Genome-wide association analyses for coat colour patterns in the autochthonous Nero Siciliano pig breed

Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.

Genome-wide association study revealed the genomic regions associated with skin pigmentation in an Ogye x White Leghorn F2 chicken population

Skin color in chickens is an economically important trait that determines the first impression of a consumer toward a broiler and can ultimately affect consumer choice in the market. Therefore, identification of genomic regions associated with skin color is crucial for increasing the sales value of chickens. Although previous studies have attempted to reveal the genetic markers associated with the skin coloration in chickens, most were limited to investigations of candidate genes, such as melanin-related genes, and focused on case/control studies based on a single or small population. In this study, we performed a genome-wide association study (GWAS) on 770 F2 intercrosses produced by an experimental population of 2 chicken breeds, namely Ogye and White Leghorns, with different skin colors. The GWAS demonstrated that the L* value among the 3 skin color traits is highly heritable, and the genomic regions located on 2 chromosomes (20 and Z) were detected to harbor SNPs significantly associated with the skin color trait, accounting for most of the total genetic variance. Particular genomic regions spanning a ∼2.94 Mb region on GGA Z and a ∼3.58 Mb region on GGA 20 were significantly associated with skin color traits, and in these regions, certain candidate genes, including MTAP, FEM1C, GNAS, and EDN3, were found. Our findings could help elucidate the genetic mechanisms underlying chicken skin pigmentation. Furthermore, the candidate genes can be used to provide a valuable breeding strategy for the selection of specific chicken breeds with ideal skin coloration.

A 20-SNP Panel as a Tool for Genetic Authentication and Traceability of Pig Breeds

Simple Summary

Given the high economic and qualitative values of local-breed meat products, it is not uncommon that substitution or mislabeling (either fraudulent or accidental) occurs at the market level. Therefore, to protect the interests of both producers and consumers, a reliable traceability tool should be developed. Nowadays, traceability usually relies on physical labeling systems (e.g., ear tags, tattoos, or electronic transponders). These systems do not, however, have good performances when dealing with carcasses or processed meat products. Molecular markers (i.e., based on the DNA sequence) can be a solution, since DNA is easily extracted from a wide variety of animal products and parts, and is not degraded during processing, even at the high temperatures involved. The aim of this study was to identify a small number of DNA mutations for breed-traceability purposes, in particular of the Italian Nero Siciliano pig and its derived products. A small panel of 12 DNA mutations was enough to discriminate Nero Siciliano pigs from other pig breeds and from wild boars.

Abstract

Food authentication in local breeds has important implications from both an economic and a qualitative point of view. Meat products from autochthonous breeds are of premium value, but can easily incur fraudulent or accidental substitution or mislabeling. The aim of this study was to identify a small number of SNPs using the Illumina PorcineSNP60 BeadChip for breed traceability, in particular of the Italian Nero Siciliano pig and its derived products. A panel of 12 SNPs was sufficient to discriminate Nero Siciliano pig from cosmopolitan breeds and wild boars. After adding 8 SNPs, the final panel of 20 SNPs allowed us to discriminate all the breeds involved in the study, to correctly assign each individual to its breed, and, moreover, to discriminate Nero Siciliano from first-generation hybrids. Almost all livestock breeds are being genotyped with medium- or high-density SNP panels, providing a large amount of information for many applications. Here, we proposed a method to select a reduced SNP panel to be used for the traceability of pig breeds.

A genome-wide association study for the number of teats in European rabbits (Oryctolagus cuniculus) identifies several candidate genes affecting this trait

In the European rabbit (Oryctolagus cuniculus), a polytocous livestock species, the number of teats indirectly impacts the doe reproduction efficiency and, in turn, the sustainable production of rabbit meat. In this study, we carried out a genome-wide association study (GWAS) for the total number of teats in 247 Italian White does included in the Italian White rabbit breed selection program, by applying a selective genotyping approach. Does had either 8 (n = 121) or 10 teats (n = 126). All rabbits were genotyped with the Affymetrix Axiom OrcunSNP Array. Genomic data from the two extreme groups of rabbits were also analysed with the single-marker fixation index statistic and combined with the GWAS results. The GWAS identified 50 significant SNPs and the fixation index analysis identified a total of 20 SNPs that trespassed the 99.98th percentile threshold, 19 of which confirmed the GWAS results. The most significant SNP (P = 4.31 × 10^-11 ) was located on OCU1, close to the NUDT2 gene, a breast carcinoma cells proliferation promoter. Another significant SNP identified as candidate gene NR6A1, which is well known to play an important role in affecting the correlated number of vertebrae in pigs. Other significant markers were close to candidate genes involved in determining body length in mice. Markers associated with increased number of teats could be included in selection programmes to speed up the improvement for this trait in rabbit lines that need to increase maternal performances.

Sicilian Black Pig: An Overview

Simple Summary

The conservation of the genetic variability of animals used for food production and non-food raw materials and services is a problem of primary importance at a global level. In recent years, conservation of biodiversity in livestock species has been favoring the need to preserve genetic variability of the autochthonous breeds, exploiting them in the context of production systems. In this context, a precious genetic reserve is represented by autochthonous breeds used for the production of typical products used in Italian gastronomic traditions, of which some organoleptic properties of their meats that could disappear due to severe selection programs are being recovered. Currently, the survival of autochthonous breeds is linked to various reasons such as their rusticity, i.e., the adaptability to difficult environmental conditions, and to the higher market value of their productions obtained according to traditional methods compared to the industrial production types. As information on autochthonous Italian pigs is limited, further research aims at making better use of these breeds and at increasing the knowledge of their genetic variability.

Abstract

The Sicilian black pig (SB) (Nero Siciliano), also known as the Nero dei Nebrodi, Nero delle Madonie, or Nero dell’Etna pig ecotype, is an autochthonous Italian breed. The origins of this breed date back to Greek and Carthaginian dominations. In ancient times, its breeding was fairly common throughout Sicily, registering only a temporary reduction during the Arab domination. This breed is known primarily for its distinctive black coat, although some individuals display wattles and a partially or wholly white face. The SB pig has a birth rate with an average per sow of 7.6 piglets, each of 1.4 kg live body weight, showing an average daily gain (ADG) of 346 g/day during the fattening period. Slaughter generally takes place at an average age of 390 days, with an average live weight of 95 kg. This breed also appears to withstand adverse climatic conditions and resist disease. The purpose of this manuscript is to offer a general overview regarding the Sicilian Black pig and to consider the recent findings related to genome investigation. The recent application of Next Generation Sequencing (NGS) technologies in the study of the genome of autochthonous breeds showed that polymorphisms of some candidate genes for production performance and phenotypic traits represent important information for selection processes. The protection of autochthonous breeds, intended as sources of genomic diversity for the further improvements of pigs for commercial use, constitutes a valuable opportunity to create new sustainable pig chains.