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With the tremendous increase in human population the demand of milk and meat is also increasing. This necessitates the centralization of animal husbandry sector both in developed and developing countries. More production has to be taken from fewer animals which seem to be possible only with the usage of advanced technologies. Earlier this seems to be impractical due to non-availability of such technologies to the farmers. Nowadays, computational power is very cheap and easily available. Artificial intelligence is one such field of computer science devoted to creating computing machines and systems that perform operations analogous to human learning and decision-making. Artificial intelligence includes the machine learning, deep learning and predictive analytics. With the implementation of various software and algorithms, the production has been increased from the farm animals along with better management and welfare. This paper illustrates the application domains and maneuvering of artificial intelligence in the animal husbandry sector. [ABSTRACT FROM AUTHOR]

An attempt was made to study the effect of different shade materials on physiological, behavioural, biochemical and hormonal responses in crossbredVrindavanicalves during the summer seasons in the Cattle and Buffalo Farm of Indian veterinary Research Institute, Izatnagar, India. During experiment, 28 crossbred calves were divided into four groups: thatch shading roof (T1), agro-net shading roof – 60% light diffusion (T2), asbestos with canvas shading roof (T3) and well-grown tree (T4). The daily macro- and microclimate data were recorded at 0900 and 1400 h. The data for each ongoing behavioural activity were recorded by closed circuit television consecutively for three days for each animal in each group from 1000 to 1700 h. Blood was also collected at 0, 15, 30, 45, 60, 75 and 90 days of the experimental period for estimation of different biochemical parameters. The microclimate, that is, maximum and minimum temperatures, relative humidity and temperature humidity index of the roof, was lower in the T2 group. There was significantly more (P < .05) time spent in shade structure by the T2 group as compared to other groups. Among the behaviour, feeding, rumination, resting and sleeping activities were more in the T2 group, whereas standing, moving, drinking, time spent near water tank and abnormal behaviour (cross-sucking, licking) were more in T3 and T4. Among the blood parameters, haemoglobin was significantly higher (P < .05) while, Serum Glutamic Oxaloacetic Transaminase and Alkaline Phosphatase were significantly lower in the T2 group. [ABSTRACT FROM PUBLISHER]

Aim: The present study was carried out on cattle and buffalo farm of Indian Veterinary Research Institute, Izatnagar (Uttar Pradesh) to determine the effect of different shade materials on physiological performance in Vrindavani crossbred calves during the summer. Materials and Methods: Twenty-eight crossbred calves were divided into four groups viz. Thatch shading roof (T1), agro-net shading roof - 60 % light diffusion (T2), asbestos with canvas shading roof (T3) and well-grown tree (T4). The recording of macro and micro climate as well as the physiological parameters viz. rectal temperature and respiration rate were recorded at 9:00 AM and 2:00 PM for 2 consecutive days at every fortnight interval. Result: The microclimate viz. maximum and minimum, relative humidity, temperature humidity index and surface temperature of the roof was lower in T2 group in the summer season. The physiological responses viz. rectal temperature and respiration rate was significantly higher in T4. Conclusion: During the summer season both thatch and agro-net shade material helped in better relieving the summer stress. [ABSTRACT FROM AUTHOR]

Aim: To find out the influence of different types of roofing materials on micro-climate in animal loose housing system during rainy season. Materials and Methods: Different shade materials were used for covered area under each of three treatments. Thatch shading roof (T ), Agro-net shading roof (T ), Asbestos with canvas shading roof (T ). Long axis of the paddock was east-to-west 1 2 3 orientation. The covered area floor space was 1.5 ×1 m (excluding manger) for each animal and open paddock was 2 × 1 m. Height of shed at eaves was 2 meter. Daily temperature (maximum and minimum) and dry bulb and wet bulb temperature of macro and micro- environment under different treatments were recorded at 9:30 AM and 2:00 PM of Indian Standard Time (IST) by using maximum and minimum thermometer and dry and wet bulb thermometer. Both inside and outside surface temperatures of shade materials were measured by infrared digital thermometer (ebro, TFI 220). The statistical procedures followed were two way ANOVA and Paired 'T' test. Results: During the experimental period, maximum temperature was recorded under asbestos and lowest temperature was in agro-net and maximum protection from high temperature was given during peak hot hours in agro-net than asbestos. THI was more (P<0.05) under asbestos than agro-net and thatch. The outside surface temperature at 9.30 AM and 2:00 PM (IST) was significantly lower (P<0.05) in agro-net than thatch and asbestos. [ABSTRACT FROM AUTHOR]

Aim: To assess the welfare of pack animal: Pony, Horse, Mule and Donkey in and around Bareilly city. Materials and Methods: The present study was carried out in Bareilly city and Izatnagar area of Bareilly district of Uttar Pradesh in the year 2009. Representative sample of 100 pack animal owners were selected to get the information regarding various social, personal and economic attributes of the pack animal. Further during interviewing different health and behavior pattern of animals was keenly examined. Analysis has been done as per standard procedures. Results: Most of the pack animal owners (98%) were aware of the freedom from hunger and thirst. Majority of respondents (96, 93, 81 & 85 percent) were aware of freedom from injury and disease, pain and discomfort, to express normal behavior and adequate space and freedom from fear and distress. Respondents (85%) believed that they themselves were responsible for the welfare of the animals. Most of the owners (48.8%) employed their animals for work for 9-10 hrs with rest (96.5%) in between work and most (88.3%) indulged into beating to compel the animals to work. All pregnant animals were put to work in the first two trimesters of pregnancy. Upon physical examination, pack animals showed abnormality in eyes (49%), abnormality in gait (40%) and limb deformity (39%). Most animals (75%) had tether lesions and 34 percent animals avoided or were aggressive to observer. Majority (74.1%) of the owners housed their animals in a part of their own residence with improper drainage and cleaning. Most of the owners (82%) consulted Veterinary doctors for treatment and believed in allopathic medicine (57%). Vaccination was not carried out on most (96%) of the animals. All the animals were feed green fodder but practice of supplementation of minerals to animals was only among 11 percent owners. Conclusions: Present findings provide baseline information on welfare activities followed by pack animal owners and status of pack animals in regards to animal welfare. Amore detailed in-depth study is needed regarding welfare issues in all varied pack animals, designing of scientific efficient carts, working hours and special requirements related to feed and other managemental practices for pack and draught animals. Rules and Regulations advocated by Government Act can be used to enforce welfare laws of the animals but thrust should be more in regard to development of awareness among owners for animal welfare. [ABSTRACT FROM AUTHOR]

