Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle.

Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the -homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average FPED (Pedigree based inbreeding coefficient), FROH (Genomic inbreeding coefficient), FHOM (Inbreeding estimated as the ratio of observed and expected homozygous genotypes), FGRM (Inbreeding estimated on genomic relationship method) and FGRM0.5 (Inbreeding estimated from the diagonal of a GRM with allele frequencies near to 0.5) were 0.009, 0.091, 0.035, -0.104 and -0.009, respectively. Our study revealed the optimum parameter setting in PLINK viz. maximal gaps between two SNPs, minimal density of SNPs in a segment (in kb/SNP) and scanning window size to identify ROH segments, which will enable ROH estimation more efficient and comparable across various SNP genotyping-based studies. The result further emphasized the significant role of genomics in unraveling population diversity, selection signatures and inbreeding in the ongoing Sahiwal breed improvement programs.

Oral Epithelial Dysplasia in Tobacco Non-habitués: A Case Report and Review of Literature.

Oral potentially malignant disorders (OPMDs) encompass a diverse group of clinical lesions, which, on histopathological evaluation, may reveal features of hyperplasia, oral epithelial dysplasia (OED), or even early invasive squamous cell carcinoma. OEDs are often perceived to be associated with a deleterious habit such as tobacco chewing. It has emerged that OEDs may occur even in the absence of a tobacco habit and could be attributed to factors such as trauma, chronic inflammation, and inherent genetic aberrations. Authors have reported a preponderance of such lesions in young females, particularly at sites distinct from those noted in habitués. Additionally, the probability of malignant transformation of OED has been reported to be higher in non-habitués as compared to habitués when lesions are left unaddressed. There remains a paucity of data regarding the exact molecular basis, behavior, and response to treatment of OED among tobacco non-habitués. In view of the increasing number of oral lesions demonstrating epithelial dysplasia in the absence of exposure to significant risk factors, we highlight the scenario with a case. A 39-year-old female, non-habitué, presented with a non-scrapable, white lesion on the maxillary buccal gingiva. Incisional biopsy revealed features of moderate epithelial dysplasia that, on further evaluation of the excisional specimen, confirmed features of severe epithelial dysplasia. Genotyping for human papillomavirus (HPV) was carried out to assess the presence of high-risk HPV strains (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68), which are usually associated with OED and/or oral squamous cell carcinomas (OSCCs) in non-habitués. A comprehensive review of various tissue and molecular factors, which play a key role in the pathophysiology of non-habit-associated OED has been illustrated in this report. While the etiological focus of OPMDs is often directed toward deleterious habits and exposure to carcinogens, it is essential to be vigilant for this entity even among non-habitués. A meticulous screening of the oral cavity, for all patients, shall facilitate the prevention and early diagnosis of OED, particularly in individuals not exposed to habit-forming risk factors.

Comparative assessment of the effective population size and linkage disequilibrium of Karan fries composite cattle revealed viable population dynamics.

Objective: Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of Linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (Ne) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for evaluation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of Ne and LD for the long-term sustainability of these breeds. Methods: The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes. Results: The average LD between SNPs was r2 = 0.13 in the present study. LD decay (r2 = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based effective population size (Ne) of KF was determined to be 78, while the Ne estimates obtained using LD-based methods were 52 (SNeP) and 219 (Genetic Optimization for Ne Estimation - GONE), respectively. Conclusion: KF cattle have an effective population size (Ne) exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for long-term sustainable development.

Comparative genetic analysis of frequentist and Bayesian approach for reproduction, production and life time traits showing favourable association of age at first calving in Tharparkar cattle.

