## 3 Molecular Methods
### Genetic Markers for Assessing Genetic Variation  
The first use of microsatellite markers as a tool for assessing the genetic diversity of domestic animals began in the early 1990s. Microsatellite markers are characterized by their short length, high polymorphism, and elevated mutation rates. They are a co-dominantly inherited simple sequence repeat (SSR) that is widely distributed in a genome [72]. They have been widely employed to analyze the genetic diversity of native pig breeds and to develop region-specific breeding strategies [15; 27; 65; 73; 74; 75], as well as to study their phylogenetic relationships [73; 76] (Table 1). [PERSON] et al. [73] and [PERSON] et al. [89] used microsatellite markers to analyze the genetic diversity of autochthonous Thai pig populations from different geographical regions and found a high degree of genetic variability within these populations. Both studies identified genetic differentiation among populations, suggesting the role of geographical isolation in their genetic structure. In addition, [PERSON] et al. [73] identified private microsatellite alleles that should be conserved in the Thai pig population. [PERSON] et al. [86] also emphasized the importance of identifying different genetic clusters within indigenous Thai pig populations for conservation. Similarly, [PERSON] et al. [74] used a panel of 19 microsatellite markers to characterize the genetic diversity, genetic clusters, and phylogenetic relationships of 15 autochthonous Vietnamese pig breeds, and proposed different conservation strategies for each breed based on the structure of the subpopulations. In the study by [PERSON] et al. [15], the authors used different marker systems, microsatellites, and SNP to analyze the genetic structure of six autochthonous pig breeds originating from three countries, i.e., Croatia, Serbia, and Slovenia. The results of their analysis show that historical and geographical factors have influenced the genetic structure of the analyzed pig breeds. The authors emphasized the need to develop conservation \begin{table}
\begin{tabular}{c c c c} \hline
**Molecular Marker** & **Year** & **Pig Bred** & **Reference** \\ \hline Microsatellite & 1994 & _Sus scrofa_ & [77] \\ Microsatellite & 1995 & Landrace, Negative, Pietrain, Large White & [78] \\ Microsatellite & 2000 & European pig breeds & [79] \\ Microsatellite & 2008 & European and Chinese pig breeds & [80] \\ Microsatellite & 2009 & Brazilian pig breeds & [81] \\ Microsatellite & 2010 & Chinese autochthonous pig breed & [82] \\ Microsatellite & 2015 & Greek black pig breed & [76] \\ Microsatellite & 2017 & Ghanaian pig breed & [83] \\ Microsatellite & 2019 & Black Slavonian pig breed & [27] \\ Single Nucleotide Polymorphisms (SNP) & 2009 & Landrace & [84] \\ Single Nucleotide Polymorphisms (SNP) & 2013 & Chinese autochthonous breeds, Asian wild boar & [85] \\ Single Nucleotide Polymorphisms (SNP) & 2015 & Duroc, Landrace, Yorkshire & [86] \\ Single Nucleotide Polymorphisms (SNP) & 2019 & European autochthonous pig breeds & [87] \\ Single Nucleotide Polymorphisms (SNP) & 2019 & Chinese autochthonous pig breeds & [9] \\ Single Nucleotide Polymorphisms (SNP) & 2024 & Korean Duroc, Landrace, Yorkshire & [88] \\ \hline \end{tabular}
\end{table} 
Table 1: Molecular markers used in genetic diversity studies of pig breeds. strategies for the preservation of genetic diversity within these autochthonous populations. [PERSON] et al. [75] analyzed microsatellite markers and mitochondrial DNA of autochthonous pig populations in the Himalayan region of India. Their results showed genetic admixture between the analyzed pig populations leading to increased genetic diversity. In the genome, SNPs represent the most common form of genetic variation. They can be directly related to the function of proteins and are found in both coding and non-coding sections of genes. Due to their widespread distribution throughout the genome, they are the most commonly used genetic markers when analyzing genetic diversity.