The domestication of animals is a process of great interest to many scientific fields, including genetics. Differences in coat colour between wild and domesticated animals have been of scientific interest for a long time. Coat colours are easily recognizable phenotypes and so have been studied since the dawn of modern genetics. Many phenotypes that are similar across species have the same genetic basis, but there are numerous exceptions. Similar phenotypes within a species can also have different genetic backgrounds. The progressive advances in genetic research methodology have given new insights into both the molecular basis for coat colours and the history of domestication over the last decades. The variation in coat colours seen today is believed to be caused mainly by human selection. Similarities in morphological changes between different species during domestication, including colour phenotypes such as white spotting, have long been noted. This is known as the domestication syndrome and two major hypotheses for this have been suggested: the neural crest hypothesis and the thyroid hormone hypothesis. This thesis gives an overview of the current knowledge about the genetic basis of coat colours in mammals, the genetic aspects of domestication of animals, and how the two are related.

Three interrelated genes postulated to affect economically important traits related to growth and/or carcass quality of beef cattle were chosen to characterize and perform association analyses for this study. Melanocortin 1 receptor (MC1R), melanocortin 4 receptor (MC4R) and agouti related protein (AGRP) play an integral role in the appetite pathway and in fat deposition.<p> We genotyped 328 crossbred steers of various coat colours that were purchased at weaning and fed until slaughter for the previously published alleles ED, E+ and e. The E+ allele was present at five percent in this population and therefore was not included in further analysis. Black cattle of ED/ED or ED/e genotype had increased backfat (P<0.05) and required significantly fewer days (15-25) (P<0.01) on feed to reach a target fat level for slaughter compared to the red cattle. Red cattle of e/e genotype were found to have significantly larger longissimus dorsi (l. dorsi) area, shipping weight and hot carcass weight. Subsequent analysis revealed that the differences were comparable whether black versus red coat colour or MC1R genotype was used as the criteria for the group of cattle.<p> MC4R sequence was obtained from 20 random crossbred steers. In addition to several previously published polymorphisms, a novel Ser330Asn polymorphism was detected. A population of 382 crossbred Canadian steers and 985 crossbred American steers was genotyped for this Ser330Asn polymorphism. A minor allele frequency of 0.01 was observed in the Canadian and 0.02 in the American steer populations. No homozygous g.989AA cattle were detected. In the Canadian population, heterozygous steers had increased grade fat (P=0.036) and decreased lean meat yield (P=0.032). Similarly in the American population, steers of the g.989GA genotype had increased backfat (P=0.031) and less desirable yield grades (P=0.022,) but also lower ribeye area measurements (P=0.031). These results suggest that genotyping for the Ser330Asn polymorphism may lead to increased quality of carcasses either through lean meat production or backfat measurements, depending on the goal of the beef operation.<p> Sequence data obtained from 38 Bos taurus beef cattle, 4 Holsteins and 4 Bos indicus cattle revealed six polymorphisms in the AGRP gene. No polymorphisms that altered amino acids were detected in Bos taurus cattle. Genotyping of 382 crossbred beef steers was performed for two polymorphisms, an intronic deletion (g.439_440delTC) and a base pair substitution in exon 4 that did not alter an amino acid (g.715G>A). An ANOVA analysis, using PROC Mixed, was performed for both polymorphisms on several growth and carcass traits. No significant differences were observed.<p> Polymorphisms in MC1R and MC4R could be used as genetic tests which may be beneficial for beef producers in North America. The significant differences observed in this study in relation to cattle growth and fat deposition would represent savings for producers when used for sorting feedlot cattle or in selection of breeding cattle.