OBJECTIVE: The present study was aimed primarily for estimating various genetic parameters (heritability, genetic correlations) of reproduction (age at first calving [AFC], first service period [FSP]); production (first lactation milk, solid-not fat, and fat yield) and lifetime traits (lifetime milk yield, productive life [PL], herd life [HL]) in Tharparkar cattle to check the association of reproduction traits with lifetime traits through two different methods (Frequentist and Bayesian) for comparative purpose. METHODS: Animal breeding data of Tharparkar cattle (n = 964) collected from Livestock farm unit of ICAR-NDRI Karnal for the period 1990 through 2019 were analyzed using a Frequentist least squares maximum likelihood method (LSML; Harvey, 1990) and a multitrait Bayesian-Gibbs sampler approach (MTGSAM) for genetic correlations estimation of all the traits. Estimated breeding values of sires was obtained by BLUP and Bayesian analysis for the production traits. RESULTS: Heritability estimates of most of the traits were medium to high with the LSML (0.20±0.44 to 0.49±0.71) and Bayesian approach (0.24±0.009 to 0.61±0.017), respectively. However, more reliable estimates were obtained using the Bayesian technique. A higher heritability estimate was obtained for AFC (0.61±0.017) followed by first lactation fat yield, first lactation solid-not fat yield, FSP, first lactation milk yield (FLMY), PL (0.60±0.013, 0.60±0.006, 0.57±0.024, 0.57±0.020, 0.42±0.025); while a lower estimate for HL (0.38±0.034) by MTGSAM approach. Genetic and phenotypic correlations were negative for AFC-PL, AFC-HL, FSP-PL, and FSP-HL (-0.59±0.19, -0.59±0.24, -0.38±0.101 and -0.34±0.076) by the multi-trait Bayesian analysis. CONCLUSION: Breed and traits of economic importance are important for selection decisions to ensure genetic gain in cattle breeding programs. Favourable genetic and phenotypic correlations of AFC with production and lifetime traits compared to that of FSP indicated better scope of AFC for indirect selection of life-time traits at an early age. This also indicated that the present Tharparkar cattle herd had sufficient genetic diversity through the selection of AFC for the improvement of first lactation production and lifetime traits.

Novel insights into genome-wide associations in Bos indicus reveal genetic linkages between fertility and growth.

Bos indicus breed Sahiwal, famous for its optimum performance, has so far been genetically improved for performance traits based on phenotypic records and the genomic knowhow regarding genes, regions and biological processes underlying the complex quantitative traits is lacking. In this context, a Genome-wide Association Study was performed for fertility and growth traits in Sahiwal cattle to shed light on its genomic profile. A total of 46 SNPs were found associated with the traits at genome-wide suggestive threshold of P ≤ 10-4. USP32, LRPPRC, PLA2G10, RRN3 and ASAP1 were identified as putative candidate genes for body weight at different ages. However, several genes mapped for growth traits like GREB1, PLA2G10, RAD51C, BIRC6, TEX14 and PEBP4 had significant physiological underpinnings in determining fertility of the animals. Moreover, Quantitative trait loci (QTL) identification revealed potential overlaps with the already reported QTLs for both fertility and growth for most of the traits. Further, candidate SNP enrichment analysis revealed an enriched biological process for birth weight with a significant reproductive role. Based on the findings, genetic linkages underlying fertility and growth could be discerned in Sahiwal population and may be utilized for improving fertility traits in future.

Bayesian estimates for genetic and phenotypic parameters of growth traits in Sahiwal cattle.

Analyses were carried out for the estimation of (co)variance components and genetic parameters for birth weight (BWT), 6-month weight (6WT), 12-month weight (12WT), 18-month weight (18WT), 24-month weight (24WT), 30-month weight (30WT), 36-month weight (36WT), weight at first service (WFS), and weight at first calving(WFC) in Sahiwal cattle. Data for 802 lifetime records (raw data) were collected over a period of 30 years (1990-2019) for various growth traits in the herd for Sahiwal cows maintained at the livestock farm unit of ICAR-NDRI Karnal, Haryana, India. Bayesian estimates using the multi-trait Gibbs sampling animal model approach were calculated in the present study. Total heritability for BWT, 6WT, 12WT, 18WT, 24WT, 30WT, 36WT, WFS, and WFC by Bayesian modeling was estimated as 0.22 ± 0.0052, 0.47 ± 0.0037, 0.30 ± 0.0025, 0.65 ± 0.0021, 0.32 ± 0.0039, 0.33 ± 0.0027, 0.39 ± 0.0031, 0.49 ± 0.0020, and 0.57 ± 0.0023, respectively, along with its Monte Carlo error in Sahiwal cattle. Direct genetic covariances between body weight traits were ranging from - 2762.5 for 18WT and WFC to 4739.6 between WFS and WFC. Environmental covariances were ranging from - 169.98 for 30WT and 36WT to 4539.4 between WFS and WFC. Family relationships as well as the existing interaction effects between two or more traits in opposite direction effect lead to negative estimates for genetic covariances between some of the combinations with various growth traits. Although most of the estimates for posteriori were somewhat skewed, the marginalization effect enabled them to fit into the Gaussian distribution, by comparing the mean, mode, and median with each other. Results suggest that genetic progress through growth traits can be achieved if the selection is carried out for highly heritable 18-month weight as well as for the selection of pubertal and fertility traits, viz., 24WT, 30WT, 36WT, WFS, and WFC with a balanced feeding and optimum management.

