Variant calling in polyploids for population and quantitative genetics

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...

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Published inApplications in plant sciences Vol. 12; no. 4; pp. e11607 - n/a
Main Author Phillips, Alyssa R.
Format Journal Article
LanguageEnglish
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
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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.
AbstractList 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.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.
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.
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.
Author Phillips, Alyssa R.
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  organization: University of California, Davis
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CitedBy_id crossref_primary_10_3390_horticulturae10101077
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Issue 4
Keywords whole genome sequence
population genetics
quantitative genetics
variant calling
polyploidy
mixed ploidy
Language English
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Notes This article is part of the special issue “Twice as Nice: New Techniques and Discoveries in Polyploid Biology.”
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Snippet Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid...
Abstract Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study...
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SubjectTerms 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
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Title Variant calling in polyploids for population and quantitative genetics
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2Faps3.11607
https://www.ncbi.nlm.nih.gov/pubmed/39184203
https://www.proquest.com/docview/3095927051
https://www.proquest.com/docview/3097151711
https://www.proquest.com/docview/3153723029
https://doaj.org/article/3cf0e25d877041bab62119c9cee2dd1a
Volume 12
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