Genomic characterization of Italian and European pig populations

Thanks to the genomic revolution we can today take advantage of molecular and bioinformatic tools for dissecting phenotypic traits and genetic differences among modern commercial pig breeds, local populations and wild boars. This is important for European autochthonous and endangered pig breeds, whose genetic architecture remains uncharacterized and breeding potential unexploited. This project aimed to investigate genomic features of autochthonous pig breeds focusing on candidate gene markers associated to disease resistance, coat colour, vertebral number and genes involved in feeding preferences. First of all, we used a genotyping approach to define the distribution of disease resistance marker alleles in Italian local pig populations, confirming the robustness of local pig breeds. Results derived from the association study between investigated disease resistance markers and production traits, suggested that it could be possible to introduce disease resistance traits in pig breeding programs without affecting productivity. Regarding the relationship between local pig populations and wild boars, we performed an analysis monitoring the allelic distribution at two evolutionary important loci, involved in coat colour and vertebral number determination. Results suggested that Sus scrofa genome is experiencing bidirectional introgression of wild and domestic alleles, with autochthonous breeds undergoing a “de-domestication” process and wild resources challenged by a “domestication” drift. In the last part of this project we evaluated the genetic variability of taste receptor genes across European pig populations. We performed a SNP discovery study to find out similarities and differences in taste sensing system among local breeds. Taste perception is connected to the diet and the environment and comparing differences between pig breeds in these genes allows to reconstruct the history of breeds and the impact of ecology in their biodiversity. Our results can be considered a basis for the use of genetic variability among local pig populations and for further studies regarding their characterization

Nero Siciliano Pig

Origins of Nero Siciliano pig date to Carthaginian domination and its rearing, after a setback during the Arab period, was rather diffused throughout Sicily. Breed rearing is nowadays limited from the farmed area to the wooded hills of north-eastern Sicily. The latest available status (2015) reported 87 registered farms with about 1100 breeding sows and 124 boars enrolled in the herdbook started in 2001, as well as the conservation programme. Coat colour is mainly black but white face and wattles are accepted. Nero Siciliano pigs have on average 7.6 piglets of 1.4 kg live body weight and the average daily gain during fattening period was on average 346 g/day for the overall fattening stage. Slaughter age of Nero Siciliano breed was on average 390 days, at an average live weight of 95 kg. Average intramuscular fat content was 4.6% and as regards fatty acid composition, average values obtained for SFA, MUFA and PUFA were 37.5, 54.2 and 8.3% in longissimus muscle and 39.0, 49.4 and 11.7% in back fat tissue, respectively. This review gives an exhaustive review of the information available for this local Italian breed

Sarda Pig

Sarda pig breed (a.k.a. Suino Sardo) is a local breed from Sardinia Island (Italy) with its ancestors dating back to the Nuragic period. It is the most recent breed interested by a conservation programme among the six Italian autochthonous pig breeds investigated by the H2020 project TREASURE and could be considered untapped in terms of information on its performances and products. Thirteen farms were registered at the last census (2015) including sixty-one breeding sows and twenty boars. It is a small size breed with black, grey, tawny or spotted coat colour. On average, age at parturition is 15.7 months, with 1.6 litters per year and 7.8 piglets per parity. Average piglet mortality is rather high in the considered studies (16.1%). The average daily gain for Sarda pig within the considered studies was 423 g/day. On average, daily feed intake in the overall fattening stage was 2.3 kg/day. Sarda pigs were slaughtered at approximately 686 days of age, at an average live weight of 193 kg. Sporadic information is available for meat quality traits. Although studies on Sarda pig are scarce, the current review gives the first insight into this local pig breed

