High-Density Linkage Map and QTLs for Growth in Snapper (Chrysophrys auratus )

G3 : Genes - Genomes - Genetics
David T AshtonMaren Wellenreuther

Abstract

Characterizing the genetic variation underlying phenotypic traits is a central objective in biological research. This research has been hampered in the past by the limited genomic resources available for most non-model species. However, recent advances in sequencing technologies and related genotyping methods are rapidly changing this. Here we report the use of genome-wide SNP data from the ecologically and commercially important marine fish species Chrysophrys auratus (snapper) to 1) construct the first linkage map for this species, 2) scan for growth QTL, and 3) search for putative candidate genes in the surrounding QTL regions. The newly constructed linkage map contained ∼11K SNP markers and is one of the densest maps to date in the fish family Sparidae. Comparisons with genome scaffolds of the recently assembled snapper genome indicated that marker placement was mostly consistent between the scaffolds and linkage map (R = 0.7), but that at fine scales (< 5 cM) some precision limitations occurred. Of the 24 linkage groups, which likely reflect the 24 chromosomes of this species, three were found to contain QTL with genome-wide significance for growth-related traits. A scan of 13 candidate growth genes located the growth horm...Continue Reading

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Datasets Mentioned

BETA
KR269817.1
AH014067.4
AH014068.4
EF462192.1

Methods Mentioned

BETA
salt extraction
electrophoresis
Genotyping

Software Mentioned

ggplot2
PLINK
FastQC
STACKs
Bowtie
ea
Genepop
LEPMAP
Geneious
GridQTL

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