The present study was aimed at the identification of population stratifying markers from the commercial porcine SNP 60K array and elucidate the genome-wide selective sweeps in the crossbred Landlly pig population. Original genotyping data, generated on Landlly pigs, was merged in various combinations with global suid breeds that were grouped as exotic (global pig breeds excluding Indian and Chinese), Chinese (Chinese pig breeds only), and outgroup pig populations. Post quality control, the genome-wide SNPs were ranked for their stratifying power within each dataset in TRES (using three different criteria) and FIFS programs and top-ranked SNPs (0.5K, 1K, 2K, 3K, and 4K densities) were selected. PCA plots were used to assess the stratification power of low-density panels. Selective sweeps were elucidated in the Landlly population using intra- and inter-population haplotype statistics. Additionally, Tajima's D-statistics were calculated to determine the status of balancing selection in the Landlly population. PCA plots showed 0.5K marker density to effectively stratify Landlly from other pig populations. The A-score in DAPC program revealed the Delta statistic of marker selection to outperform other methods (informativeness and FST methods) and that 3000-marker density was suitable for stratification of Landlly animals from exotic pig populations. The results from selective sweep analysis revealed the Landlly population to be under selection for mammary (NAV2), reproductive efficiency (JMY, SERGEF, and MAP3K20), body conformation (FHIT, WNT2, ASRB, DMGDH, and BHMT), feed efficiency (CSRNP1 and ADRA1A), and immunity (U6, MYO3B, RBMS3, and FAM78B) traits. More than two methods suggested sweeps for immunity and feed efficiency traits, thus giving a strong indication for selection in this direction. The study is the first of its kind in Indian pig breeds with a comparison against global breeds. In conclusion, 500 markers were able to effectively stratify the breeds. Different traits under selective sweeps (natural or artificial selection) can be exploited for further improvement. [ABSTRACT FROM AUTHOR]

The present investigation was done to assess the utilization patterns of antiparasitic drugs among dairy owners and their perceptions regarding resistance development. A total of 160 dairy farmers, consisting of 80 Small Dairy Farmers (SDF) and 80 Large Dairy Farmers (LDF) were selected for the study from 8 different districts of 2 states of India (Rajasthan and Uttar Pradesh). A pre-tested structured interview schedule was used for collecting data. In the study area, the majority of the dairy farmers were middle-aged males, middle-level educated and had a moderate level of experience in dairy farming. All the farmers were observed utilizing chemical antiparasitic drugs for managing parasitic infestations in dairy animals. Regarding parasite control, SDF relied on para-veterinarians, while LDF preferred self-treatment for their dairy animals. A primary source for acquiring antiparasitic drugs was pharmacy stores with and without a prescription from qualified animal health care service providers. It was found that approximately one-third of the farmers did not refer to drug labels for dose calculation. However, dairy farmers primarily relied on visual observation of animal body weight to calculate antiparasitic drug doses. The majority of the farmers stored antiparasitic drugs in their dairy farms. Moreover, the farmers expressed an average perception towards the antiparasitic resistance development. Among the various socio-economic factors, education and training were found the strongest predictors that made the highest changes in perception. The overall findings indicate that farmers were neither well-versed in the scientific practices related to the usage of antiparasitic drugs nor familiar with resistance issues. Despite this, they were continuing to acquire and administer drugs without seeking advice from the qualified veterinarians. Consequently, indiscriminate use of antiparasitic drugs in livestock sector has the potential to contribute to the emergence of resistance. It is imperative to create awareness among farmers about the importance of rational use of drugs to mitigate the risk of resistance. [ABSTRACT FROM AUTHOR]

Balancing selection is the process of selection that preserves various alleles within a population. Studying the areas undergoing balancing selection is essential, because it preserves genetic diversity in a population. Finding genes that exhibit signs of balancing selection during the domestication of cattle is the goal of this study. To identify regions where polymorphism has persisted in the cattle population for millions of years, we examined the genome of cattle. In this study, we used bovine SNP 50 k data to conduct a detailed genome-wide assessment of selection signatures for balancing selection. We have included the genotyped data from 427 animals, including five taurines, two crossbreds, and eight Indian cattle breeds. For this study, we employed Tajima's D approach to identify signature regions undergoing balancing selection. Using the NCBI database, PANTHER 17.0, and CattleQTL database, the annotation was carried out after finding the relevant areas under balancing selection. The number of genomic regions undergoing balancing selection in Ayrshire, Brown-Swiss, Frieswal, Gir, Guernsey, Hariana, Holstein Friesian, Jersey, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, Tharparkar, and Vrindavani was 11, 13, 13, 19, 18, 11, 17, 14, 14, 12, 10, 12, 13, 13, and 11, respectively. We have observed multiple immune system-related genes going through balancing selection, including KIT, NFATC2, GBP4, LRRC32, SYT7, RAG1, RAG2, LOC513659, and ZBTB17. In our study, we found that the majority of the immune-related genes and a few genes associated with growth, reproduction, production, and adaptation are undergoing balancing selection. [ABSTRACT FROM AUTHOR]

Mammalian X and Y chromosomes independently evolved from various autosomes approximately 300 million years ago (MYA). To fully understand the relationship between genomic composition and phenotypic diversity arising due to the course of evolution, we have scanned regions of selection signatures on the X chromosome in different cattle breeds. In this study, we have prepared the datasets of 184 individuals of different cattle breeds and explored the complete X chromosome by utilizing four within-population and two between-population methods. There were 23, 25, 30, 17, 17, and 12 outlier regions identified in Tajima's D, CLR, iHS, ROH, FST, and XP-EHH. Bioinformatics analysis showed that these regions harbor important candidate genes like AKAP4 for reproduction in Brown Swiss, MBTS2 for production traits in Brown Swiss and Guernsey, CXCR3 and CITED1 for health traits in Jersey and Nelore, and BMX and CD40LG for regulation of X chromosome inactivation in Nelore and Gir. We identified genes shared among multiple methods, such as TRNAC-GCA and IL1RAPL1, which appeared in Tajima's D, ROH, and iHS analyses. The gene TRNAW-CCA was found in ROH, CLR and iHS analyses. The X chromosome exhibits a distinctive interaction between demographic factors and genetic variations, and these findings may provide new insight into the X-linked selection in different cattle breeds. [ABSTRACT FROM AUTHOR]

