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多倍体中用于群体和数量遗传学的变异检测

Variant calling in polyploids for population and quantitative genetics.

作者信息

Phillips Alyssa R

机构信息

Department of Evolution and Ecology University of California, Davis Davis 95616 California USA.

出版信息

Appl Plant Sci. 2024 Jul 17;12(4):e11607. doi: 10.1002/aps3.11607. eCollection 2024 Jul-Aug.

DOI:10.1002/aps3.11607
PMID:39184203
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11342233/
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.

摘要

基因组组装和测序技术的进步使得全基因组序列（WGS）数据和参考基因组可用于研究多倍体物种。与流行的简化代表性测序方法相比，WGS数据提供的全基因组覆盖范围和更高的标记密度可以极大地增进我们对多倍体物种和多倍体生物学的理解。然而，使多倍体物种引人关注的生物学特性也给读段比对、变异鉴定和基因型估计带来了挑战。在变异检测中考虑等位基因剂量不确定性、亚基因组之间的同源性以及染色体遗传模式的差异等特征可以减少错误。在这里，我讨论了多倍体WGS数据中变异检测的挑战，并讨论了潜在的解决方案可以整合到标准变异检测流程中的哪些环节。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/195e/11342233/f20523ca4544/APS3-12-e11607-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/195e/11342233/e457c27d1fb4/APS3-12-e11607-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/195e/11342233/16ab8a4d480c/APS3-12-e11607-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/195e/11342233/f20523ca4544/APS3-12-e11607-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/195e/11342233/e457c27d1fb4/APS3-12-e11607-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/195e/11342233/16ab8a4d480c/APS3-12-e11607-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/195e/11342233/f20523ca4544/APS3-12-e11607-g001.jpg

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