimental botany · 2026Article
- Evolution of compound eye cell types shapes visual behaviors acrossbioRxiv : the preprint server for biology · 2026Article
- NodeGWAS: Leveraging graph pangenomes for sensitive and accurate association analyses across diverse diploid and polyploid species.Plant communications · 2026Article
- KCFtools: rapid alignment-free method for introgression screening and GWAS using k-mer profiles.Bioinformatics (Oxford, England) · 2026Article
- A k-mer-based genome-wide association study approach empowering gene mining in polyploids.Nature genetics · 2026Article
- kmerRRR: A k-mer based tool for functional genomics in Repeat Rich Regions.bioRxiv : the preprint server for biology · 2026Article
- k-mer-based approaches to unlock genebank genomics for targeted crop improvement.Nature genetics · 2026Review
- Integrative genomic analyses reveal candidate genes for the Ur-3 and Ur-7 rust resistance loci in common bean.The plant genome · 2026Article
- Advances in gene cloning and functional genomics approaches for wheat (Triticum aestivum L.) improvement.The plant genome · 2026Review
48 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the type of genetic variants detected in GWAS to include major deletions, insertions and rearrangements. We first use raw sequencing data directly to derive short sequences, k-mers, that mark a broad range of polymorphisms independently of a reference genome. We then link k-mers associated with phenotypes to specific genomic regions. Using this approach, we reanalyzed 2,000 traits in Arabidopsis thaliana, tomato and maize populations. Associations identified with k-mers recapitulate those found with SNPs, but with stronger statistical support. Importantly, we discovered new associations with structural variants and with regions missing from reference genomes. Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allows the detection of a wider range of genetic variants responsible for phenotypic variation.
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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 Socratic graph.