The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development. [ABSTRACT FROM AUTHOR]

Riverine Buffaloes, especially the Murrah breed because of their adaptability to harsh climatic conditions, is farmed in many countries to convert low-quality feed into valuable dairy products and meat. Here, we investigated the copy number variations (CNVs) in 296 Murrah buffalo using the Axiom® Buffalo Genotyping Array 90K (Affymetrix, Santa Clara, CA, USA). The CNVs were detected on the autosomes, using the Copy Number Analysis Module (CNAM) using the univariate analysis. 7937 CNVs were detected in 279 Buffaloes, the average length of the CNVs was 119,048.87 bp that ranged between 7800 and 4,561,030 bp. These CNVs were accounting for 10.33% of the buffalo genome, which was comparable to cattle, sheep, and goat CNV analyses. Further, CNVs were merged and 1541 CNVRs were detected using the Bedtools-mergeBed command. 485 genes were annotated within 196 CNVRs that were identified in at least 10 animals of Murrah population. Out of these, 40 CNVRs contained 59 different genes that were associated with 69 different traits. Overall, the study identified a significant number of CNVs and CNVRs in the Murrah breed of buffalo, with a wide range of lengths and frequencies across the autosomes. The identified CNVRs contained genes associated with important traits related to production and reproduction, making them potentially important targets for future breeding and genetic improvement efforts. [ABSTRACT FROM AUTHOR]

Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle. [ABSTRACT FROM AUTHOR]

The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes. [ABSTRACT FROM AUTHOR]

The main objective of the current research was to locate, annotate, and highlight specific areas of the bovine genome that are undergoing intense positive selection. Here, we are analyzing selection signatures in crossbred (Bos taurus X Bos indicus), taurine (Bos taurus), and indicine (Bos indicus) cattle breeds. Indicine cattle breeds found throughout India are known for their higher heat tolerance and disease resilience. More breeds and more methods can provide a better understanding of the selection signature. So, we have worked on nine distinct cattle breeds utilizing seven different summary statistics, which is a fairly extensive approach. In this study, we carried out a thorough genome-wide investigation of selection signatures using bovine 50K SNP data. We have included the genotyped data of two taurine, two crossbreds, and five indicine cattle breeds, for a total of 320 animals. During the 1950s, these indicine (cebuine) cattle breeds were exported with the aim of enhancing the resilience of taurine breeds in Western countries. For this study, we employed seven summary statistics, including intra-population, i.e., Tajima's D, CLR, iHS, and ROH and inter-population statistics, i.e., FST, XP-EHH, and Rsb. The NCBI database, PANTHER 17.0, and CattleQTL database were used for annotation after finding the important areas under selection. Some genes, including EPHA6, CTNNA2, NPFFR2, HS6ST3, NPR3, KCNIP4, LIPK, SDCBP, CYP7A1, NSMAF, UBXN2B, UGDH, UBE2K, and DAB1, were shown to be shared by three or more different approaches. Therefore, it gives evidence of the most intense selection in these areas. These genes are mostly linked to milk production and adaptability traits. This study also reveals selection regions that contain genes which are crucial to numerous biological functions, including those associated with milk production, coat color, glucose metabolism, oxidative stress response, immunity and circadian rhythms. [ABSTRACT FROM AUTHOR]

The study investigated the effects of FMD vaccination on acute phase response and milk composition in the HF crossbred cows (n = 12) using a cross-over experimental design. In trial 1, one group (n = 6) received inactivated trivalent oil-adjuvanted FMD vaccine [day post-vaccination, (dpv) 0], while the mock-vaccinated group received saline (n = 6). After a cooling period of 15 days, the trial was repeated by swapping groups. The body temperature, dry matter intake (DMI) and milk yield were recorded. Haemato-biochemical parameters, haptoglobin and cortisol concentrations were also assessed. A significant (p < 0.05) increase in the neutralizing antibody response to FMDV serotype O and Asia1 indicated a positive immune response. A significant (p < 0.05) increase of 0.4° to 0.6°C in the body temperature, decrease of 0.7-0.8 kg in DMI along with an increase in the serum haptoglobin, total leukocyte count and neutrophils within dpv 2 indicated acute phase response in the FMD vaccinated group. Among the milk constituents, only milk fat (p = 0.053) was significant. It was concluded that FMD vaccination induced acute phase response within dpv 3 in the crossbred cows and caused a non-significant reduction in the milk yield on the day of vaccination. [ABSTRACT FROM AUTHOR]

Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the 'null model' and positive selection as the 'signal'. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next‐generation sequencing, high‐density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large‐scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data. [ABSTRACT FROM AUTHOR]

The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India. [ABSTRACT FROM AUTHOR]

In the present study, Porcine 60K SNP genotype data from 69 Landlly pigs were used to explore Copy Number Variations (CNVs) across the autosomes. A total of 386 CNVs were identified using Hidden Markov Model (HMM) in PennCNV software, which were subsequently aggregated to 115 CNV regions (CNVRs). Among the total detected CNVRs, 58 gain, 49 were loss type while remaining 8 events were both gain and loss types. Identified CNVRs covered 12.5 Mb (0.55%) of Sus scrofa reference 11.1 genome. Comparison of our results with previous investigations on pigs revealed that approximately 75% CNVRs were novel, which may be due to differences in genetic background, environment and implementation of artificial selection in Landlly pigs. Functional annotation and pathway analysis showed the significant enrichment of 267 well-annotated Sus scrofa genes in CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Additionally, KIT and FUT1 were two major genes detected on CNVR in our population. This investigation provided a comprehensive overview of CNV distribution in the Indian porcine genome for the first time, which may be useful for further investigating the association of important quantitative traits in Landlly pigs. 115 CNVRs were identified in 69 Landlly pig population. Approximately 75% detected CNVRs were novel for Landlly population. Significant enrichment of 267 well-annotated Sus scrofa genes observed in these CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Comprehensive CNV map in the Indian porcine genome developed for the first time. [ABSTRACT FROM AUTHOR]

