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A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)
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A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)
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Journal Article
A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)
2013
Overview
Background
The construction of linkage maps is a first step in exploring the genetic basis for adaptive phenotypic divergence in closely related species by quantitative trait locus (QTL) analysis. Linkage maps are also useful for comparative genomics in non-model organisms. Advances in genomics technologies make it more feasible than ever to study the genetics of adaptation in natural populations. Restriction-site associated DNA (RAD) sequencing in next-generation sequencers facilitates the development of many genetic markers and genotyping. We aimed to construct a linkage map of the gudgeons of the genus
Gnathopogon
(Cyprinidae) for comparative genomics with the zebrafish
Danio rerio
(a member of the same family as gudgeons) and for the future QTL analysis of the genetic architecture underlying adaptive phenotypic evolution of
Gnathopogon
.
Results
We constructed the first genetic linkage map of
Gnathopogon
using a 198 F
2
interspecific cross between two closely related species in Japan: river-dwelling
Gnathopogon elongatus
and lake-dwelling
Gnathopogon caerulescens
. Based on 1,622 RAD-tag markers, a linkage map spanning 1,390.9 cM with 25 linkage groups and an average marker interval of 0.87 cM was constructed. We also identified a region involving female-specific transmission ratio distortion (TRD). Synteny and collinearity were extensively conserved between
Gnathopogon
and zebrafish.
Conclusions
The dense SNP-based linkage map presented here provides a basis for future QTL analysis. It will also be useful for transferring genomic information from a “traditional” model fish species, zebrafish, to screen candidate genes underlying ecologically important traits of the gudgeons.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
Subject
/ Alleles
/ Analysis
/ Animal Genetics and Genomics
/ Animals
/ Biomedical and Life Sciences
/ Chromosome Mapping - methods
/ Comparative and evolutionary genomics
/ DNA
/ DNA Restriction Enzymes - metabolism
/ Female
/ Genes
/ Genetics
/ Genomes
/ Genomics
/ Male
/ Microbial Genetics and Genomics
/ Quantitative Trait Loci - genetics
/ Sequence Analysis, DNA - methods
/ Studies
