Using genomic resources for linkage analysis in Peromyscus with an application for characterizing Dominant Spot

Zhenhua Shang,Ronald H Mckenzie,Jessica L Keisler,David J Horovitz,Shannon W Davis,Michael R Felder

doi:10.1186/s12864-020-06969-1

Abstract

BackgroundPeromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P. polionotus, are closely related and can generate viable and fertile hybrid offspring. The ability to generate hybrid offspring, coupled with developing genomic resources, enables researchers to conduct linkage analysis studies to identify genomic loci associated with specific traits.ResultsWe used available genomic data to identify DNA polymorphisms between P. maniculatus and P. polionotus and used the polymorphic data to identify the range of genetic complexity that underlies physiological and behavioral differences between the species, including cholesterol metabolism and genes associated with autism. In addition, we used the polymorphic data to conduct a candidate gene linkage analysis for the Dominant spot trait and determined that Dominant spot is linked to a region of chromosome 20 that contains a strong candidate gene, Sox10. During the linkage analysis, we found that the spot size varied quantitively in affected Peromyscus based on genetic background.ConclusionsThe expanding genomic resources for Peromyscus facilitate their use in linkage analysis studies, enabling the identification of loci associated with specific traits. More specifically, we have linked a coat color spotting phenotype, Dominant spot, with Sox10, a member the neural crest gene regulatory network, and that there are likely two genetic modifiers that interact with Dominant spot. These results establish Peromyscus as a model system for identifying new alleles of the neural crest gene regulatory network.

Highlights

Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies
Analysis of genomic variations between P. maniculatus and P. polionotus The ability to generate fertile and viable hybrid offspring from P. maniculatus and P. polionotus provides an opportunity to identify the genetic loci associated with phenotypic traits that differ between the two species
The first assembly of the P. maniculatus genome was used as the reference genome, and the P. polionotus sequencing reads deposited in the Sequencing Read Archive (SRA) database were mapped against the P. maniculatus reference genome

Summary

Introduction

Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P. polionotus, are closely related and can generate viable and fertile hybrid offspring. The ability to generate hybrid offspring, coupled with developing genomic resources, enables researchers to conduct linkage analysis studies to identify genomic loci associated with specific traits. Peromyscus are the most common and widely distributed mammalian species in North America and includes the deer mouse (P. maniculatus), the old-field mouse (P. polionotus), and the white-footed mouse (P. leucopos) [1]. Peromyscus are more closely related to hamsters than to Mus. Mus is an exceptional model system for biomedical research, having a wide range of genetic resources, including a fully sequenced and annotated genome, various inbred strains, and the ability to make specific genetic modifications.

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