Maternal genetic diversity and phylogenetic analysis of Indian riverine and swamp buffaloes: insights from complete mitochondrial genomes.

This study explored the genetic diversity and evolutionary history of riverine and swamp buffaloes in India, utilizing complete mitochondrial genome sequences. Through comprehensive sampling across varied agro-climatic zones, including 91 riverine buffaloes from 12 breeds and 6 non-descript populations, along with 16 swamp buffaloes of the Luit breed, this study employed next-generation sequencing techniques to map the mitogenomic landscape of these subspecies. Sequence alignments were performed with the buffalo mitochondrial reference genome to identify mitochondrial DNA (mtDNA) variations and distinct maternal haplogroups among Indian buffaloes. The results uncovered the existence of 212 variable sites in riverine buffaloes, yielding 67 haplotypes with high haplotype diversity (0.991), and in swamp buffaloes, 194 variable sites resulting in 12 haplotypes, displaying haplotype diversity of 0.950. Phylogenetic analyses elucidated the genetic relationships between Indian buffaloes and the recognized global haplogroups, categorizing Indian swamp buffaloes predominantly into the SA haplogroup. Intriguingly, the haplogroup SB2b was observed for the first time in swamp buffaloes. Conversely, riverine buffaloes conformed to established sub-haplogroups RB1, RB2, and RB3, underscoring the notion of Northwestern India as a pivotal domestication site for riverine buffaloes. The study supports the hypothesis of independent domestication events for riverine and swamp buffaloes, highlighting the critical role of genetic analysis in unraveling the complex evolutionary pathways of domestic animals. This investigation contributes to the global understanding of buffalo mitogenome diversity, offering insights into this important livestock species' domestication and dispersal patterns.

Skeletal muscle transcriptomics of sheep acclimated to cold desert and tropical regions identifies genes and pathways accentuating their diversity.

The current study attempts to investigate the differences in gene expression in longissimus thoracis muscles between sheep breeds acclimated to diverse environments. Changthangi sheep inhabits the cold arid plateau of Ladakh, at an altitude above 3000 m with prevalence of rarefied atmosphere. Muzzafarnagri sheep, on the other hand is found in the sub-tropical hot and humid plains at an altitude of about 250 m. Comparative transcriptomics was used to provide a molecular perspective of the differential adaptation of the two breeds. RNA sequencing data was generated from four biological replicates of the longissimus thoracis muscles from both breeds. The common genes expressed in both breeds were involved in muscle contraction and muscle fibre organization. The most significant pathways enriched in Changthangi muscles were glycogen metabolism, reduction of cytosolic Ca++ levels and NFE2L2 regulating anti-oxidant, while those in Muzzafarnagri were extracellular matrix organization and collagen formation. The hub genes identified in Changthangi were involved in hematopoiesis and HIF signaling pathway, suggesting the molecular acclimatization of Changthangi to the high altitude cold desert of Ladakh. The nodal genes discovered in Muzzafarnagri sheep were associated with the extracellular matrix which accentuates its significance in the development, growth and repair of muscles. The observed transcriptomic differences underscore the morphological and adaptive disparity between the two breeds. The candidate genes and pathways identified in this study will form the basis for future research on adaptation to high altitude and body size in small ruminants.

Development and validation of the Axiom-MaruPri SNP chip for genetic analyses of domesticated old world camelids.

Camels play a crucial socio-economic role in sustaining the livelihoods of millions in arid and semi-arid regions. They possess remarkable physiological attributes which enable them to thrive in extreme environments, and provide a source of meat, milk and transportation. With their unique traits, camels embody an irreplaceable source of untapped genomic knowledge. This study introduces Axiom-MaruPri, a medium-density SNP chip meticulously designed and validated for both Camelus bactrianus and Camelus dromedarius. Comprising of 182,122 SNP markers, derived from the re-sequenced data of nine Indian dromedary breeds and the double-humped Bactrian camel, this SNP chip offers 34,894 markers that display polymorphism in both species. It achieves an estimated inter-marker distance of 14 Kb, significantly enhancing the coverage of the camel genome. The medium-density chip has been successfully genotyped using 480 camel samples, achieving an impressive 99 % call rate, with 96 % of the 182,122 SNPs being highly reliable for genotyping. Phylogenetic analysis and Discriminant Analysis of Principal Components yield clear distinctions between Bactrian camels and dromedaries. Moreover, the discriminant functions substantially enhance the classification of dromedary camels into different breeds. The clustering of various camel breeds reveals an apparent correlation between geographical and genetic distances. The results affirm the efficacy of this SNP array, demonstrating high genotyping precision and clear differentiation between Bactrian and dromedary camels. With an enhanced genome coverage, accuracy and economic efficiency the Axiom_MaruPri SNP chip is poised to advance genomic breeding research in camels. It holds the potential to serve as an invaluable genetic resource for investigating population structure, genome-wide association studies and implementing genomic selection in domesticated camelid species.

