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.

Keywords: buffalo; candidate genes; evolution and domestication; genome sequencing advancement; traits.

Figure 1

Geographical distribution of buffalo population [4].

Figure 2

Cytogenetics of buffaloes (river and swamp) and cattle (Bos taurus). (A) Synteny analysis of buffaloes (river and swamp) and cattle. The cattle chromosomes are presented in red, river buffalo chromosomes in blue, and swamp buffalo chromosomes in pink and centromeres in red dots [21]. (B,C) The similar banding pattern of different chromosomes of buffaloes and cattle [20].

Figure 3

A proposed pattern of riverian and swamp buffalo migration. The dashed arrow points to an initial and independent migration way that might have led river buffaloes into Europe [45] (figure reproduced by Rehman et al., 2021, with the permission of authors).

Figure 4

Phylogenies based on mitogenome and Y-chromosome. The pairwise differences between the adjoining haplotypes are represented by the widths of the edges. (a) The network of Y-chromosome using 520 SNPs. (b) Swamp buffalo mitogenome network. Diverse haplogroups of mitogenomes and Y-chromosomes are characterized in each gray box [47] (figure reproduced by Rehman et al., 2021, with the permission of authors).