Impact and utility of shallow pedigree using single-step genomic BLUP for prediction of unbiased genomic breeding values.

In unstructured dairy programs, pedigree is usually shallow, which leads to biased prediction of breeding values using best linear unbiased prediction (BLUP). The objective of this study was to come out with a genomic prediction strategy that can utilize shallow pedigree information and predict unbiased and more accurate GEBV for sex-limited traits in a small population using single-step GBLUP (ssGBLUP). The data and models for a population under selection were simulated. Out of current 10 generations, 10th generation with 1000 candidates served as validation population. For the complete pedigree scenario, pedigree (P)BLUP estimated breeding values (EBV) were unbiased with accuracy (r) of 0.35 ± 0.02 and 0.26 ± 0.01 for 0.3 and 0.1 h2 scenario, respectively. For the shallow pedigree, biased prediction of breeding values and low accuracies were obtained with linear decline in the accuracy of EBV for removal of information on more distant pedigree. Accuracy and bias (ρ) for scenario with removing 4 distant generations from pedigree were 0.30 ± 0.02 and 0.55 ± 0.03, respectively, in moderate h2 scenario. Use of Genomic (G)BLUP, especially with "extreme phenotypic contrast selective genotyping," (TB) resulted in higher accuracy for a small reference of females; however, GEBV were highly biased. We observed that ssGBLUPF, where the numerator relationship matrix is corrected for inbreeding, resulted in more accurate and unbiased estimates of GEBV across shallow pedigree scenario, with TB all female reference (missing 4 distant generations: r = 0.50 ± 0.02; ρ = 0.96 ± 0.02). We recommend use of ssGBLUPF with two tailed selectively genotyped all female reference in shallow pedigree scenarios, to obtain unbiased and accurate GEBV for sex-limited traits, when resources are limited.

Associations between polymorphisms of LAP3 and SIRT1 genes with clinical mastitis and milk production traits in Sahiwal and Karan Fries dairy cattle.

BACKGROUND: Bovine mastitis continues to remain as the most challenging disease in dairy cattle, as a result improvement of selection methods has great economic relevance while a deeper understanding of the genetic mechanisms regulating milk production traits and mastitis is of general scientific interest. OBJECTIVES: This study aimed to evaluate the association of SNPs of the LAP3 and SIRT1 genes with estimated breeding values (EBVs) of milk production traits and clinical mastitis in dairy cattle of Indian origin. METHODS: DNA samples from 263 animals (Sahiwal and Karan Fries cattle) were genotyped by PCR-RFLP to assess their pattern of genetic variation. EBVs of milk production traits and phenotypic records of incidences of clinical mastitis were used for association analysis. RESULTS: A total of 9 SNPs were identified, including three (rs110932626: A>G, rs716493845: C>T and rs43702363: C>T) in intron 12, four (g.24904G>C, rs110839532: G>T, rs43702361: T>C and rs41255599: C>T) in exon 13 and within 3'UTR of LAP3 gene and two (rs110250233: G>A and rs42140046: C>G) in the promoter region of SIRT1 gene. Eight of these identified SNPs were chosen for subsequent genotyping and association analyses. Association analysis revealed that SNP rs41255599: C>T was significantly associated with lactation milk yield, 305-day milk yield, 305-day fat yield, 305-day solid not fat yield, lactation length and incidence of clinical mastitis (p < 0.05) in Sahiwal cattle. For Karan Fries cattle, two SNPs including rs110932626: A>G and rs43702363: C>T showed significant association with 305-day milk yield. CONCLUSION: Overall, these findings provide evidence for association of the LAP3 gene with milk production traits and clinical mastitis in dairy cattle, indicating the potential role of LAP3 variants in these traits.