Background: Elucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution to genetic diversity and association with important pathophysiological states. The present study aimed to elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X and 30X). Post-quality control, the sequence reads were aligned to the latest draft release of the Bubaline genome. The genome-wide CNVs were elucidated using a read-depth approach in CNVnator with different bin sizes. Adjacent CNVs were concatenated into copy number variation regions (CNVRs) in different breeds and their genomic coverage was elucidated. Results: Overall, the average size of CNVR was lower at 30X coverage, providing finer details. Most of the CNVRs were either deletion or duplication type while the occurrence of mixed events was lesser in number on a comparative basis in all breeds. The average CNVR size was lower at 30X coverage (0.201 Mb) as compared to 10X (0.013 Mb) with the finest variants in Banni buffaloes. The maximum number of CNVs was observed in Murrah (2627) and Pandharpuri (25,688) at 10X and 30X coverages, respectively. Whereas the minimum number of CNVs were scored in Surti at both coverages (2092 and 17,373). On the other hand, the highest and lowest number of CNVRs were scored in Jaffarabadi (833 and 10,179 events) and Surti (783 and 7553 events) at both coverages. Deletion events overnumbered duplications in all breeds at both coverages. Gene profiling of common overlapped genes and longest CNVRs provided important insights into the evolutionary history of these breeds and indicate the genomic regions under selection in respective breeds. Conclusion: The present study is the first of its kind to elucidate the high-resolution CNV map in major buffalo populations using a read-depth approach on whole genome resequencing data. The results revealed important insights into the divergence of major global buffalo breeds along the evolutionary timescale. [ABSTRACT FROM AUTHOR]

The BoLA class II DQA and DQB genes in crossbred cattle were studied using PCR-RFLP, cloning, and sequencing techniques. Seventy-two crossbred cattle (Vrindavani) were used in the current study. HaeIII and XbaI restriction enzymes digested DQA exon 2-3, revealing seven (HaeIII-A-G) and three (XbaI A-C) motifs, respectively. The BoLA-DQB gene was analyzed using PCR-RFLP with PstI and TaqI restriction enzymes, yielding five restriction motifs for each restriction enzyme (PstI-A-E and TaqI-A-E). In crossbred cattle, addition, deletion, and substitutions were observed in distinct sequences, resulting in variations in overall gene length. Changes in nucleotides at positions 64–80, 110–200, and 207–264 were largely responsible for polymorphism in DQA exon 2. The phylogenetic analysis predicted a high degree of nucleotide and amino acid changes in DQA exon 2-3 and DQB exon 2. DQA genes had a nucleotide dissimilarity of 0.3–25.4 percent, while DQB genes had a nucleotide dissimilarity of 1.5–14.3 percent. We cloned and sequenced 20 genotypes based on PCR-RFLP of the DQA and DQB genes. The current study observed variation in the DQA and DQB genes and will serve as a foundation for future research on the BoLA DQA and DQB genes. [ABSTRACT FROM AUTHOR]

The present study was conducted on the MHC class I (BoLA-A/BuLA-A) gene in Sahiwal, Jersey, Hariana, and Tharparkar breeds of cattle and Murrah, Mehsana, and Bhadawari breeds of buffalo to study the polymorphism. Exons 7–8 of the MHC class I gene was first characterized for polymorphism study in buffalo and the results reveal that this gene has a higher level of nucleotide changes than the cattle. Genes were investigated for polymorphisms in 285 animals of cattle and buffalo breeds. Molecular characterization of the MHC class I (BoLa-A/Bula-A) gene reveals a higher degree of polymorphism at the nucleotide level in cattle and buffalo. Results revealed this region has a higher level of polymorphisms in buffalo as campared to the cattle. Alul restriction patterns were monomorphic except for three different patterns but it was able to illustrate the differences in buffalo and cattle. SSCP analysis of exons 7–8 showed remarkable differences in cattle and buffalo. Sequence analysis revealed more closeness of Murrah breed with crossbred and indigenous cattle than Holstein Friesian. Exon 8 had more deletion and stop codon as compared to exon 7. The investigation confirmed that MHC class I BoLa-A/Bula-A exons 7–8 is highly polymorphic in buffalo as compared to cattle. [ABSTRACT FROM AUTHOR]

Background: The study was conducted to evaluate the effect of floor enrichment with rubber mattress of calving pen on prepartum calving behaviour of Tharparkar cow during the winter season. Methods: A total 28 Tharparkar cows were taken in study during winter season (November to March) and divided into two groups each contain 14 animals. One group placed in floor enriched with rubber mattress and other group kept on bare concrete floor calving pen. Preparturient behaviours like lying time, standing time, lying bout duration, number of lying bouts, rumination time, rumination bouts, self grooming and frequency of self grooming were evaluated on -12 hr, -7th day, -14th day and -21st day prepartum for period of 12 hr in a day. Repeated Meausures ANOVA was used for the analysis of the data. Result: It was found that lying time, lying bout duration was significantly more in rubber mattress group as compare to concrete floor. However, 12 hr before parturition standing time was significantly high compare to any other observational day within the group. Similarly, rubber mattress had positive effect on rumination time, lying duration and self grooming frequency as compare to bare concrete floor. It was concluded that rubber mattress had beneficial effect in calving pen of Tharparkar cow during winter season due to its softness and insulating property. It provided comfort and warmth to the parturient cows. which was evident by increase in rumination time, more lying duration and reduced self grooming frequency. [ABSTRACT FROM AUTHOR]

