Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Detection of Polymorphisms in FASN, DGAT1, and PPARGC1A Genes and Their Association with Milk Yield and Composition Traits in River Buffalo of Bangladesh

This study aimed to identify SNPs in the intron, exon, and UTR regions of the FASN, DGAT1, and PPARGC1A genes and to investigate their possible association with milk yield and composition traits in the riverine buffalo of Bangladesh. A total of 150 DNA samples from riverine buffalo were used for PCR amplification with five pairs of primers, followed by association studies using a generalized linear model in R. SNP genotyping was performed by direct sequencing of the respective amplicon. Traits analyzed included DMY, fat%, protein%, and SNF%. This study identified 8 SNPs in FASN (g.7163G>A and g.7271C>T), DGAT1 (g.7809C>T and g.8525C>T) and PPARGC1A (g.387642C>T, g.387758A>G, g.409354A>G, and g.409452G>A). Genotypic and allelic frequencies differed significantly for each SNP genotype and did not follow the Hardy-Weinberg principle (p < 0.01 or p < 0.001) in most cases. The g.7163G>A and g.7271C>T SNP genotypes of the FASN gene were significantly associated with milk fat%, with the latter also significantly associated with SNF%. The g.8525C>T polymorphism of the DGAT1 gene significantly affected protein% (p < 0.01). Additionally, PPARGC1A gene polymorphisms showed significant associations: g.387642C>T with fat% (p < 0.05); g.387758A>G and g.409354A>G with protein% (p < 0.001) and SNF% (p < 0.01); and g.409452G>A with DMY (p < 0.001), fat% (p < 0.05), and protein% (p < 0.01). Reconstructed haplotypes of the PPARGC1A gene were significantly associated (p < 0.01) with all traits except SNF%. These findings suggest that polymorphisms in these three candidate genes have the potential as molecular markers for improving milk yield and composition traits in the riverine buffalo of Bangladesh.

Genetic characterization and diversity assessment in 'Bhangor' indigenous swamp buffalo population using heterologous microsatellite markers

'Bhangor' newly identified swamp buffalo population from North East Indian, was characterized using microsatellite markers. Genomic DNA was isolated from blood samples of 76 unrelated animals, 15 microsatellite markers (CSSM33, BM1818, CSRM60, HEL13, ILSTS019, ILSTS025, ILSTS028, ILSTS029, ILSTS033, ILSTS036, ILSTS056, ILSTS058, ILSTS061, ILSTS089 and ETH003) were found to be highly polymorphic in the population of the selected markers. A total of 114 alleles were observed, which ranged from 3 in CSRM60 and ILSTS025 locus to 12 in ILSTS056 and ILSTS061. The mean effective number of alleles across all polymorphic loci was found to be 3.76. The overall mean expected heterozygosity and unbiased expected heterozygosity values were 0.67 and 0.68, ranging from 0.067 (ILSTS025) to 0.85 (ILSTS058) and 0.068 (ILSTS025) to 0.86 (ILSTS058), respectively. Within the population, the inbreeding estimates (FIS) ranged between -0.4352 and 0.804, with an average FIS of 0.114 ± 0.033. The outcome for infinite allele model (IAM), two-phase model (TPM) and test for mode shift revealed the absence of any recent bottleneck in the investigated buffalo population. The population was found to be in optimum diversity based on polymorphic microsatellite markers. With fast changing agro-climatic conditions; there is an urgent need to characterize the nondescript livestock populations.

ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health

Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the genomic repeat sequences all in one place without the need to switch between other resources. The user-friendly online interface allows users to browse SSRs by genomic coordinates, repeat motif sequence, chromosome, motif type, motif frequency, and functional annotation. Users may enter their preferred flanking area around the repeat to retrieve the nucleotide sequence, they can investigate SSRs present in the genic or the genes between SSRs, they can generate custom primers, and they can also execute in silico validation of primers using electronic PCR. For customized sequences, an SSR prediction pipeline called miSATminer is also built. New species will be added to this website's database on a regular basis throughout time. To improve animal health via genomic selection, we hope that ranchSATdb will be a useful tool for mapping quantitative trait loci (QTLs) and marker-assisted selection. The web-resource is freely accessible at https://bioinfo.usu.edu/ranchSATdb/.

