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Mastitis, the inflammation of the mammary gland caused by both gram-positive and gram-negative bacteria, causes the global dairy industry over $20 billion annually in losses due to changes in milk yield and quality. The goals of this research were to 1) identify genetic variants, genes, and biological pathways that are associated with mastitis, and 2) identify genetic variants, genes, and biological pathways that are associated with somatic cell count. In Chapter 3, we describe genome-wide association studies (GWAS) on 1,858 cows from two lactations with both medium (n=87,493) and high density (n=624,300) single nucleotide polymorphisms (SNP) using a single SNP mixed linear model. A total of 289 SNPs across all models reached genome-wide significance at 5% false discovery rate (FDR) and were mapped to 100 different nearby genes which have been identified in previous studies and are quantitative trait loci for somatic cell count. Significant SNPs and genes were mapped to the bovine genome to reveal corresponding genes to allow gene enrichment analysis to identify significant biological pathways associated with mastitis. In Chapter 4, we describe genetic associations affecting lactation average somatic cell count using 624,300 single nucleotide polymorphisms (SNP) on performed on 364 Holstein and Jersey cows in their first lactation. A total of 205 SNPs reached genome-wide significance at 5% FDR and were mapped to 68 unique genes.

Thesis (MscAgric (Animal Sciences))--University of Stellenbosch, 2006. / Six non-lactating, ruminally cannulated Holstein cows were used in a three part study to determine the effect of biotin supplementation to dairy cows on forage fermentation characteristics. Cows were randomly assigned to two groups in a 2 x 3 change-over experiment. All cows received oat hay ad libitum and one of two concentrate feeds, fed twice daily at 2 kg per feeding as a top dressing. The concentrates were identical in composition, except for a premix that was included to provide either 0 or 40 mg supplemental biotin/cow per day when the concentrate was fed at a rate of 4 kg/cow. Cows received the respective treatments for 28 days before being changed over to the other treatment. All cows therefore received both treatments. The first 21 days in each period were used for adaptation, while the last 7 days of the period were used for an in sacco trial, as well as for the collection of rumen liquor for two in vitro studies. The in vitro studies were a gas production trial and an in vitro digestibility trial. Forages differing in neutral detergent fibre (NDF) content were used as substrates in the study. Lucerne hay (440 g NDF/kg DM), oat hay (680 g NDF/kg DM), and wheat straw (798 g NDF/kg DM) were chosen to represent high, medium and low quality forages. In the gas production study, samples (0.5 g) of the three forages were incubated at 39ºC in buffered rumen liquor (obtained from cows in the different treatments) in glass vials. Pressure readings were taken after 12, 18, 24, 30 and 48 hours incubation using a digital pressure gauge fitted with a 21 gauge needle. Pressure readings were converted to gas volumes with the aid of a predetermined regression equation. In the in vitro digestibility trial, forage samples (0.25 g) were weighed into Ankom F57 filter bags and incubated at 39ºC in an Ankom Daisy II incubator in buffered rumen liquor. Three bags of each substrate were removed from the incubation jars after 18, 24 and 30 h incubation. Bag residues were analyzed for dry matter, organic matter and NDF. In the in sacco degradability trial, forage samples (5 g) were weighed into 100 x 200 mm Ankom Forage Bags and inserted into the rumina of the respective cow simultaneously. One bag per substrate was removed from each cow at after 4, 8, 18, 24, 30 and 48 h incubation, while two bags per substrate were removed after 72 and 96 h to ensure enough residue for subsequent chemical analysis. Samples of rumen liquor were taken at each of the mentioned incubation times for VFA analysis, while rumen pH was also measured at these times. All the data collected were subjected to a one-way ANOVA, least square means were determined and significance was declared at P<0.05. Biotin supplementation increased the rate of gas production (0-12 h) of all three substrates, as well as cumulative gas production at 48 h. No treatment effects were observed in the in vitro digestion study. Biotin supplementation increased the rate of in sacco NDF disappearance and calculated effective NDF degradability in oat hay and wheat straw, but not in lucerne hay. The rumen pH curve appeared higher for the biotin treatment than for the control and the value at the 72 h sampling time was significantly higher for the biotin treatment than for the control treatment (6.13 vs 5.94). Rumen pH tended to be higher (P<0.10) at 18 h (6.44 vs 6.23), 48 h (6.13 vs 6.00) and 96 h (6.14 vs 6.04). There was also a tendency (P<0.10) for the mean pH over the total 96 h period to be higher for the biotin treatment than for the control (6.09 vs 5.97), while the maximum and minimum pH values did not differ between treatments. Molar proportions of volatile fatty acids did not differ between treatments and the acetic acid proportion was relatively high (acetic:propionic = 74:15), which was probably because the cows were not on a very high concentrate diet. It was concluded that biotin supplementation to dairy cows may improve fermentation rates and NDF digestibility of certain forages.