Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.
Trop Anim Health Prod. 2023 Apr 11;55(3):154. doi: 10.1007/s11250-023-03557-9.
Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.
解析地方品种的遗传变异对于保护的成功至关重要。在这项研究中，我们研究了哥伦比亚克里奥尔猪（CR）的基因组变异，重点是在 34 个具有报道称对适应性和经济性状有影响的基因的外显子区域中发现的特定于品种的变异。每个 CR 品种（CM，卡萨德穆拉；SP，圣佩德雷诺；ZU，宗戈）的 7 个个体与 7 头伊比利亚猪（IB）和每个 4 个最常用的世界性品种（杜洛克猪、长白猪×大白猪和皮特兰猪）的 7 个个体一起进行了全基因组测序。CR 的分子变异性（6451218 个变异；SP 为 3919242 个，ZU 为 4648069 个，CM 为 3919242 个）与 CP 相当，但高于 IB。在所研究的基因中，SP 猪的外显子变异（178 个）少于 ZU（254 个）、CM（263 个）、IB（200 个）和单个 CP 遗传类型（201 到 335 个）。这些基因的序列变异证实了 CR 与 IB 的相似性，并表明 CR 猪，特别是 ZU 和 CM，不受其他品种的选择性渗入的影响。共鉴定出 50 个外显子变异可能是 CR 特有的，包括在瘦素受体基因第 15 号和第 16 号外显子之间的内含子中的一个高影响缺失，该缺失仅在 CM 和 ZU 中发现。在与适应性和经济性状相关的基因中鉴定出特定于品种的变异，可以加强对基因-环境相互作用在地方适应性中的作用的理解，并为 CR 猪的有效繁殖和保护指明方向。
