Abstract
The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK) (Seriola lalandi) are relative sparse. To overcome this, we aimed (1) to develop a linkage map for this species, and (2) to identify markers/variants associated with economically important traits in kingfish (with an emphasis on body weight). Genetic and genomic analyses were conducted using 13,898 single nucleotide polymorphisms (SNPs) generated from a new high-throughput genotyping by sequencing platform, Diversity Arrays Technology (DArTseqTM) in a pedigreed population comprising 752 animals. The linkage analysis enabled to map about 4,000 markers to 24 linkage groups (LGs), with an average density of 3.4 SNPs per cM. The linkage map was integrated into a genome-wide association study (GWAS) and identified six variants/SNPs associated with body weight (P < 5e-8) when a multi-locus mixed model was used. Two out of the six significant markers were mapped to LGs 17 and 23, and collectively they explained 5.8% of the total genetic variance. It is concluded that the newly developed linkage map and the significantly associated markers with body weight provide fundamental information to characterize genetic architecture of growth-related traits in this population of YTK S. lalandi.
Highlights
Despite the economic importance of Yellowtail kingfish (YTK) Seriola lalandi world-wide, there has been very limited published information regarding genetic and genomic architecture for quantitative complex traits in this species
The findings from this study provide information for future fine mapping, gene mining, polymorphism identification of causative single nucleotide polymorphisms (SNPs) and their pathways and biological functions related to complex traits of economic importance in YTK
The present study reports, for the first time in YTK: (i) a high-density SNP-based linkage map, and (ii) a set of markers significantly associated with traits of economic importance
Summary
Despite the economic importance of Yellowtail kingfish (YTK) Seriola lalandi world-wide (e.g., with a current annual production of about 4,000 tons, valuing 56 million dollars in Australia), there has been very limited published information regarding genetic and genomic architecture for quantitative complex traits in this species. The associations of DNA markers (microsatellites or SNPs) with growth and carcass traits (Gonzalez-Pena et al, 2016), disease resistance (Correa et al, 2016; Palaiokostas et al, 2016) or sexual maturity (Gutierrez et al, 2015) were reported in a number of species of commercial importance, such as salmonids and seabream Results from these studies showed that growth or disease resistance trait is generally of polygenic nature (controlled by multiple loci, each with small effects) or they possess oligogenic architecture with a few moderate-large effects quantitative trait loci (QTL) (Vallejo et al, 2017). QTL were reported to reside on two different linkage groups (LGs) for the monogenean fluke ectoparasite (Benedenia seriolae) but in a different kingfish species, i.e., Seriola quinqueradiata (Ozaki et al, 2013)
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