There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.

中文翻译：

---

眉山猪基因组揭示了亚洲猪驯化的结构变异介导的基因表达和表型差异

亚洲和欧洲猪品种之间存在广泛的基因组和表型差异，但目前的参考基因组是欧洲杜洛克猪基因组。亚洲猪农业性状遗传分析缺乏高质量的猪基因组。在这里，使用混合方法，亚洲梅山品种的高质量参考基因组 (MSCAAS v1) 与大小为 48.05 Mb 的重叠群 N50 组装在一起。作为亚洲品种的参考基因组，MSCAAS v1 优于杜洛克基因组。基因组比较揭示了眉山和杜洛克之间的 49,103 个结构变异 (SV)，其中 4.02% 是亚洲特异性 SV (AP-SV)。值得注意的是，亚洲家猪品种中存在一个 30-Mb 的 AP-SV 热点，其中富含与亚洲猪特异性表型相关的基因，但在亚洲野猪中不存在。表明亚洲家养品种有一个共同的祖先。杂交转录组学揭示了 AP-SV 在多种组织中的转录抑制作用。最后，报道了 IGF2R 内含子的转录调控，因为与家猪品种相比，藏猪的基因组 SV（274 bp 缺失）限制了其生长。总之，这项研究提供了有关猪驯化背后遗传变化的见解，并为亚洲猪的农业有价值位点的利用提供了基准设定资源。