Three interrelated genes postulated to affect economically important traits related to growth and/or carcass quality of beef cattle were chosen to characterize and perform association analyses for this study. Melanocortin 1 receptor (MC1R), melanocortin 4 receptor (MC4R) and agouti related protein (AGRP) play an integral role in the appetite pathway and in fat deposition.<p> We genotyped 328 crossbred steers of various coat colours that were purchased at weaning and fed until slaughter for the previously published alleles ED, E+ and e. The E+ allele was present at five percent in this population and therefore was not included in further analysis. Black cattle of ED/ED or ED/e genotype had increased backfat (P<0.05) and required significantly fewer days (15-25) (P<0.01) on feed to reach a target fat level for slaughter compared to the red cattle. Red cattle of e/e genotype were found to have significantly larger longissimus dorsi (l. dorsi) area, shipping weight and hot carcass weight. Subsequent analysis revealed that the differences were comparable whether black versus red coat colour or MC1R genotype was used as the criteria for the group of cattle.<p> MC4R sequence was obtained from 20 random crossbred steers. In addition to several previously published polymorphisms, a novel Ser330Asn polymorphism was detected. A population of 382 crossbred Canadian steers and 985 crossbred American steers was genotyped for this Ser330Asn polymorphism. A minor allele frequency of 0.01 was observed in the Canadian and 0.02 in the American steer populations. No homozygous g.989AA cattle were detected. In the Canadian population, heterozygous steers had increased grade fat (P=0.036) and decreased lean meat yield (P=0.032). Similarly in the American population, steers of the g.989GA genotype had increased backfat (P=0.031) and less desirable yield grades (P=0.022,) but also lower ribeye area measurements (P=0.031). These results suggest that genotyping for the Ser330Asn polymorphism may lead to increased quality of carcasses either through lean meat production or backfat measurements, depending on the goal of the beef operation.<p> Sequence data obtained from 38 Bos taurus beef cattle, 4 Holsteins and 4 Bos indicus cattle revealed six polymorphisms in the AGRP gene. No polymorphisms that altered amino acids were detected in Bos taurus cattle. Genotyping of 382 crossbred beef steers was performed for two polymorphisms, an intronic deletion (g.439_440delTC) and a base pair substitution in exon 4 that did not alter an amino acid (g.715G>A). An ANOVA analysis, using PROC Mixed, was performed for both polymorphisms on several growth and carcass traits. No significant differences were observed.<p> Polymorphisms in MC1R and MC4R could be used as genetic tests which may be beneficial for beef producers in North America. The significant differences observed in this study in relation to cattle growth and fat deposition would represent savings for producers when used for sorting feedlot cattle or in selection of breeding cattle.

Thesis(M.Sc. (Animal Production)) -- University of Limpopo, 2022 / Donkeys continue to play a significant role in draught power activities for both rural and urban regions in underdeveloped countries, where they are commonly employed for transportation of goods and movement of people at extremely low prices. The study sought to determine donkey farmers' breeding practices as well as donkey morphological characterization in three villages such as Thorp, Archibalt and Genau of the Blouberg Local Municipality. A total of 21 donkey farmers and 74 donkeys were used to collect data. The following Morphological traits characterized were; Head length (HL), Ear length (EL), Neck length (NL), Chest width (CW), Back length (Bal), Body length (BoL), Hips width (HW), Umbilical circumference (UC), Back height (BH), Height at the rump (HR), Thoracic circumference (TC), Chest depth (CD), Withers Height (WH), Front leg length (FLL), Cannon circumference (CC), Cannon length (CL), Cannon height (CH) and Body weight (BW). Descriptive statistics, Chi-square tests, Analysis of variance (ANOVA), Pearson correlation, and Rank Index were used for data analysis. Education level of the farmers in the three villages was significantly different (p<0.05) with the majority of farmers having secondary education. There was no significant difference (p>0.05) amongst the villages on different reasons behind keeping donkeys. The results showed a significant difference (p<0.05) in inbreeding knowledge by the farmers amongst the three villages. The selection criteria used across the three villages were not significantly different (p>0.05). Rank and Indices in selection of male donkeys looked at body size (0.39), growth rate (0.19), Draught power performance (0.14), and for overall preference in female donkeys it was body size (0.26), twinning ability (0.23) and mothering ability (0.15). Body size and growth rate where the most important traits to donkey farmers. The coat colours were not significantly different (p>0.05). In all the eighteen measured traits, only four (BaL, HW, BH and FLL) showed a significant difference (p<0.05) among the three villages. BW in male donkeys was not significantly correlated (p>0.05) with HL, EL, NL, BaL, HW, FLL, CC, CH, CL but was positively correlated (p<0.05) with BoL (r = 0.34), UC (r = 0.35), TC (r = 0.33), CD (r = 0.31), CW (0.94), BH (r = 0.41), HR (0.60), and WH (r = 0.58). BW in female donkeys was not significantly correlated (p>0.05) with NL, BaL, TC, and CL but positively significant correlated (p<0.05) with HL, EL, BoL, HW, UC, FLL and CC CW, BH, HR, WH and CH with correlation coefficient values ranging from 0.34 to 0.75. The farmers had no breeding program in place the donkeys were allowed to mate on their own without designed breeding program. Selection of donkeys to be part of the heard was based on physical attributes, such length It was concluded that donkey farmers in Genau, Archibalt, and Thorp villages engaged in breeding practices that could be valuable in construction of a community-based breeding program.