Environmental heat stress in dairy cattle leads to poor health, reduced milk production and decreased reproductive efficiency. Multiple genes interact and coordinate the response to overcome the impact of heat stress. The present study identified heat shock regulated genes in the peripheral blood mononuclear cells (PBMC). Genome-wide expression patterns for cellular stress response were compared between two genetically distinct groups of cattle viz., Hariana (B. indicus) and Vrindavani (B. indicus X B. taurus). In addition to major heat shock response genes, oxidative stress and immune response genes were also found to be affected by heat stress. Heat shock proteins such as HSPH1, HSPB8, FKB4, DNAJ4 and SERPINH1 were up-regulated at higher fold change in Vrindavani compared to Hariana cattle. The oxidative stress response genes (HMOX1, BNIP3, RHOB and VEGFA) and immune response genes (FSOB, GADD45B and JUN) were up-regulated in Vrindavani whereas the same were down-regulated in Hariana cattle. The enrichment analysis of dysregulated genes revealed the biological functions and signaling pathways that were affected by heat stress. Overall, these results show distinct cellular responses to heat stress in two different genetic groups of cattle. This also highlight the long-term adaptation of B. indicus (Hariana) to tropical climate as compared to the crossbred (Vrindavani) with mixed genetic makeup (B. indicus X B. taurus). [ABSTRACT FROM AUTHOR]

Copy number variations (CNVs) are major forms of genetic variation with an increasing importance in animal genomics. This study used the Illumina BovineSNP 50 K BeadChip to detect the genome-wide CNVs in the Tharparkar cattle. With the aid of PennCNV software, we noticed a total of 447 copy number variation regions (CNVRs) across the autosomal genome, occupying nearly 2.17% of the bovine genome. The average size of detected CNVRs was found to be 122.2 kb, the smallest CNVR being 50.02 kb in size, to the largest being 1,232.87 Kb. Enrichment analyses of the genes in these CNVRs gave significant associations with molecular adaptation-related Gene Ontology (GO) terms. Most CNVR genes were significantly enriched for specific biological functions; signaling pathways, sensory responses to stimuli, and various cellular processes. In addition, QTL analysis of CNVRs described them to be linked with economically essential traits in cattle. The findings here provide crucial information for constructing a more comprehensive CNVR map for the indigenous cattle genome. [ABSTRACT FROM AUTHOR]

This review deals with the various traditional and recent methods of sire evaluation. A sire evaluation is a method of prediction of sire's next-generation produced by breeding with specified females and creating their records in a specific environment. Breeding worth of progeny tested sires are obtained through sire index method that assigns ranking to each sire based on their genetic merit. Numerous sire indices are broadly classified in two type's viz., indices which are purely meant for ranking purposes and those which, besides, provide an estimate of the breeding worth of each sire. Sires can be evaluated in single or multiple herds. The statistical equations represent sire evaluation as linear or non-linear methods. Numerous methods can be incorporated as the advances are made in sire evaluation based on data structures, breeding approaches and selection methods. There are various approaches of sire evaluation such as Least Squares Method (LSM), Simple Regressed Least Squares (SRLS), Best Linear Unbiased Prediction (BLUP) and Derivative-Free Restricted Maximum Likelihood (DFREML) for single as well as multiple trait models which can be used to derive genetic worth of an individual. An efficient method of sire evaluation shows minimum within sire variance or error variance. [ABSTRACT FROM AUTHOR]

Background: The information about milk quality of different breeds of cattle and buffalo is still scanty. The objective of the study was to the compare milk fatty acid composition and mineral concentration in the crossbred cattle and indigenous cattle and buffalo reared on same farm. Methods: This study was conducted on 187 individual milk samples, which includes 124 crossbred Vrindavani cattle, 19 indigenous cattle and 44 Murrah buffaloes. Result: The Murrah buffalo milk had significantly (P≤0.05) higher concentration of fat and saturated fatty acids than indigenous or crossbred cow's milk. The mono unsaturated fatty acid (MUFA) and poly unsaturated fatty acid (PUFA) contents (C16:1, C20:2, C20:4n6 and C22:6N3) were significantly higher in indigenous cows compared to crossbreds and Murrah buffalo. The concentration of iron and zinc were significantly (P≤0.05) higher in indigenous cattle, whereas, the contents of Cu and Mn were higher in Murrah buffalo. [ABSTRACT FROM AUTHOR]

Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long‐term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non‐textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber‐producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber‐producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber‐producing animal species. [ABSTRACT FROM AUTHOR]

Lumpy skin disease (LSD) is a notifiable re-emerging transboundary viral disease of bovines that inflicts heavy losses in affected livestock farms. Genetic variations contribute substantially to the inter-individual differences in the immune response against disease agents. The present study aimed to evaluate the genetic basis of differential immune response in Vrindavani cattle by comparing the hematological, biochemical and cytokine genes' expression profiles of LSD-affected and unaffected animals. After 21 days of the outbreak at the farm, the animals were grouped as affected (those who developed symptoms) and unaffected/healthy (those who did not). Standard hematological and biochemical parameters were evaluated in both the groups. Expression profiling of important Th1 (IL2, INFG and GMCSF) and Th2 (IL4, IL6 and IL10) cytokines was also performed via a relative quantification approach using real-time PCR. Erythrogram and leucogram analyses revealed significant differences in total leucocyte count (TLC: 14.18 ± 0.74 versus 11.38 ± 0.68 x103/µL), hemoglobin (Hb: 8.66 ± 0.42 versus 10.84 ± 0.17 g%) and percentage of neutrophils (46.40 ± 1.98 versus 35.40 ± 2.11%), lymphocytes (49.40 ± 1.99 versus 62.40 ± 1.86) and monocytes (4.20 ± 0.37 versus 2.40 ± 0.40) between the affected and healthy animals, respectively. The production of liver enzymes (SGOT and SGPT) was significantly higher in affected animals (74.18 ± 4.76 and 59.51 ± 2.75) when compared to the healthy counterparts (65.95 ± 9.18 and 39.21 ± 3.31). The expression profiling of Th1 and Th2 cytokines revealed significant differences between the two groups, except IL10. The expression of IL2, GMCSF and IL6 were upregulated in healthy animals while that of INFG, IL4 and IL10 were upregulated in LSD-affected animals. The highest abundance was observed for IL2 transcripts in healthy animals among all assessed cytokines with log2fold change of 1.61 as compared to affected counterparts. Overall, the immune response in healthy animals (after exposure to LSD virus) was predominated by the expression of Th1 cell proliferation and there was an increased production of pro-inflammatory cytokines as compared to the affected counterparts. The results revealed that the effective immune response to LSD in cattle consists of changes in hematological and biochemical parameters and altered expression profile of cytokines with enhanced phagocytosis and lymphocyte recruitment. Furthermore, optimal expression of Th1 cytokines is required for maintaining optimal health against infectious insult with LSD virus in cattle. [ABSTRACT FROM AUTHOR]

