A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits

IF 3.6 1区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE

Genetics Selection Evolution Pub Date : 2023-12-07 DOI:10.1186/s12711-023-00858-3

Klavdija Poklukar, Camille Mestre, Martin Škrlep, Marjeta Čandek-Potokar, Cristina Ovilo, Luca Fontanesi, Juliette Riquet, Samuele Bovo, Giuseppina Schiavo, Anisa Ribani, Maria Muñoz, Maurizio Gallo, Ricardo Bozzi, Rui Charneca, Raquel Quintanilla, Goran Kušec, Marie-José Mercat, Christoph Zimmer, Violeta Razmaite, Jose P. Araujo, Čedomir Radović, Radomir Savić, Danijel Karolyi, Bertrand Servin

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Abstract

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. 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. 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.

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一项对欧洲地方猪品种遗传和表型多样性的荟萃分析揭示了与生产性状品种分化相关的基因组区域

现代猪品种的密集选择导致了生产性状的遗传改进，而地方猪品种的性能仍然较低。由于地方猪品种已经在广泛的系统中繁殖，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。本研究以欧洲地方猪品种为基础，利用dna库测序数据对其进行遗传表征，并利用与身高、肥胖、生长和繁殖性能性状相关的品种水平表型对其进行表型表征。这些数据使用专门的方法进行分析，以检测与表型性状相关的选择特征，以发现可能成为适应特定环境基础的潜在候选基因。对欧洲猪种遗传数据的分析揭示了以伊比利亚猪和三个现代猪种(即大白猪、长白猪和杜洛克猪)为代表的四条主要遗传变异轴。此外，品种根据其地理起源聚集在一起，例如法国加斯科尼和巴斯克品种，意大利Apulo Calabrese和Casertana品种，西班牙伊比利亚品种和葡萄牙阿连特哈诺品种。表型数据的主成分分析区分出生长潜力和繁殖性能较好的大瘦品种和生长和繁殖效率较低的小胖品种。将选择特征与表型联系起来，鉴定出16个与身高有关的显著基因组区域，24个与肥胖有关，2个与生长有关，192个与生殖有关。其中，一些区域含有可能对身高、肥胖、生长和繁殖性能性状产生生物学影响的候选基因。例如，在两个分别含有ANXA4和ANTXR1基因的区域，在含有DNMT3A和POMC基因的区域，在含有HSD17B7基因的区域，发现了身高与肥胖的强关联。在这项对欧洲地方猪品种的研究中，我们使用了一种专门的方法来检测由品种水平的表型数据支持的选择特征，以确定可能适应不同生活环境和生产系统的潜在候选基因。

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来源期刊

Genetics Selection Evolution 生物-奶制品与动物科学

CiteScore

6.50

自引率

9.80%

发文量

审稿时长

1 months

期刊介绍： Genetics Selection Evolution invites basic, applied and methodological content that will aid the current understanding and the utilization of genetic variability in domestic animal species. Although the focus is on domestic animal species, research on other species is invited if it contributes to the understanding of the use of genetic variability in domestic animals. Genetics Selection Evolution publishes results from all levels of study, from the gene to the quantitative trait, from the individual to the population, the breed or the species. Contributions concerning both the biological approach, from molecular genetics to quantitative genetics, as well as the mathematical approach, from population genetics to statistics, are welcome. Specific areas of interest include but are not limited to: gene and QTL identification, mapping and characterization, analysis of new phenotypes, high-throughput SNP data analysis, functional genomics, cytogenetics, genetic diversity of populations and breeds, genetic evaluation, applied and experimental selection, genomic selection, selection efficiency, and statistical methodology for the genetic analysis of phenotypes with quantitative and mixed inheritance.