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BACKGROUND

Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments.

RESULTS

Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene.

CONCLUSIONS

In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.

背景

现代猪种的强烈选择导致了生产性状的遗传改良，而地方猪种的表现仍然较低。由于地方猪种在粗放系统中繁殖，它们已经适应了特定的环境条件，从而产生了丰富的基因型和表型多样性。本研究基于欧洲地方猪种，这些猪种已经使用 DNA 池测序数据进行了基因特征分析，并使用与体型、肥胖、生长和繁殖性能相关的品种水平表型进行了表型特征分析。这些数据使用专门的方法进行了分析，以检测与表型性状相关的选择信号，以揭示可能导致对特定环境适应的潜在候选基因。

结果

对欧洲猪种的遗传数据分析揭示了四个主要的遗传变异轴，代表了伊比利亚和三个现代品种（即大白猪、长白猪和杜洛克猪）。此外，根据地理起源对品种进行聚类，例如法国加斯科涅和巴斯克品种、意大利阿普洛卡拉布里亚和卡塞塔纳品种、西班牙伊比利亚和葡萄牙阿连特茹品种。表型数据的主成分分析将生长潜力和繁殖性能较好的体型较大且较瘦的品种与体型较小且肥胖、生长和繁殖效率较低的品种区分开来。将选择信号与表型联系起来，确定了 16 个与体型相关的显著基因组区域、24 个与肥胖相关的区域、2 个与生长相关的区域和 192 个与繁殖相关的区域。其中，一些区域包含了对体型、肥胖、生长和繁殖性能性状可能具有生物学影响的候选基因。例如，在包含 ANXA4 和 ANTXR1 基因的两个区域中发现了与体型强烈相关的区域，在包含 DNMT3A 和 POMC 基因的一个区域中发现了与肥胖相关的区域，在包含 HSD17B7 基因的一个区域中发现了与繁殖性能相关的区域。