The study evaluated genetic progress of a breeding program for common carp undergoing four generations of selection for increased harvest body weight from 2004 to 2014. The pedigree included 17,351 individual fish which were offspring of 342 sires and 352 dams. Genetic parameters for body weight at about two years of age and survival rate during grow-out period were also estimated using the residual maximum likelihood method applied to a two-trait linear mixed model. Direct response in body weight and correlated changes in survival were measured as the differences in: i) estimated breeding values (EBVs) between the two lines; and ii) EBVs of the selection line between successive generations. Direct gain in body weight ranged from 0.20 to 0.90 genetic standard deviation units and averaged 7 % of the base population per generation (two years per generation). Correlated changes in survival were negligible, indicating that the selection program for high growth did not have any adverse effect on this trait in the present population. The heritability for body weight was moderate (0.17, s.e. 0.05), whereas the estimate for survival was low (0.05–0.17) but significantly different from zero across linear mixed and threshold generalised statistical models. Our results predict that body weight or/and other growth related traits will continue to respond to selection and that there is potential to improve survival through direct genetic means. Correlated improvement in survival to selection for increased body weight was hardly achieved, as the genetic correlation between the two traits was not different from zero. It is concluded that selection for increased harvest body weight resulted in significant improvement in growth performance of the present population of common carp Cyprinus carpio.

Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish skin color is limited. Herein, Illumina sequencing and bioinformatics were conducted on black, white, and red skin of Koi carp (Cyprinus carpio L.). A total of 590,415,050 clean reads, 446,614 putative transcripts, 4252 known and 72,907 novel lncRNAs were simultaneously obtained, including 92 significant differentially expressed lncRNAs and 722 mRNAs. Ccr_lnc5622441 and Ccr_lnc765201 were up-regulated in black and red skin, Ccr_lnc14074601 and Ccr_lnc2382951 were up-regulated in white skin, and premelanosome protein a (Pmela), Pmelb and tyrosinase (Tyr) were up-regulated in black skin. The expression patterns of 18 randomly selected differentially expressed genes were validated using the quantitative real-time PCR method. Moreover, 70 lncRNAs acting on 107 target mRNAs in cis and 79 lncRNAs acting on 41,625 target mRNAs in trans were investigated. The resulting co-expression networks revealed that a single lncRNA can connect with numerous mRNAs, and vice versa. To further reveal their potential functions, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, and membrane, pigment cell development, cAMP signaling, melanogenesis and tyrosine metabolism appear to affect skin pigmentation. Additionally, three lncRNAs (Ccr_lnc142711, Ccr_lnc17214525 and Ccr_lnc14830101) and three mRNAs (Asip, Mitf and Tyr) involved in the melanogenesis pathway were investigated in terms of potential functions in embryogenesis and different tissues. The findings broaden our understanding of lncRNAs and skin color genetics, and provide new insight into the mechanisms underlying lncRNA-mediated pigmentation and differentiation in Koi carp.

Differentiation and variation in body color has been a growing limitation to the commercial value of red tilapia. Limited microRNA (miRNA) information is available on skin color differentiation and variation in fish so far. In this study, a high-throughput Illumina sequencing of sRNAs was conducted on three color varieties of red tilapia and 81,394,491 raw reads were generated. A total of 158 differentially expressed miRNAs (|log₂(fold change)| ≥ 1 and q-value ≤ 0.001) were identified. Target prediction and functional analysis of color-related miRNAs showed that a variety of putative target genes—including slc7a11, mc1r and asip—played potential roles in pigmentation. Moreover; the miRNA-mRNA regulatory network was illustrated to elucidate the pigmentation differentiation, in which miR-138-5p and miR-722 were predicted to play important roles in regulating the pigmentation process. These results advance our understanding of the molecular mechanisms of skin pigmentation differentiation in red tilapia.