Molecular insights into Pashmina fiber production: comparative skin transcriptomic analysis of Changthangi goats and sheep.

Ladakh, one of the highest inhabited regions globally, hosts the unique Changthangi goat, renowned for producing Pashmina, the world's most luxurious natural fiber. In comparison, the fiber derived from Changthangi sheep is considered next only to Pashmina. This research endeavors to compare the skin transcriptome profiles of Changthangi goats and Changthangi sheep, aiming to discern the molecular determinants behind the recognition of Changthangi goats as the source of Pashmina. Drawing upon previously conducted studies, a collective of 225 genes correlated with fiber characteristics were extracted from the differentially expressed genes noticed between the two species (p-value of ≤ 0.05 and a log2 fold change of ≥ 1.5). These genes were analyzed using DAVID software to understand their biological functions and to identify enriched KEGG and Reactome pathways. The protein-protein interaction networks were constructed using Cytoscape, cytoHubba, and STRING to focus on key genes and infer their biological significance. Comparative transcriptome analysis revealed significantly higher expression of genes involved in signaling pathways like Wnt, MAPK, PI3K-Akt, Hedgehog, associated with fiber development and quality in Changthangi goats. These pathways play crucial roles in hair follicle (HF) formation, maintenance of epidermal stem cells, and fiber characteristics. Findings also highlight the enrichment of cell adhesion molecules and ECM-receptor interaction, emphasizing their roles in HF structure, growth, and signaling. This investigation offers an in-depth understanding of the molecular intricacies governing Pashmina production in Changthangi goats, providing valuable insights into their unique genetic makeup and underlying mechanisms influencing the exceptional quality of Pashmina fibers.

Comprehensive evaluation and validation of optimal reference genes for normalization of qPCR data in different caprine tissues.

BACKGROUND: Quantitative real-time PCR (qPCR) is a highly reliable method for validating gene expression data in molecular studies due to its sensitivity, specificity, and efficiency. To ensure accurate qPCR results, it's essential to normalize the expression data using stable reference genes. METHODS: This study aimed to identify suitable reference genes for qPCR studies in goats by evaluating 18 candidate reference genes (ACTB, BACH1, B2M, GAPDH, HMBS, HPRT1, PGK1, PPIA, PPIB, RPLP0, RPL19, RPS9, RPS15, RPS28, SDHA, TBP, UXT, and YWHAZ) in 10 different caprine tissues (heart, intestine, kidney, liver, lung, muscle, rumen, skin, spleen, and testis). An integrated tool called RefFinder, which incorporates various algorithms like NormFinder, GeNorm, BestKeeper, and ΔCt, was used to assess the stability of expression among these genes. RESULTS: After thorough analysis, ACTB, PPIB, and B2M emerged as the most stable reference genes, while RPL19, RPS15, and RPS9 were found to be the least stable. The suitability of the selected internal control genes was further validated through target gene analysis, confirming their efficacy in ensuring accurate gene expression profiling in goats. CONCLUSION: The study determined that the geometric average of ACTB, PPIB, and B2M creates an appropriate normalization factor for gene expression studies in goat tissues.

Comparative manual and digital analysis of gonial angle in lateral cephalograms for gender determination.

Human skull has always been used for victim identification in forensic odontology. The gender-dimorphic bone of the skull is the mandible. The gonial angle has frequently been investigated for gender estimation with variable results and requires further exploration. We aim to compare the efficacy of gonial angle estimation by ancient methods of lateral cephalometric tracing compared with more recent digital analysis methods for gender estimation in the Indian population. Lateral cephalograms of 191 (96 M and 95F) cases above the age of 17 years were retrieved. Cephalometric analysis of gonial angle on radiographs was done using both manual cephalometric tracing method and digitally using Adobe Photoshop software. The results were subjected to statistical analysis for evaluation. The mean gonial angle was higher in females (125.05; 123.77 and 125.28) than in males (122.583; 121.715 and 122.008) using both manual and digital methods. On applying the logistical regression analysis (LRA), the digital method showed the highest gender estimation accuracy of 60.7% followed by Burstone's analysis (57.1%) and manual conventional analysis (56.5%). Burstone's analysis (57.9%) correctly identified increased females, whereas digital analysis (62.5%) and manual conventional analysis (59.4%) accurately recognised increased males. The present study showed a higher gender estimation accuracy using digital methods as compared to manual methods, but it still lacks the credibility to be used as a sole factor for predicting the gender of an individual. Hence, a cumulative factor must be taken into consideration for gender identification which would provide more promising results.

Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India.

The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.

Identification and validation of stable reference genes for expression profiling of target genes in diverse ovine tissues.

Quantitative PCR (qPCR) is a widely-used technique for quantifying the expression of target genes across various tissues, as well as under different pathological and physiological conditions. One of the challenges associated with this method is the need to identify optimal reference genes (RGs) that maintain consistent expression levels under diverse experimental settings, thereby ensuring accurate biological interpretation. In this study, we conducted a thorough analysis of 18 candidate RGs (ACTB, BACH1, B2M, GAPDH, HMBS, HPRT1, PGK1, PPIA, PPIB, RPLP0, RPL19, RPS9, RPS15, RPS28, SDHA, TBP, UXT, and YWHAZ) across 10 ovine tissues (muscle, skin, kidney, liver, intestine, rumen, lung, testis, heart, and spleen) obtained from five individual sheep. We aimed to identify genes with stable expression across these tissues. A literature-based survey helped us shortlist candidate genes representing various functional classes from multiple livestock species. We employed four algorithms: geNorm, NormFinder, BestKeeper, and Delta Ct (ΔCt), to rank these genes based on their stability. A consistent trend in the rankings was observed across these different algorithms. RefFinder was then used for a comprehensive ranking, integrating the outputs from the various methods. ACTB, PPIB, BACH1, and B2M emerged as the most stable RGs, while RPS9, RPS15, and PGK1 displayed variable expression. We validated our findings through qPCR analysis of four target genes (ACTN2, CRYAB, DLK1, and TRIM54) in the skin samples from two different sheep breeds. Based on these results, we recommend ACTB, PPIB, BACH1, and B2M as reliable internal control genes for qPCR experiments involving diverse ovine tissues.

Effect of Submucosal Injection of Platelet-rich Plasma on the Rate of Canine Retraction - A Split-mouth Randomized Clinical Study.

Introduction: The use of platelet-rich plasma (PRP) has gained popularity in orthodontics in the past decade. PRP is an autologous concentration of platelets rich in growth factors and is hypothesized to play a role in orthodontic tooth movement (OTM) due to its bone remodeling capacity. Objective: The aim of this study was to determine the effect of PRP on the rate of tooth movement in humans. Materials and Methods: Fourteen patients requiring bilateral extraction of upper first premolars were included in the study. PRP (×4) was prepared and injected in the alveolar mucosa, distal to canine on experimental sides. Canine retraction was initiated on the same day of PRP injection using NiTi closed coil springs on both sides. The amount of canine retraction was measured and compared between both sides at the 4th, 8th, 12th, and 16th weeks by measuring the distance between lateral incisor and canine on the cast. Results: Results showed mean displacement of 1.355 mm, 1.232 mm, 1.191 mm, and 1.085 mm on experimental side and 1.265 mm, 1.126 mm, 1.031 mm, and 0.879 mm on control side at the 4th, 8th, 12th, and 16th weeks, respectively. Although increased OTM (13.85% or 1.1 times faster) was observed on experimental side at all time intervals compared to the control group, the result was not statistically significant. Conclusion: 4× concentration of PRP does not accelerate OTM significantly.

Tracing the genetic footprints: India's role as a gateway for pig migration and domestication across continents.

This study explored the maternal genetic diversity in the pig genetic resources of India by analyzing a mitochondrial D-loop fragment and comparing it with the corresponding sequences of previously published studies involving domestic pigs and wild boars. Sequencing of 103 samples representing different domestic pig populations revealed existence of 32 maternal haplotypes. The indices of haplotype and nucleotide diversity in Indian domestic pigs were 0.9421 and 0.015, respectively. Median-Joining network revealed that Indian pigs belong to Clade A and show conformity to 6 haplogroups reported worldwide (D1a, D1a1, D1a2, D1e, D1h and D3a). Among these, D1e and D1a2 were shared with Asian wild boars too. Interestingly, haplotype sharing was evident between Indian pigs and samples from other countries representing Africa, Asia, Europe and Oceania. This study substantiates India's contribution as a possible pig domestication center and highlights the importance of the Indian subcontinent in dispersal of the species to other continents. Additionally, genetic evidence suggested the influence of trading routes and historical interactions in shaping pig genetic exchange. Overall, this investigation provides valuable insights into the genetic diversity, historical migration, and domestication of Indian domestic pigs, contributing to the broader understanding of global pig genetic resources and their evolutionary history.

