Animal Molecular Breeding, 2024, Vol.14, No.6, 362-369 http://animalscipublisher.com/index.php/amb 365 Figure 2 Buffalypso animals from a local herd in Trinidad and Tobago (Adopted from Ramlachan, 2023) 4.3 Phylogenetic studies using molecular markers Phylogenetic studies using molecular markers have provided valuable insights into the evolutionary relationships among buffalo populations. A study on a lesser-known buffalo population in Central India used microsatellite markers to reveal genetic diversity and phylogenetic relationships with other well-established breeds, suggesting the need for conservation and improvement programs (Gahlyan et al., 2024). The use of SNP markers in phylogenetic studies has also been highlighted, with a 90K SNP chip distinguishing buffalo from different farms and identifying genomic regions involved in milk production (Iamartino et al., 2017). These studies underscore the importance of molecular markers in understanding the phylogenetic structure and guiding conservation strategies for water buffalo. In summary, genomic studies have revealed significant genetic diversity in water buffalo populations, with population-specific markers playing a crucial role in conservation and breeding programs. Phylogenetic studies using molecular markers have further enhanced our understanding of the evolutionary relationships among buffalo populations, supporting targeted conservation efforts. 5 Case Study: Application of SNP Markers in Water Buffalo Conservation 5.1 Identification and selection of SNP markers for genetic monitoring Single Nucleotide Polymorphisms (SNPs) are crucial molecular markers used in the genetic monitoring of water buffalo populations. The identification and selection of SNP markers involve analyzing genome sequences to detect allele differences among breeds. For instance, a study in Pakistan identified breed-specific SNP markers for the Nili, Nili-Ravi, Azakheli, and Kundi breeds, highlighting the importance of SNPs in maintaining breed diversity and aiding conservation efforts (Anas et al., 2023). Additionally, a 90K SNP genotyping assay was developed for water buffalo, which facilitates the analysis of genetic diversity and supports genomic selection approaches (Iamartino et al., 2017). These SNP markers are essential for monitoring genetic variation and ensuring the sustainable management of buffalo populations. 5.2 Analysis of population bottlenecks and inbreeding trends The analysis of population bottlenecks and inbreeding trends is vital for understanding the genetic health of water buffalo populations. Studies have shown that genetic diversity can be assessed using SNP markers, which help identify inbreeding levels and potential bottlenecks. For example, the use of microsatellite markers in Cuban water buffalo populations revealed positive inbreeding estimates in several loci, indicating a need for careful management to prevent genetic erosion (Uffo et al., 2017). Similarly, the genetic characterization of Pakistani buffalo breeds using microsatellite markers showed low genetic diversity, suggesting historical bottlenecks and the necessity for conservation strategies to mitigate inbreeding (Hussain et al., 2017).
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