Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations

Genetics
Timothy P BiltonKen G Dodds

Abstract

Next-generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high-density genetic linkage maps, which facilitate the development of nonmodel species' genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth. If unaccounted for, these errors lead to inflated genetic maps. In addition, map construction in many species is performed using full-sibling family populations derived from the outcrossing of two individuals, where unknown parental phase and varying segregation types further complicate construction. We present a new methodology for modeling low coverage sequencing data in the construction of genetic linkage maps using full-sibling populations of diploid species, implemented in a package called GUSMap. Our model is based on the Lander-Green hidden Markov model but extended to account for errors present in sequencing data. We were able to obtain accurate estimat...Continue Reading

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Citations

Aug 7, 2019·G3 : Genes - Genomes - Genetics·Ken G DoddsShannon M Clarke
Nov 17, 2019·G3 : Genes - Genomes - Genetics·Marcelo MollinariZhao-Bang Zeng
Apr 22, 2020·G3 : Genes - Genomes - Genetics·Christos PalaiokostasDirk-Jan De Koning
Apr 4, 2021·Animals : an Open Access Journal From MDPI·Fotis Pappas, Christos Palaiokostas
May 26, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Yanlin LiaoChris Maliepaard
Jul 29, 2021·The New Phytologist·Kenneth M OlsenLin-Feng Li
Sep 15, 2021·G3 : Genes - Genomes - Genetics·Vander Fillipe de SouzaCynthia Maria Borges Damasceno

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Methods Mentioned

BETA
genotyping

Software Mentioned

JoinMap
JM
Lep
LM2
Bowtie2
Tassel3
GUSMap ( Genotyping Uncertainty with Sequencing data and linka...
GM
Linux
R

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