Analysis of genetic structure and genetic diversity in Diannan small-ear pig

The Diannan small-ear pig, an indigenous breed in Yunnan of China, has significant conservation and utilization value due to its unique economic traits. To investigate the population genetic diversity and structure of this breed, this study applied Illumina Porcine 50K SNP chip to detect genome-wide SNPs in 424 Diannan small-ear pigs. Using PLINK software, a total of 29,468 SNPs were detected. The results showed that the average polymorphism information content (PIC) was 0.21, the minor allele frequency (MAF) was 0.18, and the average expected heterozygosity (H_e) was 0.24, indicating a moderately low level of genetic diversity in the Diannan small-ear pigs population. Subsequently, the phylogenetic tree was constructed using MEGA X software, showing that the Diannan small-ear pigs could be divided into eight linages. Computed with Plink software, the distance matrix was built from pairwise identity by state (IBS) proportions. The results revealed that the average IBS proportion across all individual pairs was 0.23. Analysis of genetic relationships within the population with GCTA software revealed that most Diannan small-ear pigs exhibited moderate genetic proximity. Additionally, a total of 5,301 runs of homozygosity (ROH) segments were identified. 59.54% of those ROHs ranged from 0 to 5 Mb in length. The average inbreeding coefficient based on ROH was 0.006, indicating a low level of inbreeding in the Diannan small-ear pigs population. This study provides a worthwhile genetic foundation for the future conservation and utilization of Diannan small-ear pigs. These findings indicated that the Diannan small-ear pig conservation farm could introduce other more gene flows from other subpopulations to promote population genetic diversity based on preserving their unique and desirable traits, and integrate modern biotechnology for breeding organisms like genomic selection to promote its potential for the discovery and utilization of the merit phenotype-related genes, contributing to the long-term scientific protection and sustainable development and utilization of this valuable genetic resource.