Bioscience Evidence 2025, Vol.15, No.6, 291-302 http://bioscipublisher.com/index.php/be 299 males again and again. We can also bring in local breeds that are not used much. Using molecular markers, such as SNPs and microsatellites, can help us check genetic diversity. These tools also help us find rare alleles that need protection (Smith et al., 2020). Improving crossbreeding plans can increase heterosis. It can also bring good traits from different breeds or groups into the target population. But crossbreeding needs careful control. If not, we may lose important adaptive genes in local breeds. Genomic selection uses high-throughput genotyping and whole-genome data. It can speed up genetic progress. At the same time, it can help keep and monitor genetic diversity (Jones et al., 2021). 7.4 Potential application of genetic resources of wild water buffaloes in domestic improvement The unique alleles and adaptive characteristics contained in wild water buffaloes (such as disease resistance, environmental tolerance, and strong reproductive capacity, etc.) have greater application value in the context of climate change and the intensification of disease challenges. Through carefully designed genetic infiltration schemes, wild genetic variations can be reasonably introduced into domesticated populations to counteract genetic erosion or inbreeding effects caused by high-intensity selection (Zhong et al., 2020; Kherwar and Bhattarai, 2021; Rehman et al., 2021; Si et al., 2024). To effectively utilize wild genetic resources, it is necessary to carry out systematic molecular research to identify and characterize the genetic differences between wild and domestic water buffaloes. Establishing DNA sample banks, genomic reference libraries and genotype databases will help screen candidate genes and alleles for the genetic infiltration of target traits. 8 The Future Direction of Genetic Diversity Research on Water Buffaloes 8.1 The need to conduct large-scale whole-genome resequencing for all buffalo lineages Large-scale whole-genome resequencing of domestic water buffaloes of river and marsh types and their wild relatives is necessary for fully capturing their genetic diversity, identifying rare alleles and finely analyzing population structure (Rafiepour et al., 2020; Rehman et al., 2021; Arshad et al., 2025). Some resequencing studies involving multiple varieties and tens to hundreds of individuals have identified millions of single nucleotide variations and revealed the differentiation patterns among varieties, but these results still represent only a small part of global genetic diversity (Luo et al., 2020; Bian et al., 2024; Si et al., 2024). High-resolution genomic data can precisely locate genomic regions related to local environmental adaptation, disease resistance and production traits. 8.2 Develop high-density SNP chips for buffalo populations Although some SNP chips for cattle have been used in water buffaloes at present, their applicability is limited due to the low polymorphism level and the existence of many information-free loci in the water buffalo genome. The development of buffaloe-specific SNP chips (such as the 90K SNP chip) has demonstrated higher resolution in population structure analysis, trait mapping and genomic selection, but further optimization is still needed to cover the genetic diversity of more species and subspecies (Khan et al., 2022). Chip customization based on the genetic structure of river type, marsh type and their hybrid water buffaloes will achieve more accurate genotyping, enhance the ability to conduct GWAS on complex traits, and support the implementation of genomic selection breeding. High-density SNP arrays can also detect homozygous blocks, linkage disequilibrium patterns and selection imprints more effectively. 8.3 The integration of phenotypic, ecological and genomic data is used for the discovery of adaptive traits By integrating GWAS with environmental association analysis, transcriptome analysis and other methods, researchers can identify candidate genes and regulatory networks that affect milk production capacity, disease resistance, growth rate and environmental adaptability (Mishra et al., 2023; Dai et al., 2025; Shen et al., 2025). Establishing a large-scale and standardized phenotypic database, combined with high-precision environmental data, will help to analyze genotype-environmental interactions and identify the key gene loci that enable water buffaloes to maintain resilience under climate change and various environmental pressures.
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