The present broad range of sheep phenotypic variation is the consequence of selection for various production characteristics such as wool, milk, meat, and natural adaptability to diverse situations. In the current study, the genomic data of 79 animals from three Indian sheep breeds (Changthangi, Deccani, and Garole) were explored to decipher regions under positive selection for various productive traits using various statistical tools. We found 61, 102 regions using Tajima's D, CLR and 58, 38, and 71 regions using FST, FLK, and hapFLK, respectively, under selective sweep. Significant candidate genes related to various important traits, such as KLHL for fibre diameter and the OMA1 gene for feed-induced thermogenesis in Changthangi, were identified. In addition, the SYCP2 and NAPAS3 genes were found to be associated with seasonal reproductivity, and BMPR1B for fertilization capacity in Garole. In a previous study, the HSPA6 gene (Garole) was found to be associated with thermo-tolerance in the Angus sheep breed. The outcomes discussed here provide a basis for detecting selective sweeps that underlie genetic variations of traits that have functional importance. [ABSTRACT FROM AUTHOR]

Classical Swine Fever (CSF) is a contagious viral disease of pigs which is endemic in several parts of the world, including India. Prophylactic vaccination using live attenuated vaccine is the preferred method of control. However, there is significant inter-individual variation in the antibody response to vaccination. In this study, we measured the E2 antibody blocking percentage after 21 days of CSF vaccination in a mixed pig population consisting of Landrace, indigenous Ghurrah pigs, and their crossbreds. A Genome Wide Association Study (GWAS) carried out using single-SNP and haplotype based methods detected a 1.6 Mb region on SSC2 (28.92−30.52 Mb) as significantly associated with antibody response to CSF vaccination. The significant region and 1 Mb flanking sequences encompass 3 genes – EIF3M, DNAJC24 and ARL14EP, which code for proteins involved in Pestivirus replication and host immune response system. Our results combined with previous studies on immune response of pigs present this region as a suitable candidate for future functional investigations. [ABSTRACT FROM AUTHOR]

The present study was undertaken to identify the microRNAs (miRNAs) expressed in the mammary tissue of a bubaline heifer. Small RNAs were isolated from the mammary gland tissue and enriched for miRNA fraction. The linker-ligated small RNAs were reverse transcribed to synthesize cDNA and amplified by PCR. The PCR products were ligated to the pGEM-T Easy vector; cloned into DH5 alpha cells and sequenced. Sequencing of 40 clones, randomly chosen from this library, produced 115 concatemerized short sequences. The short sequences were checked for their matches with the help of refseq_rna database, EST database (NCBI) and Ensembl. The analysis was performed for more than 90% identity with miRNAs across different species in miRBase. Alignment of putative small RNA sequences with the bovine genome was attempted in GenBank (NCBI) and Ensembl using BLAST. The small RNA sequences with a partial matches within the bovine genome and/or with flanking sequences (upstream or downstream) were analyzed for hairpin structures using the Mfold web server. Reverse complements were also assessed for the homology search. miRNA sequences showing only a partial match with already reported sequences were considered as a putative bubaline miRNAs. Six developmentally important putative miRNA precursors were identified from this study using cloning and sequencing followed by the Bioinformatics approach. This study will help in the elucidation of pathways involving miRNAs in bubaline species at the heifer stage. [ABSTRACT FROM AUTHOR]

Environmental temperature is one of the major factors to affect health and productivity of dairy cattle. Gene expression networks within the cells and tissues coordinate stress response, metabolism, and milk production in dairy cattle. Epigenetic DNA methylations were found to mediate the effect of environment by regulating gene expression patterns. In the present study, we compared three Indian native zebu cattle, Bos indicus (Sahiwal, Tharparkar, and Hariana) and one crossbred Bos indicus × Bos taurus (Vrindavani) for stress gene expression and differences in the DNA methylation patterns. The results indicated acute heat shock to cultured PBMC affected their proliferation, stress gene expression, and DNA methylation. Interestingly, expressions of HSP70, HSP90, and STIP1 were found more pronounced in zebu cattle than the crossbred cattle. However, no significant changes were observed in global DNA methylation due to acute heat shock, even though variations were observed in the expression patterns of DNA methyltransferases (DNMT1, DNMT3a) and demethylases (TET1, TET2, and TET3) genes. The treatment 5-AzaC (5-azacitidine) that inhibit DNA methylation in proliferating PBMC caused significant increase in heat shock-induced HSP70 and STIP1 expression indicating that hypomethylation facilitated stress gene expression. Further targeted analysis DNA methylation in the promoter regions revealed no significant differences for HSP70, HSP90, and STIP1. However, there was a significant hypomethylation for BDNF in both zebu and crossbred cattle. Similarly, NR3C1 promoter region showed hypomethylation alone in crossbred cattle. Overall, the results indicated that tropically adapted zebu cattle had comparatively higher expression of stress genes than the crossbred cattle. Furthermore, DNA methylation may play a role in regulating expression of certain genes involved in stress response pathways. [ABSTRACT FROM AUTHOR]

• "Inter-calving intervals reflect cattle reproductive capacity, influencing the sustainability of livestock production through impacts on lactation dynamics." • "Identification of numerous Quantitative Trait Loci (QTLs) associated with reproductive phenotypes in dairy cattle offers valuable insights for enhancing breeding strategies and genetic selection." • "Studying QTLs linked to reproductive traits not only informs livestock breeding practices but also contributes to advancements in biotechnology and broader fields like human health and conservation." From an economic standpoint, reproductive characteristics are fundamental for sustainable production, particularly for monotocous livestock like cattle. A longer inter-calving interval is indicative of low reproductive capacity. This issue changes the dynamics of current and future lactations since it necessitates more inseminations, veterinary care, and hormone interventions. Various reproductive phenotypes, including ovulation, mating, fertility, pregnancy, embryonic growth, and calving-related traits, are observed in dairy cattle, and these traits have been associated with several QTLs. Calving ease, age at puberty, scrotal circumference, and inseminations per conception have been associated with 4437, 10623, 10498, and 2476 Quantitative Trait Loci (QTLs), respectively. This data offers valuable insights into enhancing and comprehending reproductive traits in livestock breeding. Studying QTLs associated with reproductive traits has far-reaching implications across various fields, from agriculture and animal husbandry to human health, evolutionary biology, and conservation. It provides the foundation for informed breeding practices, advances in biotechnology, and a deeper understanding of the genetic underpinnings of reproduction. [ABSTRACT FROM AUTHOR]

Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (HO) and expected heterozygosity (HE) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by FROH, FHOM, FGRM and FUNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations. [ABSTRACT FROM AUTHOR]

• The study aimed to elucidate genetic diversity and selective sweeps in 82 Sahiwal cattle using ddRAD data. • A declining trend in the effective population size (74 in most recent generation) observed in the population which necessitates a breeding plan to maintain a sufficiently large Ne. The genomic inbreeding coefficients ranged from −0.0289 to 0.0725. • The LD estimates revealed a minimum of 114,800 SNP markers and at least 14,350 informative markers necessary for GWAS analysis and genomic selection studies, respectively. • We found 146 regions undergoing selective sweeps using five distinct statistical tests and these regions, located in non-overlapping. • We identified various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK) , as well as production traits (NRXN1, PLCE1, GHR). The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (F HOM , F UNI , F ROH , and F GROM), ranged from −0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075–35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population. [ABSTRACT FROM AUTHOR]

This study details about the phenotypic and molecular characteristics of multidrug‐resistant (MDR) Escherichia coli in the fresh community pond water (n = 257) collected from three districts of West Bengal, India. In total, 57 isolates were MDR of which 38 emerged as extended spectrum and 7 as AmpC‐type β‐lactamase producers in phenotypic assay. Among β‐lactamase genes, blaCTXM‐1was predominant (87.71%) followed by blaAmpC (77.2%) and blaTEM‐1 (22.8%). Six MDR strains carried metallo‐β‐lactamase (MBL, blaNDM‐1) gene. Tissue culture plate assay confirmed strong biofilm (SP) production in four MDR and one non‐MDR isolates. In PCR‐based replicon typing (PBRT), multiple plasmids of diverse replicon types (Frep, FIB, I1, FIA, K/B, HI1, and Y) were identified. The enterobacterial repetitive intergenic consensus–polymerase chain reaction (ERIC‐PCR)‐based phylogenetic analysis revealed a high degree of genetic divergence among the MDR isolates. Multiplex PCR‐based phylogrouping categorized 11 isolates as virulent (B2/D/F), which carried blaCTXM‐1 gene and three had blaNDM‐1 gene. Relative transcriptional activity of AcrAB efflux pump was significantly elevated among the SP and MBL producers. The presence of MDR E. coli isolates, particularly those resistant to carbapenem, in pond water used for daily domestic and household work, is a cause of concern as these pathogens may sneak into human food chain causing life‐threatening infections. Practitioner Points: Multidrug‐resistant biofilm producing E. coli isolated from community pond water.A few of them were carbapenem‐resistant and belonged to virulent (B2/D) types.Expression of AcrAB efflux pumps was found significantly elevated among biofilm producers and carbapenem‐resistant population. [ABSTRACT FROM AUTHOR]

The objective of this study was to calculate the extent and decay of linkage disequilibrium (LD) in 96 crossbred Vrindavani cattle genotyped with Bovine SNP50K Bead Chip. After filtering, 43,821 SNPs were retained for final analysis, across 2500.3 Mb of autosome. A significant percentage of SNPs was having minor allele frequency of less than 0.20. The extent of LD between autosomal SNPs up to 10 Mb apart across the genome was measured using r2 statistic. The mean r2 value was 0.43, if pairwise distance of marker was less than10 kb and it decreased further to 0.21 for 25–50 kb markers distance. Further, the effect of minor allele frequency and sample size on LD estimate was investigated. The LD value decreased with the increase in inter-marker distance, and increased with the increase of minor allelic frequency. The estimated inbreeding coefficient and effective population size were 0.04, and 46 for present generation, which indicated small and unstable population of Vrindavani cattle. These findings suggested that a denser or breed specific SNP panel would be required to cover all genome of Vrindavani cattle for genome wide association studies (GWAS). [ABSTRACT FROM AUTHOR]

This study describes comparative occurrence and characterization of multidrug-resistant (MDR) Escherichia coli and Klebsiella pneumoniae (KP) in healthy cattle (HC) and cattle with diarrhea (DC) in India. During 2018–2020, 72 MDR isolates, including 35 E. coli (DC: 27; HC 8) and 37 K. pneumoniae (DC: 34; HC: 3), from 251 rectal swabs (DC: 219; HC: 32) were investigated for extended-spectrum beta-lactamase (ESBL), AmpC type β-lactamase and carbapenemase production, antimicrobial susceptibility profile, biofilm production, and efflux pump activity. Fifty-five MDR isolates were ESBL producers (ESBLPs) (DC: 50; HC: 5) and ESBLPs from DC were coresistant to multiple antibiotics. The blaCTX-M gene (50) was the most frequently detected β-lactamases followed by blaAmpC (22), blaTEM1 (13), blaCMY-6 (6), blaOXA1 (5), blaPER (2), blaDHA, and blaFOX and blaSHV12 (1 each). Plasmid-mediated quinolone resistance determinants qnrB, qnrS, qnrA, and qepA were detected in 18, 16, 2, and 3 isolates, respectively. Twenty three isolates revealed mutation in gyrA and parC genes. Tetracycline-resistance markers tetA, tetB, tetC, and tetE were detected in 33, 10, 3, and 2 isolates, respectively. Only one of the 41 imipenem-resistant isolates harbored blaNDM-5 and two were colistin-resistant. Altogether, 20 MDR isolates were strong biofilm producers and 19 harbored different virulence factors. This is the first ever report from India on the presence of MDR Enterobacteriaceae with resistance to even last-resort antimicrobials in the bovine diarrhea. [ABSTRACT FROM AUTHOR]