Genome-Wide Association Studies in Indian Buffalo Revealed Genomic Regions for Lactation and Fertility.

Murrah breed of buffalo is an excellent dairy germplasm known for its superior milk quality in terms of milk fat and solids-not-fat (SNF); however, it is often reported that Indian buffaloes had lower lactation and fertility potential compared to the non-native cattle of the country. Recent techniques, particularly the genome-wide association studies (GWAS), to identify genomic variations associated with lactation and fertility traits offer prospects for systematic improvement of buffalo. DNA samples were sequenced using the double-digestion restriction-associated DNA (RAD) tag genotyping-by-sequencing. The bioinformatics pipeline was standardized to call the variants, and single-nucleotide polymorphisms (SNPs) qualifying the stringent quality check measures were retained for GWAS. Over 38,000 SNPs were used to perform GWAS on the first two principal components of test-day records of milk yields, fat percentages, and SNF percentages, separately. GWAS was also performed on 305 days' milk yield; lactation persistency was estimated through the rate of decline after attaining the peak yield method, along with three other standard methods; and breeding efficiency, post-partum breeding interval, and age at sexual maturity were considered fertility traits. Significant association of SNPs was observed for the first principal component, explaining the maximum proportion of variation in milk yield. Furthermore, some potential genomic regions were identified to have a potential role in regulating milk yield and fertility in Murrah. Identification of such genomic regions shall help in carrying out an early selection of high-yielding persistent Murrah buffaloes and, in the long run, would be helpful in shaping their future genetic improvement programs.

Tumor-associated macrophages: Harbingers of aggressiveness in oral squamous cell carcinoma.

BACKGROUND: The significance of the tumor microenvironment (TME) as a modulator of tumor behavior was acknowledged by Hanahan and Weinberg in 2011 as the emerging hallmarks and enabling characteristics of the hallmarks of cancer. Subsequently, the role of inflammation, in conferring aggressiveness to a tumor, was regarded as a fundamental process in the evolution of the TME. Tumor-associated macrophages (TAMs) are distinctly polarized inflammatory cells and key shapers of a protumorigenic microenvironment. AIMS: The aim of the study was to evaluate the distribution of TAMs and the expression of CD-163 as a marker to evince tumor aggressiveness, in oral squamous cell carcinoma (OSCC). SETTINGS AND DESIGN: A retrospective institutional study was approved by the institutional ethics committee, and random sampling was carried out. Cases fulfilling the inclusion criteria were subjected to S(site), T(tumor), N( node), M( metastasis), P(pathology) STNMP staging along with immunohistochemical evaluation of CD-163. METHODS: Samples for this study included 58 archival cases of OSCC. Demographic details were recorded, and the STNMP stage ascertained, following which, each case was reevaluated histopathologically for the invasive front. Cases with sufficient stroma and demonstrating the invasive front were further subjected to immunohistochemical evaluation of CD-163 for TAMs. The density of CD-163-positive cells was assessed by three pathologists, independently, in a double-blinded evaluation using Image-J©. STATISTICAL ANALYSIS: Descriptive data were evaluated and analyzed statistically using Spearman's/Pearson's correlation tests based on the distribution of data. RESULTS: The density of TAMs was noted to be directly proportional to the STNMP stage. In addition, a strong positive, statistically significant correlation was noted between the density of TAMs and tumor size, nodal status and STNMP stage. CONCLUSION: The crucial role of the tumor microenvironment must be considered when evaluating OSCC. TAMs prove to be a reliable marker for assessing tumor aggressiveness and could aid in improved prognostication of OSCC, while also being potential targets for therapy.

Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle.

BACKGROUND: In the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip. RESULT: De-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent. CONCLUSION: The key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.

The Stromal Dictators in a Concomitant Case of Oral Submucous Fibrosis - Oral Squamous Cell Carcinoma.

Oral submucous fibrosis (OSMF) is a potentially malignant disorder, characterized by alteration in the connective tissue stroma. Its association with oral squamous cell carcinoma (OSCC) has been recognized and conferred a special status as a distinct disease entity with improved prognosis as compared to conventional squamous cell carcinoma. Such cases of concomitant presentation of OSMF and OSCC have not yet been defined, leading to ambiguity regarding the evaluation. The concomitant occurrence of OSMF-OSCC is associated with histopathological features, unlike OSMF, yet similar to an aggressive presentation of OSCC. An indepth evaluation of the connective tissue, along with other tumor characteristics such as tissue hypoxia, inflammatory cell population, neoangiogenesis, and stromal cells fortify the possibility of these cases of concomitance being as aggressive, if not more, as compared to conventional OSCC. Thus, recognizing such cases along with the evaluation of probable prognostic indicators is necessary to improve the current understanding of tumorigenesis and progression in concomitant cases of OSMF-OSCC.