Transcriptomics reveals key genes responsible for functional diversity in pectoralis major muscles of native black Kadaknath and broiler chicken.

RNA sequencing-based expression profiles from pectoralis major muscles of black meat (Kadaknath) and white meat (broiler) chicken were compared to identify differentially expressed genes. A total of 156 genes with log2 fold change ≥ ± 2.0 showed higher expression in Kadaknath and 68 genes were expressed at a lower level in comparison to broiler. Significantly enriched biological functions of up-regulated genes in Kadaknath were skeletal muscle cell differentiation, regulation of response to reactive oxygen, positive regulation of fat cell differentiation and melanosome. Significant ontology terms up-regulated in broiler included DNA replication origin binding, G-protein coupled receptor signaling pathway and chemokine activity. Highly inter-connected differentially expressed genes in Kadaknath (ATFs, C/EPDs) were observed to be important regulators of cellular adaptive functions, while in broiler, the hub genes were involved in cell cycle progression and DNA replication. The study is an attempt to get an insight into the transcript diversity of pectoralis major muscles of Kadaknath and broiler chicken. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03682-0.

Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys.

To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.

Functional Quality Characteristics of the Meat from a Dual-Purpose Poultry Crossbreed Suitable for Backyard Rearing in Comparison to Commercial Broilers.

Backyard poultry farming contributes to food security, nutrition, and the regular income of rural farmers in India. Their products have a niche market here and fetch higher prices than those of commercial poultry. Improved varieties are being developed to overcome the slow growth, late sexual maturity, and low production of indigenous breeds, while retaining their positive attributes. A comprehensive study was conducted to analyze the functional attributes of meat from the Jabalpur color (JBC), a colored, improved dual-purpose synthetic line, developed by Nanaji Deshmukh Veterinary Science University, Jabalpur, India. The birds were managed in a deep litter system under a backyard type of housing (night shelter and free range). Primal meat cuts (breast and thigh) of the male birds (n = 20/group) were evaluated at the age of marketing. The corresponding attributes were compared with the results obtained for commercial Cobb (400) broilers. The protein concentration of JBC breast (25.65 ± 0.39 g/100 g of tissue) and thigh (19.04 ± 0.23 g/100 g of tissue) meat was superior (p ≤ 0.05) to that of Cobb broilers. Established assays (in vitro) identified a better (p ≤ 0.05) antioxidation capacity in the JBC meat. High-performance liquid chromatography confirmed a considerable quantity of functional biomolecules (carnosine, anserine, and creatine) in the JBC breast and thigh meat extracts. The average carnosine concentration (mg/g of tissue) was 2.66 ± 0.09 and 1.11 ± 0.04 in the JBC breast and thigh meat, respectively. The mRNA expression was quantified by qRT-PCR for the carnosine-related genes: ß-alanine transporter (SLC36A1), carnosine-synthesizing enzyme (CARNS1), and carnosine-degrading enzyme (CNDP2); this explained the comparable carnosine in the JBC and Cobb meat. Meat extracts from both genetic groups (JBC and Cobb) had high anti-glycation potential. Higher protein content and antioxidant capacity, along with the bioactive dipeptides in the JBC meat, herald exciting research opportunities for its use in improving the traditional backyard poultry farming system.

Ecofriendly fabrication of cobalt nanoparticles using Azadirachta indica (neem) for effective inhibition of Candida-like fungal infection in medicated nano-coated textile.

This study involves the formulation of cobalt nanoparticles by means of ethanolic Azadirachta indica (neem) extract (CoNP@N). Later, the formulated buildup was incorporated into cotton fabric in order to mitigate antifungal infection. Optimization of the formulation was carried out by considering the effect of plant concentration, temperature, and revolutions per minute (rpm) used, through design of the experiment (DOE), response surface methodology (RSM), and ANOVA of the synthetic procedure. Hence, graph was potted with the aid of effecting parameters and the related factors (size of particle and zeta potential). Further characterization of nanoparticles was performed through scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Attenuated total reflection-Fourier transform infrared (ATR-FTIR) was considered for the detection of functional groups. The structural property of CoNP@N was calculated with the aid of powder X-ray diffraction (PXRD). The surface property was measured with the use of a surface area analyzer (SAA). The values of Inhibition concentration (IC50) and zone of inhibition (ZOI), were calculated, so as to determine the antifungal property against both the strains (Candida albicans, MTCC 227and Aspergillus niger, MTCC 8652). The further nano-coated cloth was subjected to a durability test, and hence the cloth was washed (through the purpose of time 0; 10; 25; and 50 washing cycles), and then its anti-fungal operation to a couple of strains was retained. Primarily, 51 µg/ml of cobalt nanoparticles incorporated on the cloth was retained but after 50 washing cycles in 500 ml of purified water, the cloth showed more efficiency contrary to C. albicans than towards A. niger.

