A Candidate Gene Association Study for Economically Important Traits in Czech Dairy Goat Breeds

Milk production is influenced by many factors, including genetic and environmental factors and their interactions. Animal health, especially udder health, is usually evaluated by the number of somatic cells. The present study described the effect of polymorphisms in the ACACA, BTN1A1, LPL, and SCD genes on the daily milk yield, fat, and protein percentages and somatic cell count. In this study, 590 White Shorthaired (WSH) and Brown Shorthaired (BSH) goats were included. SNP genotyping was performed by PCR-RFLP and multiplex PCR followed by SNaPshot minisequencing analysis. The linear mixed model with repeated measurement was used to identify the genetic associations between the studied genes/SNPs and chosen traits. All selected genes were polymorphic in the tested goat populations and showed significant associations with milk traits. Only BTN1A1 (SNP g.599 A > G) showed a significant association with the somatic cell score. After Bonferroni correction, a significant effect of LPL g.300G > A on daily milk yield and fat percentage, LPL g.185G > T on protein percentage, and LPL G50C, SCD EX3_15G > A, and SCD EX3_68A > G on fat percentage was found. The importance of environmental factors, such as the herd-year effect, month of milking, and lactation order on all milk performance indicators was confirmed.

Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle

Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq in Longissimus thoracis muscle of 194 Nelore steers for association with three meat quality traits (intramuscular fat, meat pH, and tenderness) and the concentration of 13 minerals (Ca, Cr, Co, Cu, Fe, K, Mg, Mn, Na, P, S, Se, and Zn). We identified seven sets of co-expressed genes (modules) associated with at least two traits, which indicates that common pathways influence these traits. From pathway analysis of module hub genes, we further found an over-representation for energy and protein metabolism (AMPK and mTOR signaling pathways) in addition to muscle growth, and protein turnover pathways. Among the identified hub genes FASN, ELOV5, and PDE3B are involved with lipid metabolism and were affected by previously identified eQTLs associated to fat deposition. The reported hub genes and over-represented pathways provide evidence of interplay among gene expression, mineral concentration, and meat quality traits. Future studies investigating the effect of different levels of mineral supplementation in the gene expression and meat quality traits could help us to elucidate the regulatory mechanism by which the genes/pathways are affected.