Unravelling genes associated with coat colour and coat colour patterns in indigenous South African meat-type goats.

Abstract

Small ruminants such as goats are a vital part of the economy, especially that of farmers in rural communities, where people have successfully bred these animals for sustenance despite the limiting conditions found in extensive production systems which offer little protection from harsh environmental conditions and limited feed. South African meattype ecotypes, which are primarily found in communal production systems have managed to strive under such adverse conditions due to their high genetic diversity and adaptability to a wide range of environments. Due to these characteristics, the ecotypes are economically important as a livestock species because they hold high production potential, especially in the face of drastically changing environmental conditions caused by global warming and an increase in meat demand due to the rising human population. However, the lack of both information about proper breeding strategies, and investment capital within communal goat production systems inhibits the adoption of modern technologies, necessary to implement improved breeding schemes that utilise genetic, and phenotypic information to employ genomic selection. Thus, it is necessary to generate low-cost and easy-adoption selection technologies according to low-input communal production system requirements. A key step towards this goal is the description of the genetic composition of village goat populations. This genetic description involves the study of the genes that influence goat production traits. The detection of genes responsible for economical traits such as coat colour can help open opportunities towards implementing improved selection schemes with improved selection accuracy and intensity allowing for the early selection of reproducers within communal goat production systems. This study used 51 767 SNPs from 329 indigenous goats with various coat colour and coat colour patterns to investigate genes responsible for goat coat colour. Case/control GWASs carried out for all the coat colours/patterns using the GAPIT revealed several genes associated with various coat colours including white (CDK5), red (CELF5, TLE6), black (CACNA2D1), grey (GSK3B), and coat colour patterns such as white-body red head (CADPS2, SLC13A1), speckled (KIT, TYRP1), patchy (GNAI3), belted (TYRP1), whitesided (AHCY), and blacklegged (AHCY). Golden Helix SVS’s univariate method from the copy number analysis module (CNAM) detected 2 047 CNVs and 279 CNVRs overlapping 5 222 genes involved in several biological processes, molecular functions, cellular components, and pathways. Several coat colour genes overlapping these CNVRs included GSK3B, Notch1, Notch2, CDK5, ADAMTS20, TYRO3, MAP2K1, ITCH, ASIP, AHCY, SLC45A3, EDNRA, ADCY2, and TYR. Candidate coat colour genes were found to be under selection within (iHS) and between (XP-EHH) the goats. These genes were involved in melanogenesis pathways such as the MAPK signalling pathway (DUSP16, KDR, FGF10, MAP3K7), the PI3K-Akt pathway (CDKN1B, COL6A3, CRK, CREB5), the Wnt signalling pathway (SERPINF1, WNT2), the Notch signalling pathway (HEY2), and Melanogenesis (TYRP1). In addition, genes associated with various traits such as metabolism (FXN, FTO, IRX3, EDNRA), reproduction (PGR), growth and development (SMARCAD1), immune response (ACAD8, DLG4, GPS2), and environmental adaptation (CNR1) were detected, suggesting a possible link between coat colour and goat productivity. This study’s findings were in line with previous studies which have revealed that coat colour is a polygenic trait whose variation is influenced by the epistatic effects of multiple genes involved in various regulatory pathways that affect melanogenesis. Coat colour is a key factor driving the economic efficacy of indigenous goats. Therefore, knowledge of its genetic mechanisms is vital as it will allow farmers to utilize breeds with specific environmental adaptations in selection strategies for genetic improvement.