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Near Infrared spectroscopy (NIRS) offers an easy to use and cost-effective tool for quantitative and qualitative application in animal science. Of special interest could be considered the use of NIRS for tracing meat origin on the basis of breed specification. The aim of this study was to investigate the potential use of meat NIRS as a “fingerprint” of autochthonous pig breeds. The research considered intact and grounded sample of Longissimus Dorsi (n=371) collected from 11 European local pig breeds from the TREASURE project, namely: Alentejana (ALE), Bisara (BIS), Crna Slawonska (CRN), Gascon (GAS), Iberian (IBE), Krskopolje (KRS), Lithuanian Wattle (LIA), Lithuanian White (LIH), Negre Mallorqui (NEG), Schwabish Hallisches (SCH) and Turopolje (TUR). For each muscle sample, two aliquots were scanned using FT-NIRS Antaris II model (Thermo Fisher Scientific) in absorbance mode considering the infrared region (3999 to 9999 cm-1) and averaged. Discriminant analysis of principal components (DAPC) on meat NIRS was used to assess: i) breed traceability and ii) similarity among breeds. DAPC was applied on standardised (centred and scaled) spectra using the R package. For breed traceability, cross- validation was applied: five samples per breed were sampled at random, without replacement, and used in validation. The procedure was repeated ten times and each breed was analysed separately. In this case, all breeds were present in the training set. Similarity among breeds was assessed by excluding each breed from the training set and assigning the samples in the validation set to the breeds in the training one. Overall correct classification was 68.0 and 77.6% for intact and grounded meat, respectively. Alentejana had 100% correct classification for both intact and grounded meat. For CRN, KRS, LIA, LIH and NEG use of grounded meat spectra resulted in higher classification rates from 44 to 64% for intact and from 66 to 90% for grounded meat), while for GAS the opposite was found (80% for intact vs. 70% for grounded). For the rest of the breeds slight or no differences were observed between intact and grounded samples and classification rates ranged between 66 (CRN and SCH) to 72% (BIS). The lowest classification rates were observed in both cases for CRN. Similarity among breeds was greatly varied upon dataset used (e.g. ALE samples were classified as IBE (40%), TUR (40%) and SCH (10%) using intact meat while 100% were classified as CRN using grounded meat). Our results mark NIRS as a promising tool for traceability of pig breed meat origin and support the use of grounded over intact samples.

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).

Transcriptomic and phenotypic changes in young bull liver caused by low-impact and nutraceutical diets. International Plant and Animal Genome (PAG)

13 Pág., Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products., This work has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 634476 for the project with acronym TREASURE. The content of this article reflects only the authors’ view and the European Union Agency is not responsible for any use that may be made of the information it contains. MŠ and MČP received core-financing by the Slovenian Research Agency (grant number P4-0133).

The aim of the study was to investigate the influence of breed and sex on carcass and meat quality traits of purebred Black Slavonian pigs and their crossbreds with Duroc. The study included 30 purebred Black Slavonian pigs and 30 crossbred pigs with Duroc (both experimental groups with equal number of gilts and barrows) reared under extensive keeping conditions. Feeding was based on cereal mixture (50% corn, 30% barley, 10% oats, 10% soybean) supplemented with alfalfa. During the winter period, pigs were fed alfalfa hay. When pigs reached a predetermined slaughter weight of approximately 130 kg, they were transported to the commercial abattoir and slaughtered after stunning with CO2 (90%). At the slaughter line following carcass traits were measured: carcass weight, carcass lengths, muscle and backfat thickness, surfaces of LD (longissimus dorsi) muscle and belonging backfat, as well as ham length and circumference. Meat quality traits measured included pH values and electric conductivity (at m. semimembranosus and LD muscle), meat colour (L*a*b*), cooking loss and instrumental tenderness. Crna slavonska purebreds had significantly higher backfat surface, as well as ham length and circumference. Breed did not influence other carcass traits. Purebred Black Slavonian pigs had higher pH45 values in LD muscle and pH24 values in SM muscle than crossbred pigs. Also, they exhibited lower L* values and higher a* values in SM than the crossbreds. However, the experimental groups did not differ in L* values measured in LD muscle, while crossbreds had higher a* values in the same muscle compared to purebred animals. Significant effect of sex was found for carcass length (both a and b), and ham length and circumference, where barrows exhibited higher values in all traits. The results of the study indicate that crossing the Black Slavonian pig with Duroc does not compromise meat quality of the crossbred animals, however, it does not improve its carcass traits when reared in the extensive system.