Animal Molecular Breeding, 2024, Vol.14, No.6, 362-369 http://animalscipublisher.com/index.php/amb 363 2 Water Buffalo: Biodiversity and Population Structure 2.1 Global distribution and domestication history Water buffaloes (Bubalus bubalis) are primarily distributed across Asia, where they play a significant role in agriculture due to their contributions to milk, meat, and draft power (Mishra et al., 2023). The domestication of buffaloes dates back approximately 3000 to 6000 years, with two main types recognized: the river buffalo, which is more common in India and Pakistan, and the swamp buffalo, found mainly in Southeast Asia (Figure 1) (Rehman et al., 2021). The genetic diversity within these populations is influenced by their domestication history and geographical distribution, which has led to distinct phenotypic and genetic characteristics (Anas et al., 2023). Figure 1 Geographical distribution of buffalo population (Adopted from Rehman et al., 2021) 2.2 Genetic variation across populations Genetic variation in water buffalo populations is crucial for their conservation and breeding. Studies using microsatellite markers have revealed significant genetic diversity within and between populations. For instance, research on Turkish water buffalo populations identified a high level of polymorphism and genetic diversity, indicating the presence of at least two major genetic clusters (Ünal et al., 2021). Similarly, Iranian buffalo populations also exhibit high genetic diversity, with a mean heterozygosity index indicating substantial variation within and between populations (Mahdiyeh et al., 2019). The use of molecular markers such as ISSR and microsatellites has been effective in assessing genetic diversity, which is essential for understanding population structure and planning conservation strategies (Gargani et al., 2010; Aytekin et al., 2011). 2.3 Significance of biodiversity in sustainable breeding Biodiversity in water buffalo populations is vital for sustainable breeding programs. High genetic diversity allows for the selection of traits that improve productivity, disease resistance, and adaptability to environmental changes (Kenchaiwong et al., 2023). For example, the identification of SNP markers in Pakistani buffalo breeds has highlighted the potential for marker-based breeding programs aimed at enhancing milk production and disease resistance (Anas et al., 2023). Moreover, understanding the genetic architecture through whole-genome sequencing can aid in the development of breeding strategies that enhance the resilience and performance of buffalo populations globally (Rehman et al., 2021). Conservation efforts must focus on maintaining genetic diversity to ensure the long-term sustainability and productivity of water buffaloes (Gahlyan et al., 2024). In summary, the global distribution and domestication history of water buffaloes have led to significant genetic variation across populations. This genetic diversity is crucial for sustainable breeding and conservation efforts, ensuring the continued economic and agricultural importance of water buffaloes worldwide. 3 Molecular Markers: Tools for Genetic Analysis 3.1 Overview of molecular marker types Molecular markers are essential tools in genetic analysis, providing insights into genetic diversity, population structure, and evolutionary relationships. Among the most commonly used markers are Simple Sequence Repeats (SSRs), Single Nucleotide Polymorphisms (SNPs), and Amplified Fragment Length Polymorphisms (AFLPs). SSRs, also known as microsatellites, are highly polymorphic and widely used for assessing genetic diversity due
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