Comparative Genomics, Evolutionary and Gene Regulatory Regions Analysis of Casein Gene Family in Bubalus bubalis

Abstract

Buffalo is a luxurious genetic resource with multiple utilities (as a dairy, draft, and meat animal) and economic significance in the tropical and subtropical regions of the globe. The excellent potential to survive and perform on marginal resources makes buffalo an important source for nutritious products, particularly milk and meat. This study was aimed to investigate the evolutionary relationship, physiochemical properties, and comparative genomic analysis of the casein gene family (CSN1S1, CSN2, CSN1S2, and CSN3) in river and swamp buffalo. Phylogenetic, gene structure, motif, and conserved domain analysis revealed the evolutionarily conserved nature of the casein genes in buffalo and other closely related species. Results indicated that casein proteins were unstable, hydrophilic, and thermostable, although αs1-CN, β-CN, and κ-CN exhibited acidic properties except for αs2-CN, which behaved slightly basic. Comparative analysis of amino acid sequences revealed greater variation in the river buffalo breeds than the swamp buffalo indicating the possible role of these variations in the regulation of milk traits in buffalo. Furthermore, we identified lower transcription activators STATs and higher repressor site YY1 distribution in swamp buffalo, revealing its association with lower expression of casein genes that might subsequently affect milk production. The role of the main motifs in controlling the expression of casein genes necessitates the need for functional studies to evaluate the effect of these elements on the regulation of casein gene function in buffalo.

Evidence-Based Tracking of MDR E. coli from Bovine Endometritis and Its Elimination by Effective Novel Therapeutics

“…Pattern motifs in the current study were found similar to those reported on different species in literature by using MEME [ 27 , 40 , 41 ]. The present study revealed that the 23S rRNA nucleotides sequence of the local E. coli isolate showed 98% similarity to the nucleotide sequence of the reference E. coli strain (accession number CP067311.1).…”

“…Emerging resistance of the pathogen to chloramphenicol, gentamicin, and oxytetracycline is alarmingly evident [ 49 ]. Gentamicin resistance in E. coli has also been reported by Sabat et al [ 40 ]. Additionally, high chloramphenicol resistance in the E. coli isolates that originated from livestock was reported previously [ 50 ].…”

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 ].…”

Comparative metabolomics analysis of milk components between Italian Mediterranean buffaloes and Chinese Holstein cows based on LC-MS/MS technology

“…Among domestic ruminants, buffalo and cow differ in their milk composition in terms of fat and total solids, especially protein content (4.3% vs 3%) [1][2][3][4]. Italian Mediterranean buffalo (Bubalus bubalis) is an excellent buffalo breed with the highest milk yield (2000-2400 kg in 305 days of milking) [5][6][7][8][9], and relative high fat content (8%-9%) and protein content (4%-5%) (http://www.gxbri.com/index.htm). One of the most famous Italian dairy products "Mozzarella di bufala Campana" is processed from Italian Mediterranean buffalo milk, which is honored by the Protected Designation of Origin (PDO) label since 1996 [10,11].…”