Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families. We completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection. A large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs affecting body growth. Discovery of these common QTLs between families and growth-related traits represents an important step towards understanding of quantitative genetic variation in common carp.

The differentiation of skeletal muscle-derived satellite cells (MDSCs) is important in controlling muscle growth, improving livestock muscle quality, and healing of muscle-related disease. MicroRNAs (miRNAs) are a class of gene expression regulatory factors, which play critical roles in the regulation of muscle cell differentiation. This study aimed to compare the expression profile of miRNAs in MDSC differentiation, and to investigate the miRNAs which are involved in MDSC differentiation. Total RNA was extracted from MDSCs at three different stages of differentiation (MDSC-P, MDSC-D1 and MDSC-D3, representing 0, 1 and 3 days after differentiation, respectively), and used to construct small RNA libraries for RNA sequencing (RNA-seq). The results showed that in total 617 miRNAs, including 53 novel miRNA candidates, were identified. There were 9 up-expressed, 165 down-expressed, and 15 up-expressed, 145 down-expressed in MDSC-D1 and MDSC-D3, respectively, compared to those in MDSC-P. Also, 17 up-expressed, 55 down-expressed miRNAs were observed in MDSC-D3 compared to those in MDSC-D1. All known miRNAs belong to 237 miRNA gene families. Furthermore, we observed some sequence variants and base edits of the miRNAs. GO and KEGG pathway analysis showed that the majority of target genes regulated by miRNAs were involved in cellular metabolism, pathways in cancer, actin cytoskeleton regulation and the MAPK signaling pathway. Regarding the 53 novel miRNAs, there were 7 up-expressed, 31 down-expressed, and 8 up-expressed, 26 down-expressed in MDSC-D1 and MDSC-D3, respectively, compared to those in MDSC-P. The expression levels of 12 selected miRNA genes detected by RT-qPCR were consistent with those generated by deep sequencing. This study confirmed the authenticity of 564 known miRNAs and identified 53 novel miRNAs which were involved in MDSC differentiation. The identification of novel miRNAs has significantly expanded the repertoire of bovine miRNAs and could contribute to advances in understanding muscle development in cattle.