School of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, PR China.
College of Animal Science, South China Agricultural University, Guangzhou, PR China.
Animal. 2022 Aug;16(8):100591. doi: 10.1016/j.animal.2022.100591. Epub 2022 Jul 21.
Sujiang pigs are a synthetic breed derived from Jiangquhai, Fengjing, and Duroc pigs. In this study, we sequenced the genome of 62 pigs with a coverage depth of 10× to 20×, including 27 Sujiang and 35 founder breed pigs, and we collected 360 global pigs' genome sequence data from public databases including 39 Duroc pigs. We obtained a high-quality variant dataset of 365 Sujiang pigs by imputing the porcine 80 K single nucleotide polymorphism (SNP) Beadchip to the whole-genome scale with a total of 422 pigs as a reference panel. A dataset of 365 imputated Sujiang pigs was used to perform single-trait genome-wide association study (GWAS) and meta-analyses for growth and fatness traits. Single-trait GWAS identified 1 907, 18, and 14 SNPs surpassing the suggestively significant threshold for backfat thickness, chest circumference, and chest width, respectively. Meta-analyses identified 2 400 genome-wide significant SNPs and 520 suggestively significant SNPs for backfat thickness and chest circumference, and 719 genome-wide significant SNPs and 1 225 suggestively significant SNPs for all seven traits. According to the meta-analysis of backfat thickness and chest circumference, a remarkable region of 2.69 Mb on Sus scrofa chromosome 4 containing FAM110B, IMPAD1, LYN, MOS, PENK, PLAG1, SDR16C5 and XKR4 was identified as a candidate region. The haplotype heat map of the 2.69 Mb region verified that Sujiang pigs were derived from Duroc and Chinese indigenous pigs, especially Jiangquhai pigs. The Kruskal-Wallis test showed that haplotypes of the 2.69 Mb region significantly affected backfat thickness and chest circumference traits. We then focused on PLAG1, an important growth-related gene, and identified two synonymous SNPs with obvious differences among different breeds in the PLAG1 gene. We then performed genotyping of 365 Sujiang, 150 Duroc, 95 Jiangquhai, and 100 Fengjing pigs to confirm the above result and verified that the two variants significantly affected phenotypes of growth and fatness traits. Our findings not only provide insights into the genetic architecture of porcine growth and fatness traits but also provide potential markers for selective breeding of these traits in Sujiang pigs.
苏姜猪是由姜曲海猪、枫泾猪和杜洛克猪合成的品种。本研究对 62 头猪进行了测序，测序深度为 10×至 20×，包括 27 头苏姜猪和 35 头原始品种猪，并从公共数据库中收集了 360 头全球猪的基因组序列数据，其中包括 39 头杜洛克猪。我们通过将猪 80K SNP BeadChip 导入全基因组范围，以总共 422 头猪作为参考面板，获得了 365 头苏姜猪的高质量变异数据集。使用 365 头 imputed Sujiang 猪数据集进行单性状全基因组关联研究（GWAS）和生长和脂肪性状的荟萃分析。单性状 GWAS 鉴定出 1907、18 和 14 个 SNP 分别超过背部脂肪厚度、胸围和胸宽的提示性显著阈值。荟萃分析鉴定出背部脂肪厚度和胸围的 2400 个全基因组显著 SNP 和 520 个提示性显著 SNP，以及所有 7 个性状的 719 个全基因组显著 SNP 和 1225 个提示性显著 SNP。根据背部脂肪厚度和胸围的荟萃分析，在Sus scrofa 染色体 4 上鉴定出一个包含 FAM110B、IMPAD1、LYN、MOS、PENK、PLAG1、SDR16C5 和 XKR4 的 2.69 Mb 显著区域，该区域可能是一个候选区域。2.69 Mb 区域的单倍型热图验证了苏姜猪来源于杜洛克猪和中国本土猪，尤其是姜曲海猪。Kruskal-Wallis 检验表明，2.69 Mb 区域的单倍型显著影响背部脂肪厚度和胸围性状。然后我们关注了 PLAG1 这个重要的生长相关基因，并在 PLAG1 基因中发现了两个不同品种之间有明显差异的同义 SNP。然后我们对 365 头苏姜猪、150 头杜洛克猪、95 头姜曲海猪和 100 头枫泾猪进行了基因分型，以证实上述结果，并验证了这两个变体显著影响生长和脂肪性状的表型。我们的研究结果不仅为猪生长和脂肪性状的遗传结构提供了深入了解，还为苏姜猪这些性状的选择性育种提供了潜在的标记。
