Variant calling in polyploids for population and quantitative genetics

• Published in: Applications in plant sciences Vol. 12; no. 4; pp. e11607 - n/a
• Main Author: Phillips, Alyssa R.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.07.2024; Wiley
• Subjects: Algorithms; Chromosomes; Gene mapping; genome; genome assembly; Genomes; Genomics; genotype; Genotypes; Homology; mixed ploidy; Nucleotide sequence; nucleotide sequences; Polymorphism; Polyploidy; Population genetics; Population studies; Quantitative genetics; Software; species; uncertainty; variance; variant calling; whole genome sequence; whole genome sequence; population genetics; quantitative genetics; variant calling; polyploidy; mixed ploidy
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11607

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.