Abstract
QTL is a chromosomal region including single gene or gene clusters that determine a quantitative trait. While feed efficiency is highly important in aquaculture fish, little genetic and genomic progresses have been made for this trait. In this study, we constructed a high-resolution genetic linkage map in a full-sib F1 family of crucian carp (Carassius auratus) consisting of 113 progenies with 8,460 SNP markers assigning onto 50 linkage groups (LGs). This genetic map spanned 4,047.824 cM (0.478 cM/marker) and covered 98.76% of the crucian carp genome. 35 chromosome-wide QTL affecting feed conversion efficiency (FCE, 8 QTL), relative growth rate (RGR, 9 QTL), average daily gain (ADG, 13 QTL) and average daily feed intake (ADFI, 5 QTL) were detected on 14 LGs, explaining 14.0–20.9% of the phenotypic variations. In LGs of LG16, LG25, LG36 and LG49, several QTL affecting different traits clustered together at the identical or close regions of the same linkage group. Seven candidate genes, whose biological functions may involve in the energy metabolism, digestion, biosynthesis and signal transduction, were identified from these QTL intervals by comparative genomics analysis. These results provide a basis for elucidating genetic mechanism of feed efficiency and potential marker-assisted selection in crucian carp.
Highlights
Feed efficiency is economically important trait to animal producers because feed represents the major input in production, and the relevant discharge pollution is a major concern[1]
Genetic linkage maps are essential for quantitative trait loci (QTL) mapping for marker-assisted selection (MAS)[49], and this is mainly due to the fact that high-resolution genetic linkage is one of the best tools for fine Quantitative trait loci (QTL) mapping[50]
We constructed a high-density linkage map containing 8,460 SNP markers grouped into 50 linkage groups (LGs) (Supplementary Table S1, Fig. 2) using 2b-RAD technology, which is in agreement with the haploid chromosome number of crucian carp[51]
Summary
Feed efficiency is economically important trait to animal producers because feed represents the major input in production, and the relevant discharge pollution is a major concern[1]. Feed efficiency is such a major trait and hard to be improved by those traditional methods such as inbreeding, selection, crossbreeding and hybridization when involving in production. The purpose of improvement in feed efficiency could be achieved by selecting animals that are genetically superior. Progresses to identify genetic markers involved in feed efficiency have been made especially in livestock, which focused on cattle and pigs by genome association studies[31,32] and QTL mapping using microsatellite[33] or SNP markers[34]. It is obviously that improvements for the efficiency of feed utilization would lead to increasing the producer’s profitability in aquaculture, genetic studies on feed efficiency have received less attention than other economic traits in fish production system because of the difficulties in obtaining phenotype data. Due to financial returns strongly influenced by feed efficiency, this trait needs further attention and studies in more aquaculture species[39]
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