Nero Casertano Pig

The present chapter aims to present the history, current status and information of Nero Casertano pig breed investigated in the project TREASURE. As for most of the other Italian local pig breed conservation program started in 2001 and in 2015, 20 farms of Nero Casertano pigs with about 545 breeding sows and 20 boars were registered. The average age of sows at the first parturition is 16 months, whereas age at culling is 59 months. On average Nero Casertano pigs have 1.2 litters per year with 7.6 piglets. The farrowing interval (305 days on average) is prolonged compared to modern pig breeds. The fattening phase of Nero Casertano pigs is generally characterised by slower growth, and the animals were slaughtered at around 375 days of age, with an average live weight of 154 kg and a dressing yield of 81%. The breed is characterised by a high level of backfat thickness. The breed is traditionally raised with the semi-extensive system, and the most recognised trait of the Nero Casertano pig is the ‘marbling’ of the meat. This current review provides a comprehensive insight into the information for this local pig breed

Mora Romagnola Pig

Mora Romagnola breed, one of the Italian local pig breeds, owes its name to its colour, dark brown tending to black. Currently 31 farms are registered in the herdbook started in 2001 with about 270 breeding females and 67 boars. During the 1990s, only 18 animals were left, all concentrated in one single farm. The breed was investigated within the H2020 project TREASURE, and a collection and review of available literature data on reproductive and productive traits of Mora Romagnola pig breed were carried out. The average age of sows at first parturition was 22 months, whereas age at culling was 58 months. On average, Mora Romagnola pig breed has 8.0 piglets per parity with 1.4 parities per year. Slaughter weight was on average 163 kg with a dressing yield of 80%. Few information is available for meat quality traits. Although studies on Mora Romagnola pig are scarce, the current review gives the first insight into this local pig breed

Apulo-Calabrese Pig

The aim of the present chapter is to present history and current status of Apulo-Calabrese pig breed, one of the local pig breeds investigated in the project TREASURE. Apulo-Calabrese breed is one of the Italian autochthonous pig breeds. Its origin dates back to the Roman times, but it suffered a drastic decline during the past century and the recovery started in the 1990s. A herd book for this breed was established in 2001, but its performances and products are practically untapped. There are 45 registered farms with around 500 breeding sows and 100 boars. Apulo-Calabrese pig is characterised by black coat colour. On average sows of Apulo-Calabrese pig breed have 1.7 litters per year with 6.9 piglets. Regarding growth performances, the potential of Apulo-Calabrese pigs in ad libitum conditions of feeding is high (≈762 g/day in middle fattening stage) although information on feed intake and feed nutritional value was scarce, which limits the evaluation of growth potential. Data on body composition, carcass traits and meat and fat quality are scarce. The present review gives a first insight into this local pig breed

Cinta Senese Pig

Cinta Senese is an Italian autochthonous pig breed, one of the local pig breeds investigated in the project TREASURE. The present chapter aims to present history and status of Cinta Senese pig breed, its phenotypic characteristics, geographical location, production system and the quality of its main products. Reproductive performance was estimated by several data: sow age at first parturition, litters/sow/year, piglets alive/litter, weaning weight, stillborn/litter, death rate percentage at weaning, duration of lactation, length of farrowing and sow age at culling. Growth performance was estimated by means of average daily gain in lactation and from birth to slaughter, growing at early, middle, late and overall fattening stage and average daily feed intake in late and overall fattening stage. Carcass traits were evaluated by means of age and weight at slaughtering, hot carcass weight, carcass yield, loin eye area and back fat thickness at the first thoracic vertebra, last rib and above gluteus medius muscle. Meat quality traits of the longissimus muscle were evaluated by means of the following: pH at 45 minutes and 24 hours after slaughtering, instrumental measurements of colour (CIE L*, a*, b*) and intramuscular fat content. Fatty acid composition was evaluated in back fat tissue

Next generation semiconductor based sequencing of the donkey (Equus asinus) genome provided comparative sequence data against the horse genome and a few millions of single nucleotide polymorphisms

Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be similar to 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources

Investigation of genetic markers for resistance to infectious diseases in different pig breeds: antagonism with production and performance traits?

Infectious diseases have devastating economic impacts on the pig breeding industry worldwide. A few genetic markers associated with disease resistance have been recently identified and used in Marker Assisted Selection (MAS) in a few pig populations as part of disease control programs