Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy.
Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy.
Animal. 2024 Nov;18(11):101335. doi: 10.1016/j.animal.2024.101335. Epub 2024 Sep 19.
The Italian pig farming industry is unique in its focus on raising heavy pigs primarily for the production of high-quality dry-cured hams. These products require pigs to be slaughtered at a live weight of around 170 kg at 9 months of age. The primary breeds used in this system are Italian Duroc, Italian Landrace, and Italian Large White which are crossed to produce lines that meet standard requirements. Over the past four decades, selection and breeding programmes for these breeds have been subjected to distinct selective pressures to highlight the characteristics of each breed. In this study, we investigated the genome of these breeds by analysing high-density single nucleotide polymorphism data from over 9 000 pigs to scan for signatures of selection using four different methods, two within breeds and two across breeds. This allowed to identify the genomic regions that differentiate these breeds as well as any relevant genes and biological terms. On a global scale, we found that the Italian Duroc breed exhibited a higher genetic differentiation from the Italian Landrace and Italian Large White breeds, with a pairwise F value of 0.20 compared with the 0.13 between Italian Landrace and Italian Large White. This may reflect either their different origins or the different breeding goals, which are more similar for the Italian Landrace and Italian Large White breeds. Despite these genetic differences at a global level, few signatures of selection regions reached complete fixation, possibly due to challenges in detecting selection linked to quantitative polygenic traits. The differences among the three breeds are confirmed by the low level of overlap in the regions detected. Genetic enrichment analyses of the three breeds revealed pathways and genes related to various productive traits associated with growth and fat deposition. This may indicate a common selection direction aimed at enhancing specific production traits, though different biological mechanisms are likely targeted by the same directional selection in these three breeds. Therefore, these genes may play a critical role in determining the distinctive characteristics of Italian Duroc, Italian Landrace, and Italian Large White, and potentially influence the traits in crossbred pigs derived from them. Overall, the insights gained from this study will contribute to understanding how directional selection has shaped the genome of these heavy pig breeds and to better address selection strategies aimed at enhancing the meat processing industry linked with dry-cured ham production chains.
意大利的养猪业独具特色，专注于饲养体重较大的猪，主要用于生产高品质的风干火腿。这些产品要求猪在 9 个月大、活重达 170 公斤时进行屠宰。该系统主要使用的品种有意大利杜洛克猪、意大利长白猪和意大利大白猪，它们被杂交以生产符合标准要求的品系。在过去的四十年中，这些品种的选择和育种计划受到了不同的选择性压力，以突出每个品种的特点。在这项研究中，我们通过分析来自 9000 多头猪的高密度单核苷酸多态性数据，使用四种不同的方法（两种在品种内，两种在品种间）来扫描选择的特征，以研究这些品种的基因组。这使得我们能够识别出区分这些品种的基因组区域，以及任何相关的基因和生物学术语。在全球范围内，我们发现意大利杜洛克猪与意大利长白猪和意大利大白猪品种的遗传分化程度更高，其 F 值为 0.20，而意大利长白猪和意大利大白猪品种的 F 值为 0.13。这可能反映了它们不同的起源，也可能反映了它们不同的育种目标，因为意大利长白猪和意大利大白猪品种的目标更为相似。尽管在全球范围内存在这些遗传差异，但很少有选择区域的特征达到完全固定，这可能是由于检测与数量性状相关的选择存在挑战。三个品种之间的差异通过检测到的区域的低重叠度得到证实。对三个品种的遗传富集分析揭示了与生长和脂肪沉积相关的各种生产性状的途径和基因。这可能表明存在一个共同的选择方向，旨在增强特定的生产性状，尽管这些品种的同一定向选择可能针对不同的生物学机制。因此，这些基因可能在决定意大利杜洛克猪、意大利长白猪和意大利大白猪的独特特征方面发挥关键作用，并可能影响源自它们的杂交猪的性状。总的来说，这项研究的结果将有助于理解定向选择如何塑造这些大型猪品种的基因组，并更好地解决旨在增强与风干火腿生产链相关的肉类加工行业的选择策略。
