Heritability and quantitative trait locus analyses of intermuscular bones in mirror carp (Cyprinus carpio)

Abstract

Common carp (Cyprinus carpio) is one of the major aquaculture species in the world and accounts for approximately 8% of the total aquaculture production. The presence of intermuscular bones (IMBs) dramatically affects the economic value of this fish in the market. To understand the genetic variation in IMBs in common carp, in this study, we estimated the heritability and carried out quantitative trait locus (QTL) mapping of IMBs in mirror carp. We used 30 full-sib families including 871 individuals to calculate the heritability and genetic correlation and found that the heritability of the total IMB count, Y-shaped (YS) IMB count and I-shaped (IS) IMB count were moderate and significant (P < 0.001), and the values were 0.15 ± 0.08, 0.44 ± 0.12 and 0.23 ± 0.08, respectively. The phenotypic correlation among these three traits was significant, while only the genetic correlation between the IMB count and YS IMB count was significant. QTL mapping was performed with 8 families including 522 individuals, and 8 QTLs were discovered for IMBs, YS IMBs and IS IMBs, including one QTL for IMBs that explained 16.20% of the phenotypic variance, 4 QTLs for YS IMBs that explained 56.26% of the phenotypic variance, and 3 QTLs for IS IMBs that explained 38.24% of the phenotypic variance. Within the QTL regions, 29 genes with functions such as osteogenesis; osteoblast, osteoclast and chondrocyte development and differentiation; and fin or limb development were identified as candidate genes for IMB development. These results provide insight into the genetic mechanism underlying IMB development in common carp.