Genome-wide analysis reveals genetic characteristics and selection signatures in Yantai Black Pig of Shandong, China

Background Yantai Black pig (YT), renowned for its disease resistance and superior meat quality, is a Chinese indigenous pig breed that has developed through natural and artificial selection over an extended period. In recent years, the YT population has dwindled due to the introduction of cosmopolitan pig breeds and the outbreak of African swine fever, putting them at risk of extinction. Meanwhile, there is still a lack of research on its genome. We conducted a genomic comprehensive analysis by high-density SNP chip on 102 YT and comparing them with resequencing genomic data from 20 YT and 16 wild boar (WB). Results The effective population size (Ne), polymorphic marker ratio (P _N ), expected heterozygosity (He), and observed heterozygosity (H _O ) of this population were 5.0, 0.917, 0.374, and 0.361, respectively, with an average inbreeding coefficient of 0.151 within the population. Based on genomic information, this population was classified into eight different families with boars. It was found that YT was population independent of WB, exhibiting genetic differentiation within the population. Moreover, a total of 125 selected candidate genes were identified by using three methods: F _ST , π ratio, and Tajima's D. Functional enrichment analysis identified several annotated genes that might affect growth and development ( DCC , NFKBIZ , TNR , LRRC4C , ERBB4 , TMEM182 , SPRY1 , and MYC), reproduction ( INHBA , COL12A1 , ADRA2A , and DROSHA ), meat quality ( NRG1 , GRM8 , GRIK2 , EFNA5 , COL9A1 , and CHL1 ), and immune response ( SEMA3E , RUNX2 , GRIN3A , PKN2 , SEMA3C , PTPN6 , and SOCS6 ). Conclusion The findings indicated that YT exhibited a decrease in the level of genetic diversity and was a relatively independent indigenous pig breed. It should be protected scientifically and effectively as a valuable germplasm resource. Selection signatures in genomic regions linked to important economic traits in YT. Our results will provide a valuable basis for the future effective protection, breeding, and utilization of YT.