ArticleApplications in plant sciences
Variant calling in polyploids for population and quantitative genetics.
Article in Applications in plant sciences. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A pangenome-based approach reveals genes associated with polyploidy and apomixis in Eragrostis curvula.The plant genome · 2026Article
- NodeGWAS: Leveraging graph pangenomes for sensitive and accurate association analyses across diverse diploid and polyploid species.Plant communications · 2026Article
- Functional divergence of BnaWRKY7 homologs drives phytosterol variations in polyploid Brassica napus.Journal of advanced research · 2026Article
- The genomic basis of adaptive leaf variation in the Galápagos giant daisies.Nature communications · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
- Molecular identification and diversity assessment of Tyrrhenian Romulea species (Iridaceae).PloS one · 2026Article
- ChoCallate: a computational pipeline for consensus germline variant calling in genomic sequencing data.PeerJ · 2026Article
- Genomic resources for Australian alfalfa (Medicago sativa L.) genomics: reformatted reference genome, annotated variants, gene presence-absence and diversity analysis from genome re-sequencing.BMC plant biology · 2025Article
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Genetic and genomic resources for turfgrasses: status, applications, and prospects.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- A New Set of SSR Markers Combined in One Reaction for Efficient Genotyping of the Hexaploid European Plum (Plants (Basel, Switzerland) · 2025Article
- Variant calling in polyploids for population and quantitative genetics.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
1 author.
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Abstract
Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.
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