Revelation of genes associated with energy generating metabolic pathways in the fighter type Aseel chicken of India through skeletal muscle transcriptome sequencing.

In this study, comparative analysis of skeletal muscle transcriptome was carried out for four biological replicates of Aseel, a fighter type breed and Punjab Brown, a meat type breed of India. The profusely expressed genes in both breeds were related to muscle contraction and motor activity. Differential expression analysis identified 961 up-regulated and 979 down-regulated genes in Aseel at a threshold of log2 fold change ≥ ±2.0 (padj<0.05). Significantly enriched KEGG pathways in Aseel included metabolic pathways and oxidative phosphorylation, with higher expression of genes associated with fatty acid beta-oxidation, formation of ATP by chemiosmotic coupling, response to oxidative stress, and muscle contraction. The highly connected hub genes identified through gene network analysis in the Aseel gamecocks were HNF4A, APOA2, APOB, APOC3, AMBP, and ACOT13, which are primarily associated with energy generating metabolic pathways. The up-regulated genes in Punjab Brown chicken were found to be related to muscle growth and differentiation. There was enrichment of pathways such as focal adhesion, insulin signaling pathway and ECM receptor interaction in these birds. The results presented in this study help to improve our understanding of the molecular mechanisms associated with fighting ability and muscle growth in Aseel and Punjab Brown chicken, respectively.

Unraveling the genetic mechanisms governing the host response to bovine anaplasmosis.

Bovine anaplasmosis caused by Anaplasma marginale is a tick-borne disease of livestock with widespread prevalence and huge economic implications. In order to get new insights into modulation of host gene expression in response to natural infections of anaplasmosis, this study is the first attempt that compared the transcriptome profiles of peripheral blood mononuclear cells (PBMCs) of A. marginale infected and healthy crossbred cattle. Transcriptome analysis identified shared as well as unique functional pathways in the two groups. Translation and structural constituent of ribosome were the important terms for the genes abundantly expressed in the infected as well as healthy animals. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes revealed that immunity and signal transduction related terms were enriched for the up-regulated genes in the infected animals. The over-represented pathways were cytokine-cytokine receptor interaction and signaling pathways involving chemokines, Interleukin 17 (IL17), Tumour Necrosis Factor (TNF), Nuclear Factor Kappa B (NFKB) etc. Interestingly, many genes previously associated with parasite-borne diseases such as amoebiasis, trypanosomiasis, toxoplasmosis, and leishmaniasis were profusely expressed in the dataset of the diseased animals. High expression was also evident for the genes for acute phase response proteins, anti-microbial peptides and many inflammatory cytokines. Role of cytokines in mediating communication between immune cells was the most conspicuous gene network identified through the Ingenuity Pathway Analysis. This study provides comprehensive information about the crosstalk of genes involved in host defense as well as parasite persistence in the host upon infection with A. marginale.

Genetic diversity and differentiation of Thutho cattle from northeast India using microsatellite markers.

Cattle are losing maximum breeds among the world's livestock. Genetic variability data is essentially required for conservation decision-making. Thutho is a recently registered Indian cattle breed (INDIA_CATTLE_1400_THUTHO_03047) from the northeast region (NE), a biodiversity hotspot. Genetic diversity in the Thutho population and its differentiation from the only other cattle breed of NE (Siri) and cattle (Bachaur) of the neighboring region was established using highly polymorphic, FAO-recommended microsatellite markers. Numerous alleles (253) were detected across the 25 loci. The mean observed and expected numbers of alleles in the population were 10.12 ± 0.5 and 4.5 ± 0.37, respectively. The observed heterozygosity (0.67 ± 0.04) was lower than the expected heterozygosity (0.73 ± 0.03) which indicated a departure from the Hardy-Weinberg equilibrium. A positive FIS value (0.097) confirmed the heterozygote deficiency in the Thutho population. Genetic distance, phylogenetic relationships, differentiation parameters, population assignment, and Bayesian analysis explicitly ascertained the unique genetic identity of the Thutho cattle. The population did not suffer any bottlenecks in the past. Thutho has minimum diversity among the three populations; hence, its scientific management needs to be initiated immediately. Interestingly, genetic variation is enough for formulating breeding programs for managing, improving, and conserving this precious indigenous cattle germplasm.