Breed traceability of buffalo meat using microsatellite genotyping technique

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.

Comparative characteristics of the genetic structure of the Syrian cattle breed compared to Holstein and Aberdeen-Angus breeds

OBJECTIVES

The objective of this study was to perform a comparative analysis of allelic diversity to reveal population-genetic characteristics of animal breeds, namely Shami (SH), Holstein (HLS), and Aberdeen-Angus (A-A).

MATERIALS AND METHODS

The genetic materials of SH breed animals represented by wool with hair follicles were collected from 39 SH heads in Syria. Also, genetic materials of HLS breed of American selection (n = 55, HLS) and bulls and cows of A-A breed bred at breeding enterprises in Russia (n = 30, A-A) were collected. Genetic differences between the cattle groups were studied using 11 microsatellite markers.

RESULTS

The cattle breed in Syria was characterized by high genetic diversity, 107 alleles, while the average number of alleles per microsatellite locus was 9.23, which is significantly higher than that in the animals of HLS (6.18) and A-A (5.00). When analyzing the genetic equilibrium for individual locus in SH breed, a deviation from equilibrium at four loci was revealed: TGLA227, SPS115, TGLA122, and ETH225; at one locus in HLS breed: SPS115, for A-A breed: at two loci, i.e., TGLA122 and ETH225. When assessing the level of genetic consolidation, a deficiency of heterozygotes was observed in two of the three studied breeds: 4.8% for SH and 8.0% for A-A. A slight excess of heterozygotes was found in the HLS breed at the level of 0.2%. The average comparative measurement of genetic variation in different populations value for 11 loci for all breeds was 0.069, which indicates that 93.1% of the total variability is due to the intra-breed diversity, and only 6.9% is due to the differences between breeds.

CONCLUSION

The analysis of the animals belonging to their breed has shown a 100% genetic consolidation and the compliance of individual animals with the respective breeds. The study of genetic distances, adjusted for small samples, revealed the smallest genetic distance between the SH breed and HLS breed, equaling 0.107. The A-A breed, which has its separate origin and has never been imported into the Syrian Arab Republic, adjoins this cluster as an independent branch. Microsatellites can be used as an essential criterion for assessing the population-genetic characteristics of groups of cattle of various breeds (degree of polymorphism, level of heterozygosity, fixation indices, genetic group membership).

Artificial intelligence based muzzle recognition technology for individual identification of animals

India is witnessing raising interest in animal identification and traceability in recent years. Identification and tagging of productive bovines across India with the internationally accepted 12 digit unique animal identification number using bar coded ear tags under the national program of Department of Animal Husbandry and Dairying, Government of India has brought about visible change in the mindset of the stakeholders. Country is realizing the benefits of the system and steadily embracing it. But the animal identification verification system is lacking in the country and this gap can be filled by the artificial intelligence based muzzle identification technique reported in this work. Field test indicated 98% successful identification of all accepted images and 100% successful identification of all test animals. None of the images were cross assigned to any other individual. Mobile based operations without requirement of any consumables and laboratory test makes the technique field-friendly. System can be handy to agencies involved in animal identification and traceability in India and abroad.