Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

SIMPLE SUMMARY: Recent advancements in high-throughput technologies like whole-genome sequencing, genome-wide association study (GWAS), gene expression profiling, next-generation sequencing (RNA and DNA), and genome-wide CHIP-seq scanning are used to detect genetic variants and study gene regulation, gene functioning, and single nucleotide polymorphism (SNP) ordering resources. These techniques offer a wide range of whole-genome data and high coverage to genomic, epigenomic, transcriptomic, and proteomic information related to cellular interactions, functioning, and behavior. In buffaloes, candidate gene studies use the available genetic resources to uncover the functional candidate genes and their interactions associated with buffalo productivity, including production, adaptation, and disease resistance. Thus, the whole-genome and candidate gene approach to next-generation data could help elucidate the inheritance of complex traits, full genomic coverage, and the genetic dissection of productivity-related attributes, which could ultimately help accelerate genetic progress in buffaloes. ABSTRACT: The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.