Mapping quantitative trait loci and identifying candidate genes affecting feed conversion ratio based onto two linkage maps in common carp (Cyprinus carpio L)

Abstract Feed efficiency is an economically important trait in aquaculture, which can be measured traditionally as feed conversion ratio (FCR). Because of the difficult measurement, genome-wide selection using quantitative trait loci (QTLs) affecting FCR may be an alternative for genetic improvement. In the present investigation, QTLs for FCR based on two mapping panels (mirror carp and hybrid carp panels) were found in common carp ( Cyprinus carpio L.). After that, candidate genes were identified by comparative genomics. A total of nine QTLs, two genome-wide and seven linkage group-wide, were detected in eight linkage groups (LGs) in the mirror carp panel (FAM-A, n = 68) and nine QTLs, four genome-wide and five linkage group-wide, were detected on eight linkage groups of the hybrid carp panel (FAM-B, n = 92). Two genome-wide QTLs affecting FCR were identified in two LGs (Lg1 and Lg21) in FAM-A, which explained 32.3% and 35.6% of the phenotypic variation respectively; four genome-wide QTLs affecting FCR were detected in four LGs (LG5, LG21, LG24, and LG33) in FAM-B which explained 29.3%–33.4% of the phenotypic variation. All of eight QTL regions from FAM-A were aligned to the high-resolution linkage map with whole genomic scaffold and all genes mapped on, and 18 genes associated with growth or metabolic function were identified using the whole-genomic browser on http://www.carpbase.org/gbrowse.php . We believe that these 18 genes are valuable candidate genes affecting feed efficiency, that might be used in MAS programs to improve performance in common carp. Statement of relevance All animal experiments was carried out in accordance with the National Institutes of Health guide for the care and use of Laboratory animals (NIH Publications No. 8023, revised 1978) and it is hereby clearly indicated that such guidelines had been followed.