## 3 Molecular Methods
### Genomic Approaches in Genetic Diversity Analysis  
The development of whole-genome sequencing (WGS), genome-wide association studies (GWASs), and copy number variation (CNV) analysis have provided tools for studying the genomic architecture of autochthonous pig breeds (Table 2). Furthermore, the application of these methods improves the maintenance and efficiency of breeding programs for autochthonous pig breeds. As the field of genomics continues to evolve, it will play an important role in shaping the future of pig breeding and production. \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Genomic Approaches** & **Year** & **Pig Bred** & **Reference** \\ \hline Whole-genome & 2012 & Duroc & [94] \\ Sequencing (WGS) & 2020 & European & \\  & sequencing (WGS) & autochthonous pig breeds & [6] \\ Genome-Wide & 2020 & Different pig breeds (57) & [95] \\ Association Studies & 2020 & _Sus scrofa_ & [96] \\ Genome-Wide & 2022 & Suhuai, Chinese Min Zhu, Large White & [43] \\ Association Studies & 2021 & Meishan, Enshi Black, Duroc, Large White & [97] \\  & 2022 & Luchuan and Duroc breeds & [98] \\  & Pangenome analysis & 2023 & Euroasia pig breeds & [99] \\ Copy Number & 2023 & Chinese autochthonous pigs, Asian wild bours & [100] \\  & & & \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Genomic approaches in the study of genetic diversity of pig breeds. Whole-genome sequencing (WGS) is a comprehensive method that provides insight into functional genomic variation in pigs. [PERSON] et al. [6] analyzed the genome of 23 pig breeds, including wild boar, to identify signatures of selection that can explain the phenotypic diversity of the pig breeds analyzed. The authors used whole-genome sequencing data obtained through a DNA pool sequencing approach. The result of their study was the identification of selection signatures covering 502 unique genomic windows. The authors also compared the results with SNP chip data and showed that the two approaches can capture different types of information. A similar approach was used in the study by [PERSON] et al. [19], who performed a meta-analysis of the genetic and phenotypic diversity of European autochthonous pig breeds. The authors combined DNA pool sequencing data from nineteen European autochthonous breeds and seven commercial pig breeds to identify selection signatures associated with potential candidate genes for adaptation to specific environmental conditions and production systems. In their study, [PERSON] et al. [95] used a whole-genome approach in five pig populations to discover the genomic differences between autochthonous Chinese pigs and the Large White breed. The authors also identified 1289 non-synonymous SNPs for growth and feed conversion in Large White, which can be labeled as useful molecular markers. [PERSON] et al. [101] analyzed the genomic breed composition of the autochthonous Chinese Ningxiang pig breed using genomic SNP information. For their analysis, the authors used SNPs with different densities to construct SNP panels that can be used as the most effective and economical SNP panels for the Ningxiang pig. The results of their study showed that the constructed reference panel (10K SNP panel) provides insight into the genomic composition of the Ningxiang breed with high accuracy and can be used for the development of low-cost, low-density chips. Similarly, [PERSON] et al. [11] evaluated the genetic diversity and population structure of the Tongcheng pig breed to develop and implement a conservation program and ensure acceptable genetic diversity to avoid inbreeding depression in the population. The authors used a whole-genome approach and analyzed 51,315 SNPs, of which 26,999 SNPs were identified in the Tongcheng pig breed. Genome-wide association studies (GWAS) provide valuable insights into genetic diversity monitoring and selection signature identification in pig breeds, crucial for their integration into breeding programs and conservation strategies.