## 3 Molecular Methods
### Genomic Approaches in Genetic Diversity Analysis
The application of GWAS can help in the identification of breed-specific SNPs [11], the monitoring of inbreeding and genetic drift [96], and the identification of important genetic variants of pig breeds [102]. The study by [PERSON] et al. [96] identified six biological phenotypes by breed traits and several production traits of 57 pig breeds. The GWAS approach identified 37 candidate genes in the analyzed pig breed, of which 10 were newly discovered candidate genes. The authors found that the use of GWAS allows efficient mapping of complex traits in a modest number of breeds with high density of genomic variants. [PERSON] et al. [103] used a GWAS approach to detect and characterize the runs of homozygosity and estimate genomic inbreeding in a Chinese Laiwu pig breed. The authors used a high-throughput reduced-representation sequencing method developed for outbred populations to detect genomic regions with a high frequency of runs of homozygosity (ROH) regions in the Laiwu pig population. This approach shows that the Laiwu populations were affected by ancient inbreeding events and identified 13 ROH islands containing genes associated with disease resistance and biosynthetic processes. In the study by [PERSON] et al. [104], the Porcine SNP60K BeadChip was used for a genome-wide assessment of different breeds, including commercial, village, autochthonous, and feral pigs in South Africa. The results obtained show the peculiarities of South African pig populations compared to other global populations, and provide fundamental insights for breed characterization and the implementation of conservation measures. The study of genetic diversity in pig breeds has been significantly advanced by the application of pangenomic and epigenomic approaches. The \"pangenome\" concept describes the entire collection of genes within a species, including the core genes and accessory genes that differ between populations. This approach can be used to identify genetic differences that contribute to breed-specific variations and adaptations [105]. Inheritable chemical modifications of DNA and histones, such as DNA methylation and histone modifications, are part of the epigenome and control gene expression without altering the DNA sequence. Epigenomic studies provide insight into how environmental factors influence gene activity and phenotypic diversity. The integration of these two approaches will lead to a more comprehensive understanding of the genetic and regulatory mechanisms of genetic diversity and adaptation [106]. The first published paper using the pangenome approach to analyze the pig genome was conducted by [PERSON] et al. [107]. By analyzing the genetic variation of nine pig breeds from Europe and Asia, the authors found a large number of novel SNPs and structural variants. They also found hundreds of millions of base pairs and protein-coding genes that are missing in the reference genome Sus scrofa 11.1 (GCF\({}_{-}\)00003025.6) but are associated with important economic traits. Several papers [99; 108; 109; 110] used the pangenome approach to study genetic diversity within pig breeds. [PERSON] et al. [110] constructed the pangenome based on 32 pig breeds in Eurasia and analyzed coding sequence variations (presence/absence variations, PAVs) important for pig phenotypic diversity, and identified 3438 novel genes missing from the current reference genome and 308.3-Mb nonreference sequences. Similarly, [PERSON] et al. [109] constructed a pig pangenome and genome variation map of 599 deep-sequenced genes and identified 546,137 structural variations that affect adaptability to different environments and production systems. Their study showed also that core genes necessary for key biological functions are conserved in all breeds and that accessory genes enable the expression of certain breed-specific traits.