Animal breed identification has wide and important application prospects in the field of genetic breeding. It not only provides effective genetic information for the selection and breeding of superior animals (Behl et al., 2006), but also provides new methods for the traceability of animal products (Dalvit et al., 2007). Meanwhile, it plays a vital role in biological science research (Yaro et al., 2017), pedigree identification (Dreger et al., 2016) and breed resource conservation (Weigend et al., 2004).The earliest breed identification was mainly carried out in a morphological manner (Ceccobelli et al., 2016).
The domestic pig (Sus scrofa) and subfamilies have a long-term and
extensive gene flow, especially in Southeast Asia. Demographically, as a
gateway of southern China, Yunnan province with unique geographical
location and complex climate system, but genomic, genetic introgression
of Yunnan indigenous pigs is insufficient. Here, we analyzed population
structure, differentiation, gene flow, adaptive introgression, signature
selection and gene function of Yunnan indigenous pigs, European
commercial and other Southeast Asia pigs using a pig genomics reference
panel (PGRP v1) from pig Genotype-Tissue Expression project (PigGTEx).
In this study, we clarified that the Diannan small-ear pig owned
particular genetic information in the whole genome; we provided evidence
of the introgression events from the Vietnam pig to the Diannan
small-ear pig. We also outlined at least two conceptual routes of gene
flow to Diannan small-ear in Southeast Asia. Three introgressed loci
with similar chromosome positions and strong signature selection
harbored the NAF1, NPY1R and NPY5R genes, which related to fat mass,
immunity, and litter weight of pig complex trait using multiple
bio-functionalization databases. Conclusively, these results laid the
foundation for understanding introgression from Southeast Asia pigs to
Yunnan indigenous pigs and provided a new insight into explaining the
biological function of genes through multiple databases.
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