The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population’s structure and relationships.

Mutations in the porcine KIT gene (Dominant white locus) have been shown to affect coat colours and colour distribution in pigs. We analysed this gene in several pig breeds and populations (Sicilian black, completely black or with white patches; Cinta Senese; grey local population; Large White; Duroc; Hampshire; Pietrain; wild boar; Meishan) with different coat colours and patterns, genotyping a few polymorphisms. The 21 exons and parts of the intronic regions were sequenced in these pigs and 69 polymorphisms were identified. The grey-roan coat colour observed in a local grey population was completely associated with a 4-bp deletion of intron 18 in a single copy KIT gene, providing evidence that this mutation characterizes the I(d) allele described in the early genetic literature. The white patches observed in black Sicilian pigs were not completely associated with the presence of a duplicated KIT allele (I(p) ), suggesting that genetic heterogeneity is a possible cause of different coat colours in this breed. Selection signature was evident at the KIT gene in two different belted pig breeds, Hampshire and Cinta Senese. The same mutation(s) may cause the belted phenotype in these breeds that originated in the 18th-19th centuries from English pigs (Hampshire) and in Tuscany (Italy) in the 14th century (Cinta Senese). Phylogenetic relationships of 28 inferred KIT haplotypes indicated two clades: one of Asian origin that included Meishan and a few Sicilian black haplotypes and another of European origin.

This study evaluates the potential of Fourier transformation near-infrared reflectance spectroscopy to estimate the nutritional value and the chemical composition of natural pastures. Variability from all samples of pastures available is considered in order to assess the applicability of the calibration models in the future predictions. Chemical components (dry matter, crude protein, ash, ether extract, crude fibre, fibrous fractions) of grass samples were determined by applying official methods, and milk and meat forage units were calculated. Calibration and validation models were developed between chemical-nutritional parameters and NIRS spectral data using partial least square regression (PLS). The capacity of methods has been achieved using two validation approaches: the first using an independent dataset for prediction and the second by crossvalidation process. The results are evaluated in term of coefficient of determination, root-meansquare error and residual prediction deviation. Despite the wide variability of the data set, the results of FT-NIRS have been able to estimate the chemical composition of natural and naturalised pasture with good accuracy and precision, while for nutritional value parameters, a further evaluation may be useful.

The objective of this work was to evaluate, under indoors and outdoors rearing, the effect of crossing Cinta Senese (CS) with Italian Large White (ILW) and Italian Duroc (ID) breeds. Starting from 72 d of age, 9 CS, 8 ILWxCS and 7 IDxCS were reared outdoors (OUT) in 3 paddocks of 2 ha and 8 CS, 10 ILWxCS and 8 IDxCS pigs were reared indoors (IN) in three pens of 20 m 2 . All pigs, fed the same commercial diets, were weighed and measured periodically and were slaughtered at a target live weight of 150 kg. Indoor-pigs grew faster than the outdoor ones and crossbred pigs showed higher average daily gain than CS breed (476, 437 and 387 g/d for IDxCS, ILWxCS and CS, respectively). Rearing system had moderate or null effect on carcass and sample cut composition whereas the OUT pigs, when compared to IN ones, showed higher moisture and lower IMF in Longissimus L. and Psoas M. muscles and higher cooking loss of meat (22.1 vs 18.4 %) that resulted also less red (a* 10.94 vs 12.04). CS had more fat in carcass and more bone in sample cut than the crossbreeds. ILWxCS showed lower IMF content and higher moisture in muscles and brighter and less red meat than the other breeds, while IDxCS produced the most tender meat after cooking. The use of Italian Duroc could be profitable on Cinta Senese to improve the farming performance without worsening the fresh meat quality.

The aim of the present work was to estimate genetic variability in Chianina (CH), Marchigiana (MC) and Romagnola (RO) breeds using pedigree information. Different approaches based on probability of identity-by-descent (effective population size through an increase in inbreeding Ne) or probability of gene origin (total number of founders f, effective number of founders fe, ancestors fa and founder genomes fg) were used. Reference populations were defined using female animals born between 1996 and 2000 where both parents are known. Generation intervals were 5.35, 4.93 and 5.15 years for CH, MC and RO, respectively. The total number of founders were 7092, 11947, 3928, for CH, MC and RO, respectively. Complete generation equivalent showed the relative high quality of pedigree information: 5.66 for CH, 4.54 for MC and 4.95 for RO. For CH, MC and RO, respectively, a fe value of 152.1, 70.9 and 89.8, a fa value of 73.6, 48.0 and 59.5 and a fg value of 39.5, 25.0 and 38.5, were calculated. When inbreeding was used effective population sizes were 138, 122 and 124 for CH, MC and RO, respectively. Parameters derived from the probabilities of gene origin were variable among the investigated breeds and the results for MC demonstrate the need to pay specific attention to breeding strategies