Muscle transcriptome signature and gene regulatory network analysis in two divergent lines of a hilly bovine species Mithun (Bos frontalis).

A massive bovine, Bos frontalis, also known as Mithun or Gayal, found at higher altitude is very promising meat and milk animal. For candidate gene and marker discovery, RNA-seq data was generated from longissimus dorsi muscle tissues with Illumina-HiSeq. Such markers can be used in future for genetic gain of traits like feed conversion efficiency (FCE) and average daily gain (ADG). Analysis revealed 297differentially expressed genes (DEGs) having 173 up and 124 down-regulated unigenes. Extensive conservation was found in genic region while comparing with Bos taurus. Analysis revealed 57 pathways having 112 enzymes, 72 transcriptional factors and cofactors, 212 miRNAs regulating 71 DEGs, 25,855 SSRs, mithun-specific 104,822 variants and 7288 indels, gene regulatory network (GRN) having 24 hub-genes and transcriptional factors regulating cell proliferation, immune tolerance and myogenesis. This is first report of muscle transcriptome depicting candidate genes with GRN controlling FCE and ADG. Reported putative molecular markers, candidate genes and hub proteins can be valuable genomic resources for association studies in genetic improvement programme.

Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis).

BACKGROUND: Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh. However, the origin of this species is still disputed and information on its genomic architecture is scanty so far. We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun. Recently, the first genome assembly of gayal, mithun of Chinese origin, was published. However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse geographical locations and for building a superior consensus assembly. We, therefore, performed deep sequencing of the genome of an adult female mithun from India, assembled and annotated its genome and performed extensive bioinformatic analyses to produce a superior de novo genome assembly of mithun. RESULTS: We generated ≈300 Gigabyte (Gb) raw reads from whole-genome deep sequencing platforms and assembled the sequence data using a hybrid assembly strategy to create a high quality de novo assembly of mithun with 96% recovered as per BUSCO analysis. The final genome assembly has a total length of 3.0 Gb, contains 5,015 scaffolds with an N50 value of 1 Mb. Repeat sequences constitute around 43.66% of the assembly. The genomic alignments between mithun to cattle showed that their genomes, as expected, are highly conserved. Gene annotation identified 28,044 protein-coding genes presented in mithun genome. The gene orthologous groups of mithun showed a high degree of similarity in comparison with other species, while fewer mithun specific coding sequences were found compared to those in cattle. CONCLUSION: Here we presented the first de novo draft genome assembly of Indian mithun having better coverage, less fragmented, better annotated, and constitutes a reasonably complete assembly compared to the previously published gayal genome. This comprehensive assembly unravelled the genomic architecture of mithun to a great extent and will provide a reference genome assembly to research community to elucidate the evolutionary history of mithun across its distinct geographical locations.

High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis).

The current study aimed at genomic characterization and improved understanding of genetic diversity of two Indian mithun populations (both farm, 48 animals and field, 24 animals) using genome wide genotype data generated with Illumina BovineHD BeadChip. Eight additional populations of taurine cattle (Holstein and NDama), indicine cattle (Gir) and other evolutionarily closely related species (Bali cattle, Yak, Bison, Gaur and wild buffalo) were also included in this analysis (N = 137) for comparative purposes. Our results show that the genetic background of mithun populations was uniform with few possible signs of indicine admixture. In general, observed and expected heterozygosities were quite similar in these two populations. We also observed increased frequencies of small-sized runs of homozygosity (ROH) in the farm population compared to field mithuns. On the other hand, longer ROH were more frequent in field mithuns, which suggests recent founder effects and subsequent genetic drift due to close breeding in farmer herds. This represents the first study providing genetic evidence about the population structure and genomic diversity of Indian mithun. The information generated will be utilized for devising suitable breeding and conservation programme for mithun, an endangered bovine species in India.