Fig. 5

Differential regulation of TNNC1 expression may result in differences in meat quality between eastern and western pigs. a Genome browser view of the differential ATAC-seq peak near the TNNC1 promoter. b Haplotypes of the TNNC1 gene body and enhancer across all eastern and western pigs. c Characteristics of the skeletal muscle in Luchuan and Duroc pigs. In the sub-panel of fiber density, structural differences in skeletal muscle are revealed by the environmental scanning electron microscope. In the sub-panel of capillary density, scanning electron microscope images of the muscle fiber bundle in Luchuan and Duroc pigs show the orientation and tortuosity of branching vessels at different hierarchies. In the sub-panel of ATPase staining, black arrows exemplify the slow muscle fibers which are lightly stained due to lower ATPase activity, while red arrows exemplify the fast muscle fibers which are heavily stained due to higher ATPase activity, magnification of ×40. d Expression of slow muscle (Myh7) and fast muscle (Myh2, Myh4, and Myh1) markers after siRNA knockdown of Tnnc1 in C2C12 cells. e Measuring the same markers as d after overexpression of Tnnc1 in C2C12 cells. f ATPase staining of mice skeletal muscle two weeks after in vivo injection of AAV-mediated non-target control (NT siRNA) and Tnnc1 siRNA, respectively. g Barplots comparing the intensity of ATPase staining for samples under the same treatment as in f. h Comparing the expression level of Tnnc1 before and after Cebpa knockdown in C2C12 cells. i A model of potential selection on a regulatory mutation in one enhancer of the TNNC1 gene in the Luchuan pig. The Luchuan allele generates a stronger CEBPA transcription factor binding motif, which increases the expression of TNNC1, resulting in a higher proportion of slow-twitch muscle and meat quality improvement, including better color appearance, higher water-holding capacity, tenderness, and marbling (See Discussion for more details). The regulatory allele might be further favored during selection by a higher expression of CEBPA in the Luchuan breed. The sequence divergence between the Luchuan and Duroc breeds is shaded in light yellow