Bioscience Evidence 2025, Vol.15, No.6, 291-302 http://bioscipublisher.com/index.php/be 295 With the growth of molecular genetics and genomics, many breeding programs now try to increase production but also avoid losing too much genetic diversity. High-density SNP chips and reference genomes make it possible to track genetic changes, find key alleles, and set up more accurate breeding plans. By using genomic selection together with marker-assisted breeding and inbreeding control, researchers can speed up genetic improvement while still keeping enough diversity in the population. 5 Comparative Genomic Analysis: Wild and Domestic Buffalo Populations 5.1 Key genomic differentiation patterns: allele frequency, heterozygosity, and effective population size Wild water buffaloes are seen as important ancestral gene pools, so they usually show high genetic diversity at the species level. But their population is now very small and highly scattered. Because of this, their heterozygosity keeps dropping, and the runs of homozygosity keep growing. These patterns suggest that they went through strong bottlenecks in the past and also experienced inbreeding. Domestic water buffaloes (both river and marsh types) show a different and more mixed situation. Some of them, like the Italian Mediterranean river buffalo, still keep a fairly high heterozygosity (Ho ≈ 0.46). But others have much lower genetic diversity. This often happens in groups that live in isolated areas or have been under strong human selection pressure for a long time. Factors such as the founder effect, artificial selection, and geographic isolation all play a role in this decline (Pineda et al., 2024; Si et al., 2024; Pauciullo et al., 2025). FST values between wild buffalo, river buffalo, and marsh buffalo around the world show that their genetic differentiation ranges from moderate to high. The gap between river buffaloes and marsh buffaloes is especially large. For wild water buffaloes, their very small population and fragmented habitats mean their effective population size (Ne) is low. With such a small Ne, they are easily affected by genetic drift and may lose some useful adaptive alleles. Domestic buffaloes generally have larger populations, but Ne can still fall in certain breeds, especially those that have been under strong selection or kept in closed breeding systems. For example, some buffalo breeds in Iran show an Ne as low as 32, which suggests that better germplasm management is needed to avoid further loss of genetic diversity. 5.2 Selection signals related to domestication (such as milk production, draft capacity, disease resistance) Strong selective sweeps (selective sweeps) were detected in several gene regions related to milk production in river-type buffaloes, including CSN2 (β -casein) and DGAT1, which have key effects on milk quantity and milk composition (Si et al., 2024; Li et al., 2025; Pauciullo et al., 2025) (Figure 1). Genetic diversity often decreases around these areas, reflecting the long-term and intense artificial breeding of dairy breeds such as Murrah and Italian Mediterranean buffaloes. Similarly, genes related to coat color (such as MC1R), reproductive performance and metabolic pathways also have hard selective sweeping and soft selective sweeping, further promoting the differentiation between domestic buffaloes and wild ancestors (Luo et al., 2020). Marshy buffaloes are mainly selected for draft capacity and environmental adaptability, and their genomes also show selection signals related to muscle development, energy metabolism and stress response (Zhang et al., 2022). Comparative genomic studies have also found that river-type and marshy water buffaloes exhibit convergent selection for traits such as disease resistance and environmental adaptability, and some loci even show parallel evolution with cattle species. 5.3 Evaluation of gene infiltration and Hybridization between wild and domestic water buffaloes Genomic work with SNP chips and whole-genome sequencing shows that gene flow is common in places where the two buffalo ranges meet, or where domestic buffalo enter wild areas (Si et al., 2024; Pauciullo et al., 2025). In countries such as the Philippines and Brazil, researchers have also found gene introgression between river-type and swamp-type buffalo (Pineda et al., 2024). This introgression can add more genetic diversity and bring in useful alleles. But it may also break the genetic identity of wild buffalo. Most of this hybridization comes from human actions. Some crossings are planned to improve breeds, but many others happen by accident because people disturb habitats or change grazing patterns. With high-density SNP tools
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