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

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.

Molecular Characterization of TGF-Beta Gene Family in Buffalo to Identify Gene Duplication and Functional Mutations

“…The advancements in high-throughput genome sequencing technologies, typically the next-generation sequence data availability, make it easy to scan the genetic variability of genes, such as SNPs ordering with their functional effect which control a specific phenotypic trait that allow to understand animals’ genetics at molecular level [ 27 , 28 , 29 , 30 , 31 , 32 ]. For farm animals, the candidate gene studies analyze available genetic resources to identify functional genes and their potential association with productivity traits, such as disease resistance, production ability, and adaptation [ 29 ]. In buffaloes, comparative genomics offers an opportunity to explore the genetics of economically important physiological traits though discovering novel genes and their regulatory mechanisms, which significantly contributes to the development of the buffalo industry [ 32 ].…”

Generation of Heritable Prominent Double Muscle Buttock Rabbits via Novel Site Editing of Myostatin Gene Using CRISPR/Cas9 System

“…Humans are entirely reliant on livestock for their daily food supply, which comes in the form of eggs, meat, and milk ( 30 – 33 ). Thus, genetic alteration offers an opportunity for significant production and gains in a short time ( 34 , 35 ).…”

Genomic Identification, Evolution, and Expression Analysis of Bromodomain Genes Family in Buffalo

“…Bioinformatics, combined with next-generation sequencing, can provide high-throughput genomic data. These data can be used to identify the genes for the favorable traits in buffalo, for instance, the systematic analysis of candidate genes for buffalo milk production and fertility traits [ 23 , 24 ], whole-genome sequencing and characterization for selective breeding in buffalo [ 25 ], and characterization of the diacylglycerol acyltransferases gene family, collagen gene family, and heat-shock protein gene family [ 26 , 27 , 28 ]. The above studies, together with a nearly complete genome map of the buffalo [ 29 , 30 , 31 , 32 ], make it possible to study gene families at the genome-wide level in buffalo.…”