The aim of this PhD thesis was the study of the genomic, biological and phenotypic background of bovine cheese-related traits. The primary goal of this PhD thesis was to unravel the genomic background of bovine milk technological and cheese-related traits to specific chromosomic regions (CHAPTERS 1 to 3). To achieve this, the cow’s ability to produce cheese was decomposed into 11 milk coagulation (MCP) and curd-firming properties (CFt), and 7 cheese yield and milk component recoveries into the curd (REC) traits. Besides, to tackle the problem of the large number of variables required to describe the cow’s ability to produce cheese, posing restrictions in the construction of selection indices, and thereby selection decisions, factor analysis (FA) was used (CHAPTERS 4 and 5).
The MCP traits were: 3 traditional single point lacto-dynamographic properties (RCT: rennet coagulation time, min; k20: time to a curd firmness (CF) of 20 mm, min; a30: CF 30 min after rennet addition), 6 parameters modeling 360 CF data for each milk sample (CFP: potential asymptotic CF at infinite time, mm; kCF: curd firming instant rate constant, %×min-1; kSR: syneresis instant rate constant, %×min-1; RCTeq: RCT from modeling; CFmax: maximum CF, mm; tmax: time at CFmax, min), milk- protein (%) and pH. The 3 CY traits were the weight (wt) of fresh curd (%CYCURD), curd solids (%CYSOLIDS), and curd moisture (%CYWATER) as % of wt of milk processed. The 4 REC (RECFAT, RECPROTEIN, RECSOLIDS, and RECENERGY) were calculated as the % ratio between the nutrient in curd and the corresponding nutrient in processed milk. For FA 26 traits related to milk yield and quality (including milk protein fractions), MCP-CFt and CY-REC traits were analyzed.
Single marker genome-wide association analyses (GWAS) complemented by gene-set enrichment and pathway-based analyses were conducted. In total, 1,152 Italian Brown Swiss cows reared in 85 herds were genotyped with the Illumina SNP50 Beadchip v.2. Single marker regression GWAS were fitted using the GenABEL R package (GRAMMAR-GC). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases were queried for the enrichment analyses.
In GWAS (CHAPTERS 1 and 2), sharp peaks were detected on Bos taurus autosome (BTA) 6, at 84 to 88 Mbp, with the highest peak detected at 87.4 Mbp in the region harboring the casein genes and more precisely of κ-CN (CSN3). Marker Hapmap52348-rs29024684 (~87.4 Mbp), closely located to the casein genes on BTA6, was strongly associated with RECFAT (P = 1.91×10-15) and CFP (P = 1.62×10-17). Evidence of quantitative trait loci at 82.6 and 88.4 Mbp on the same chromosome was found. On BTA11, marker ARS-BFGL-NGS-104610 (~104.3 Mbp) was highly associated with RECPROTEIN (P = 6.07×10-36). Apart from BTA6 and 11, SNP located in 15 more chromosomes (1, 2, 9, 12, 13, 14, 15, 16, 18, 19, 20, 23, 26, 27 and 28) were significantly associated to the MCP-CFt and CY-REC traits.
The gene-set enrichment and pathway-based analysis (CHAPTER 3) revealed 21 GO and 17 KEGG categories significantly associated (false discovery rate controlled at 5%) with 7 of the traits (RCT, RCTeq, kCF, %CYSOLIDS, RECFAT, RECSOLIDS and RECENERGY), with some being in common between traits. The significantly enriched categories included calcium signaling pathway, salivary secretion, metabolic pathways, carbohydrate digestion and absorption, the tight junction and the phosphatidylinositol pathways, as well as pathways related to the bovine mammary gland health status, and contained a total of 150 genes located in all chromosomes but 9, 20, and 27.
In FA (CHAPTERS 4 and 5), ten mutual orthogonal Fs were obtained using a varimax rotation. The 10 Fs explaining 74% of the original variability. Those Fs captured basic concepts of the “milk to cheese” process. More precisely, the first four Fs, sorted by variance explained, were able to capture the underlying structure of the CY percentage (F1%CY), the CF process with time (F2CFt), the milk and solids yield (F3Yield) and the presence of nitrogen (N) into the cheese (F4Cheese N). Moreover, 4 Fs (F5 αs1-β-CN, F7β-κ-CN, F8αs2-CN, F9αs1-CN-P) were related to the basic milk caseins (as1-CN, as2-CN, β-CN, κ-CN, and the phosphorylated form of as1-CN) and 1 factor was associated with the α-LA whey protein (F10α-LA). A factor describing the udder health status of a cow (F6Udder health), mainly loaded on lactose, other nitrogen compounds and SCS, was also obtained.
In general, FA results were coherent to the given name of the factor. Stage of lactation had a significant effect for the majority of the Fs, followed by parity. Moreover, considerable genetic correlations existed among the Fs (CHAPTER 4). All Fs showed significant associations (P < 5 ×10-5) in GWAS, but F5Yield. High peaks on BTA6 (~87Mbp) and at the tail of BTA11 (~104Mbp) were mainly associated to F6β-κ-CN and F1Cheese N, respectively. In addition, 33 GO terms and 6 KEGG categories were mainly enriched for F8αs2-CN, but also for F1%CY, F4Cheese N, and F10α-LA. Biological pathways were mainly related to the broader categories of ion activity, neurons and the tight junction. Moreover, the considerably large number of enriched GO and KEGG terms for F8αs2-CN suggests that, perhaps, more focus should be given on αs2-CN (CHAPTER 5)
