Unravelling the complex genetic basis of growth in New Zealand silver trevally (Pseudocaranx georgianus)

Abstract

Growth directly influences production rate and therefore is one of the most important and well-studied trait in animal breeding. However, understanding the genetic basis of growth has been hindered by its typically complex polygenic architecture. Here, we performed quantitative trait locus (QTL) mapping and genome-wide association studies (GWAS) for 10 growth traits that were observed over two years in 1,100 F1 captive-bred trevally (Pseudocaranx georgianus). We constructed the first high-density linkage map for trevally, which included 19,861 single nucleotide polymorphism (SNP) markers, and discovered eight QTLs for height, length and weight on linkage groups 3, 14 and 18. Using GWAS, we further identified 113 SNP-trait associations, uncovering 10 genetic hot spots involved in growth. Two of the markers found in the GWAS co-located with the QTLs previously mentioned, demonstrating that combining QTL mapping and GWAS represents a powerful approach for the identification and validation of loci controlling complex traits. This is the first study of its kind for trevally. Our findings provide important insights into the genetic architecture of growth in this species and supply a basis for fine mapping QTLs, marker-assisted selection, and further detailed functional analysis of the genes underlying growth in trevally.