College of Animal Science and Technology, Guangxi University, Nanning, China.
Anim Genet. 2022 Aug;53(4):513-517. doi: 10.1111/age.13224. Epub 2022 May 30.
In China there are approximately 100 pig breeds, which show great diversity in their appearance. However, information on genome selection signatures, such as spine curvature, is scarce. Therefore, we used the fixation index (F ) and cross-population extended haplotype homozygosity (XPEHH) methods to explore the genome selection signatures of spine curvature in six breeds of Chinese indigenous pig. We identified 396 and 389 single nucleotide polymorphisms using the F and XPEHH methods, respectively. We detected 19 selection signatures and 28 genes located in the selected regions. Five candidate genes (MAP3K7, CUX1, GRIN2B, ALPL and MACF1) were identified in the selection signatures. Additionally, 719 high-frequency runs of homozygosity regions, 17 unique runs of homozygosity regions, 78 genes and 27 pathways were identified in the runs of homozygosity analysis. The TGF-beta signaling pathway and eight genes related to the spine formation, spine defects and intervertebral disk degeneration were identified, comprising ACVR1, FMOD, ITGA4, MAPK8, PDGF, RPL3, SULF1 and UBE2D1. In summary, we identified 13 candidate genes related to spine curvature in Chinese indigenous pigs.
在中国，大约有 100 个猪品种，它们在外貌上表现出很大的多样性。然而，关于脊柱弯曲等基因组选择特征的信息却很少。因此，我们使用固定指数（F）和跨群体扩展单倍型纯合度（XPEHH）方法来探索中国本土猪六个品种的脊柱弯曲的基因组选择特征。我们分别使用 F 和 XPEHH 方法鉴定了 396 个和 389 个单核苷酸多态性。我们检测到 19 个选择特征和位于所选区域的 28 个基因。在选择特征中鉴定出 5 个候选基因（MAP3K7、CUX1、GRIN2B、ALPL 和 MACF1）。此外，在纯合性分析中还鉴定出了 719 个高频纯合区域、17 个独特的纯合区域、78 个基因和 27 条途径。鉴定出了 TGF-β信号通路和与脊柱形成、脊柱缺陷和椎间盘退化相关的 8 个基因，包括 ACVR1、FMOD、ITGA4、MAPK8、PDGF、RPL3、SULF1 和 UBE2D1。总之，我们鉴定出了 13 个与中国本土猪脊柱弯曲相关的候选基因。
