Abstract
Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9–15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.
Highlights
Aquatic products are an important source of nutrition for people around the world, especially in food-deficient countries (Easterling, 2007; Rice and Garcia, 2011)
Songpu mirror carp (SMC) is a strain derived from a European subspecies (C. carpio) of common carp, which is one of the most valuable fish species for freshwater breeding as well as one of the species that is highly promoted to culture in China
We identified three genes, argonaute RISC component 1 (AGO1), free fatty acid receptor 3-like (FFAR3), and AT rich interactive domain 1A (ARID1A) at qFCE1-32, quantitative trait loci (QTL) qFCE2-32, and qFCE332 on LG32, respectively
Summary
Aquatic products are an important source of nutrition for people around the world, especially in food-deficient countries (Easterling, 2007; Rice and Garcia, 2011). The long-term challenge for aquaculture breeders is to improve the yieldrelated traits in fish to meet the growing demand for fish products while minimizing their impact on the environment (Wringe et al, 2010; Laghari et al, 2013). As feed cost comprises about 65–75% of the total production cost in most aquaculture industries, an effective way to solve this problem is to breed fish with high feed conversion efficiency (FCE) (Gjedrem and Baranski, 2009). Feed conversion efficiency is defined as the ratio of feed intake to weight gain in animals (Sherman et al, 2009; Ferreira et al, 2016). The aim of improvement in FCE could be achieved by breeding to select genetically superior animals
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