An Analysis of DNA Sequence Polymorphism in the Swamp Buffalo Toll-like Receptor (TLR2) Gene

Toll-like receptors (TLRs) are transmembrane proteins important for directing immune responses. Their primary role is to recognize pathogens based on single-nucleotide polymorphism (SNP) characteristics. TLR2 is categorized as a pattern recognition receptor (PRR) that is important for the recognition of pathogens. Nucleotide variation in the coding region determines the conformation of the TLR protein, affecting its protein domain efficiency. This study aimed to identify SNPs in the coding region of TLR2 to enhance available genetic tools for improving health and production in swamp buffalo. A total of 50 buffaloes were randomly sampled from the northeastern part of Thailand for genomic DNA extraction and sequencing. Nucleotide sequences were aligned and compared with cattle and river buffalo based on the database. The results showed, there were 29 SNP locations in swamp buffalo and 14 different locations in both cattle and buffaloes. Haplotype analysis revealed that 27 haplotypes occurred. Swamp buffalo were identified from 13 SNPs based on biallelic analysis, which found eight synonymous and five nonsynonymous SNPs. Nucleotide diversity (π) was 0.16, indicating genetic diversity. Genetic diversity (haplotype diversity; HD) was high at 0.99 ± 0.04. This indicates a high probability that the two sample haplotypes are different. The π and HD values are important indicators of the genetic diversity of the swamp buffalo population. In summary, the Thai swamp buffalo population detected a polymorphism of the coding region of the TRL2 gene. Therefore, further, in-depth study of the relationship between these genes in the immune system and disease resistance should be recommended.

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

Water buffalo (Bubalus bubalis), belonging to the Bovidae family, is an economically important animal as it is the major source of milk, meat, and drought in numerous countries. It is mainly distributed in tropical and subtropical regions with a global population of approximately 202 million. The advent of low cost and rapid sequencing technologies has opened a new vista for global buffalo researchers. In this study, we utilized the genomic data of five commercially important buffalo breeds, distributed globally, namely, Mediterranean, Egyptian, Bangladesh, Jaffrarabadi, and Murrah. Since there is no whole-genome sequence analysis of these five distinct buffalo breeds, which represent a highly diverse ecosystem, we made an attempt for the same. We report the first comprehensive, holistic, and user-friendly web genomic resource of buffalo (BuffGR) accessible at http://backlin.cabgrid.res.in/buffgr/, that catalogues 6028881 SNPs and 613403 InDels extracted from a set of 31 buffalo tissues. We found a total of 7727122 SNPs and 634124 InDels distributed in four breeds of buffalo (Murrah, Bangladesh, Jaffarabadi, and Egyptian) with reference to the Mediterranean breed. It also houses 4504691 SSR markers from all the breeds along with 1458 unique circRNAs, 37712 lncRNAs, and 938 miRNAs. This comprehensive web resource can be widely used by buffalo researchers across the globe for use of markers in marker trait association, genetic diversity among the different breeds of buffalo, use of ncRNAs as regulatory molecules, post-transcriptional regulations, and role in various diseases/stresses. These SNPs and InDelscan also be used as biomarkers to address adulteration and traceability. This resource can also be useful in buffalo improvement programs and disease/breed management.

Effect of Packaging Type and Aging on the Meat Quality Characteristics of Water Buffalo Bulls

Simple Summary

The water buffalo is found worldwide, but mainly in Asian countries, i.e., India, Pakistan, and China. Buffalo meat can be a viable option to fulfill the future protein demands of the world’s population. Presently, very little information is available regarding buffalo meat quality attributes under different packaging types. Therefore, this study was designed to evaluate the effect of packaging type and aging time on the meat quality characteristics (instrumental color, WBSF, cooking loss, thiobarbituric acid reactive substances (TBARS), and total volatile basic nitrogen (TVB-N) of longissimus lumborum steaks. The results showed that vacuum packaging and aging were the most effective in decreasing the WBSF values of buffalo meat.

Abstract

The present study determined the effect of the packaging type and aging time on the meat quality of water buffalo (Bubalus bubalis) bulls. A total of n = 36 longissimus lumborum (LL) muscles from n = 18 buffalo bulls were obtained. Half LL muscles were packed in modified atmosphere packaging (Hi-O₂ MAP), vacuum packaging (VP), and oxygen-permeable packaging (OP) on day 1, while the other half were aged for 7 days. Meat instrumental color, cooking loss, Warner–Bratzler shear force (WBSF), thiobarbituric acid reactive substances (TBARS), and total volatile basic nitrogen (TVB-N) of the LL steaks were analyzed, both on unaged and aged buffalo meat. Color CIE L* and C* values on all display days and a* on the first 4 days of the simulated retail display under Hi-O₂ MAP packaging were significantly higher than those of the VP and OP. WBSF and TBARS values were also higher under Hi-O₂ MAP as compared to the other packaging. Steaks under OP exhibited lower cooking loss but higher TVB-N values than the MAP and VP. The 7-day-aged buffalo meat indicated higher instrumental color (L*, a* and C*), cooking loss, and lower WBSF values than fresh meat. This study concluded that Hi-O₂ MAP improved the color; however, it negatively influenced the buffalo meat’s WBSF and TBAR values. Furthermore, VP and aging were the most effective in decreasing the WBSF values of buffalo meat.