Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain.
Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
PLoS One. 2019 Jun 27;14(6):e0218862. doi: 10.1371/journal.pone.0218862. eCollection 2019.
The selection in commercial swine breeds for meat-production efficiency has been increasing among the past decades, reducing the intramuscular fat content, which has changed the sensorial and technological properties of pork. Through processes of natural adaptation and selective breeding, the accumulation of mutations has driven the genetic divergence between pig breeds. The most common and well-studied mutations are single-nucleotide polymorphisms (SNPs). However, insertions and deletions (indels) usually represents a fifth part of the detected mutations and should also be considered for animal breeding. In the present study, three different programs (Dindel, SAMtools mpileup, and GATK) were used to detect indels from Whole Genome Sequencing data of Iberian boars and Landrace sows. A total of 1,928,746 indels were found in common with the three programs. The VEP tool predicted that 1,289 indels may have a high impact on protein sequence and function. Ten indels inside genes related with lipid metabolism were genotyped in pigs from three different backcrosses with Iberian origin, obtaining different allelic frequencies on each backcross. Genome-Wide Association Studies performed in the Longissimus dorsi muscle found an association between an indel located in the C1q and TNF related 12 (C1QTNF12) gene and the amount of eicosadienoic acid (C20:2(n-6)).
在过去的几十年里，商业猪种的选育一直在提高肉用生产效率，这降低了肌肉内脂肪含量，从而改变了猪肉的感官和技术特性。通过自然适应和选择性繁殖的过程，突变的积累推动了猪种之间的遗传分化。最常见和研究最多的突变是单核苷酸多态性（SNP）。然而，插入和缺失（indels）通常占检测到的突变的五分之一，也应该考虑用于动物繁殖。在本研究中，使用了三个不同的程序（Dindel、SAMtools mpileup 和 GATK）从伊比利亚公猪和长白母猪的全基因组测序数据中检测 indels。共有 1,928,746 个 indels 在三个程序中都被发现。VEP 工具预测，1,289 个 indels 可能对蛋白质序列和功能有很大影响。在来自三个不同回交群体的猪中对与脂质代谢相关的基因内的 10 个 indels 进行了基因分型，在每个回交群体中获得了不同的等位基因频率。在背最长肌中进行的全基因组关联研究发现，位于 C1q 和肿瘤坏死因子相关 12（C1QTNF12）基因内的一个 indel 与二十碳二烯酸（C20:2(n-6)）的含量有关。
