Animal Molecular Breeding, 2024, Vol.14, No.6, 362-369 http://animalscipublisher.com/index.php/amb 364 to their abundance and variability in the genome (Uffo et al., 2017; Singh et al., 2018; Ünal et al., 2021). SNPs are single base-pair variations in the DNA sequence and are valuable for high-resolution mapping and genomic selection, offering insights into breed-specific traits and genetic characterization (Mishra et al., 2020; Anas et al., 2023). AFLPs, although less frequently used in buffalo studies, provide a broad genome coverage and are useful for detecting genetic variation without prior sequence information (Aytekin et al., 2011). 3.2 Advantages and limitations of molecular markers in buffalo studies Molecular markers offer several advantages in buffalo genetic studies. SSRs are favored for their high polymorphism and ease of use with PCR, making them ideal for genetic diversity and population structure analysis (Singh et al., 2018; Ünal et al., 2021). SNPs provide high-throughput and precise genetic information, which is crucial for genomic selection and understanding breed-specific traits (Mishra et al., 2020; Anas et al., 2023). However, each marker type has limitations. SSRs require prior knowledge of the genome and can be labor-intensive to develop. SNPs, while informative, require extensive sequencing efforts and bioinformatics resources for analysis. AFLPs, although useful for initial diversity assessments, may lack the resolution needed for detailed genetic studies (Aytekin et al., 2011). 3.3 Role of next-generation sequencing in marker discovery Next-generation sequencing (NGS) technologies have revolutionized the discovery and application of molecular markers in buffalo genetics. NGS allows for the rapid and comprehensive identification of SNPs across the genome, facilitating detailed genetic mapping and trait association studies. Techniques such as ddRAD sequencing enable the discovery of trait-specific SNPs, enhancing the understanding of genetic traits like milk production and disease resistance (Mishra et al., 2020). NGS also supports the development of high-density SNP arrays, which are instrumental in genomic selection and conservation strategies (Anas et al., 2023). The integration of NGS in buffalo studies accelerates marker discovery and enhances the precision of genetic analyses, supporting both conservation and breeding programs. In summary, molecular markers such as SSRs and SNPs are invaluable in buffalo genetic studies, each offering unique advantages and facing specific limitations. The advent of NGS has significantly enhanced marker discovery, providing detailed insights into genetic diversity and aiding in the development of effective conservation and breeding strategies (Ramlachan, 2023; Gahlyan et al., 2024). 4 Insights into Genetic Variation in Water Buffalo 4.1 Genomic studies and key findings on genetic diversity Genomic studies on water buffalo have utilized various molecular markers to assess genetic diversity. For instance, a study on Turkish water buffalo populations using 20 microsatellite markers revealed significant genetic diversity, identifying at least two major genetic clusters among the populations (Ünal et al., 2021). Similarly, research on Cuban water buffalo using 30 microsatellite markers highlighted the genetic variability within the population, which is crucial for conservation and breeding strategies (Uffo et al., 2017). In Pakistan, genomic characterization of buffalo breeds identified numerous breed-specific single-nucleotide polymorphisms (SNPs), emphasizing the need for conservation programs for distinct breeds like the Nili (Anas et al., 2023). Additionally, a 90K SNP genotyping assay developed for water buffalo has been instrumental in exploring genetic diversity and aiding in genetic selection (Mishra et al., 2020). 4.2 Population-specific markers and their applications Population-specific markers have been identified in various studies, providing insights into the genetic makeup of different buffalo populations. In Pakistan, SNP markers specific to breeds such as Nili, Nili-Ravi, Azakheli, and Kundi were identified, which can be used for breed characterization and conservation efforts (Anas et al., 2023). In Trinidad and Tobago, microsatellite markers were used to genetically characterize the Buffalypso population, aiding in the establishment of conservation genetics programs (Figure 2) (Ramlachan, 2023). The use of heterologous microsatellite markers has also been effective in assessing genetic variability in buffalo species, supporting conservation and genetic improvement programs (Singh et al., 2018).
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