Luchuan pig genome project

Here we focus on the domestication of pig, one of the most important livestock animals and biomedical models. We integrate comparative genomics, whole-genome re-sequencing and transcriptional and epigenomic profiling to study the genetic basis underlying the phenotypic differences between the Eastern and Western pigs. We present a high-resolution phased chromosome-scale reference genome with contig N50 of 18.03 Mb for the Luchuan pig (a Chinese indigenous breed) and catalogued high-quality SNPs and indels from Western and Eastern breeds. To further study the role of cis-regulatory variants in phenotypic differentiation, we profiled transcriptome and chromatin accessibility across multiple tissues in the two pig breeds. We found that open chromatin regions in the skeletal muscle showed strongest enrichment of genetic differentiation regions. As one concrete example, a differential distal cis-regulatory SNP for higher skeletal muscle expression of TNNC1 in Luchuan may contribute to increased composition of slow muscle fibers, leading to meat flavors preferred by Eastern cuisine culture.