A high-density genetic linkage map and QTL identification for growth traits in dusky kob (Argyrosomus japonicus)

Abstract

High-density genetic linkage maps provide a foundational genomic resource for quantitative trait locus (QTL) mapping, candidate gene localisation, and comparative genomic analysis. Data from such studies, in turn, can be incorporated into marker or genomics assisted selective breeding strategies for increased efficiency of aquaculture production. This study aimed to construct the first high-density genetic linkage map for dusky kob (Argyrosomus japonicus) a commercially important marine finfish in Asia, Australia, and South Africa. Using 2b-restriction site-associated DNA (2b-RAD) sequencing for genome-wide single nucleotide polymorphism (SNP) genotyping, in three full-sib F1 families (Family 1, n = 69 offspring; Family 2, n = 73 offspring; and Family 3, n = 70 offspring), led to the discovery and genotyping of 22,789 SNPs. Among these, 3992 quality filtered and informative SNPs were mapped to 24 linkage groups (LGs), aligning with the species' proposed haploid chromosome number. The total integrated genetic map spanned a length of 2550 cM with an average marker spacing of 0.68 cM, achieving a genome coverage of 98.61%. Male and female specific maps highlighted differential map lengths and recombination rates between the sexes, with the female map slightly longer and a lower recombination frequency than for the male. QTL analysis for growth-related traits, weight (W), standard length (sL), and Fulton's condition factor (K), identified a total of 25 QTLs of which five QTLs were found to be consistently shared across the traits. Collectively, these shared QTLs explained a substantial proportion of the phenotypic variance, accounting for between 9.30 and 19.30% of the observed variation, suggesting potential major genes for growth. These QTL regions led to the discovery of 65 potential candidate genes, including 11 genes that were specifically located within the shared QTLs. These genes were linked to essential biological processes, including metabolism, immunity, stress response, development, and vascular function. The establishment of this high-density genetic linkage map represents an important genomic resource for comprehending the genetic determinants of economically important traits in A. japonicus, with implications for advancing and optimising ongoing marker-assisted selection (MAS) initiatives in the species.