The improvement in imputation accuracy diminished across different methods of selecting SNPs with increased panel density. 5 O'Brien, A.C., Judge, M.M., Fair, S. & Berry, D.P. (2019) High imputation accuracy from informative low-to-medium density single nucleotide polymorphism genotypes is achievable in sheep1. Genomic technologies have not penetrated enough in livestock, especially in developing nations where animals from a particular breed/population cannot be concurrently genotyped mainly due to financial constraints. [Extracted from the article]

Domestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and F ST , to detect selection signatures. A total of 179, 56, and 231 regions revealed 518, 277, and 267 candidate genes identified by iHS, ROH, and F ST methods, respectively. We found several candidate genes (e.g., NCR3 , ARID5A , HIST1H2BN , DEFB4 , DEFB7 , HSPA1L , HSPA1B, and DNAJB4) related to production traits and the adaptation of indigenous breeds to local environmental constraints such as heat stress and disease susceptibility. However, further studies are warranted to refine the findings using a larger sample size, whole-genome sequencing, and/or high density genotyping. • The combination of various statistical approaches could facilitate the wider spectrum of detection of both recent and ancient selection signatures. • The identified candidate genes provide insights into the adaptation and production performance of various cattle breeds. • Our observations can provide valuable knowledge for GWAS, genomic selection, implementing breeding schemes and conservation programmes. [ABSTRACT FROM AUTHOR]

• Indian pig breeds were found to be evolutionarily closer to Chinese than European pig breeds. • · Genetic diversity in Indian and Chinese breeds was found to be lower than European breeds. • In Indian pigs genes for adaptation to tropical climate and low input scavenging system were under positive selection. In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25–25.25 Mb region of SSC18, 123.25–124 Mb region of SSC15 and 118.75–119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16 , FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction. [ABSTRACT FROM AUTHOR]

• The review highlights the potential applications of genomic techniques in conservation purposes as well as discusses few case studies regarding the applications of conservation genomics in livestock and wildlife species. • Advancements in next-generation sequencing (NGS) technologies has generated a massive amount of data that is more fine-scaled and accurate and has thus resulted in more and more species becoming "genome enabled" • The conservation genetics-based "one gene, many individuals" strategy has given way to a conservation genomics-based "few individuals, several genes" approach. Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field. [ABSTRACT FROM AUTHOR]

[Display omitted] • Composition of dairy, swine and poultry farm wastewater is discussed. • Annamox and genetically modified bacteria-based treatment strategies are covered. • Microalgal, oxidation and membrane-based wastewater treatment are also discussed. • Bioplastic, biofertilizer and biofuel can be produced from farm wastewater. • Microalgal-microbial fuel cells can be developed using livestock wastewater. Livestock and poultry wastewater poses a potent risk for environmental pollution accelerating disease load and premature deaths. It is characterized by high chemical oxygen demand, biological oxygen demand, suspended solids, heavy metals, pathogens, and antibiotics, among other contaminants. These contaminants have a negative impact on the quality of soil, groundwater, and air, and is a potential hazard to human health. Depending on the specific characteristics of wastewater, such as the type and concentration of pollutants present; several physical, chemical and biological strategies have been developed for its treatment. This review aims at providing comprehensive overview of the profiling of livestock wastewater from the dairy, swine and poultry sub-sectors along with the biological, physico-chemical, AI-based and integrated treatment methodologies, and valorisation for the generation of value-added products such as bioplastics, biofertilizers, biohydrogen and microalgal-microbial fuel cells. Additionally, future perspectives for efficient and sustainable wastewater treatment are contemplated. [ABSTRACT FROM AUTHOR]

The present study was conducted on crossbred (Vrindavani) cattle calves to evaluate the effect of modified housing using different roofing materials on growth and physiological performance of calves during the rainy season. A total of twenty four calves (9-11 months old) were randomly selected and allocated in 4 groups viz. control (C): corrugated cemented sheet (CCS) as roofing material, T1: the CCS roof was painted black inside and white outside, T2: polycarbonate plastic sheet as roof and T3: polycarbonate roof with adjustable height. The overall average temperature was significantly (P<0.05) lower in T1 (26.89±0.04), followed by T3 (28.18±0.11), T2 (29.74±0.19) and C (30.55±0.06). Similarly temperature of the inner surface of roof was significantly (P<0.05) lower in T1 followed by T3 and higher in C during every fortnight. Overall average relative humidity (per cent) was significantly (P<0.05) lower in T3 (77.08±0.31) as compared to T1 (80.50±0.26), T2 (82.10±0.76) and C (82.92±0.12). Overall average THI was significantly (P<0.05) lower in T3 (76.56 ±0.23) followed by T1 (76.96 ± 0.07), T2 (78.35 ± 0.23) and C (79.30 ± 0.18). Total body weight gain (kg) was higher in T1 (32.67±0.76), followed by T3 (31.67±0.84), T2 (31.00±1.24) and C (30.83±0.48), however the difference was non-significant. The overall FCR was significantly lower (P<0.05) in T1 (9.94±0.24), T3 (10.01±0.14) followed by T2 (10.89±0.16) as compared control (11.76±0.18). The overall average rectal temperature and average respiration rate was significantly higher (p<0.05) in C (39.32±0.05 ºC, 26.07±0.29/min), followed by T2 (39.18±0.04 ºC, 24.17±0.37/min) and lower in T1 (38.98±0.03 ºC, 22.56±0.26/min) and T3 (39.06±0.03 ºC, 22.43±0.25/min). It may be inferred that the micro-environment was more conducive in T1 and T3 than control; hence the reflective paints on roof and adjusted higher height of polycarbonate roof may be the desirable choice for animal housing in view of mitigating heat stress during the hot-humid climate. [ABSTRACT FROM AUTHOR]

• Haplotype structure was elucidated in Vrindavani cattle via sliding window approach. • Haplotype-based association analysis was undertaken with (re)production traits. • Haplotypes showed significant association with AFC, TLMY, PY, DD, ICP and SP. • Overlapping candidate genes revealed pathways affecting the (re)production performance. Haplotype-based association analysis promises to reveal important information regarding the effect of genetic variants on economic traits of interest. The present study aimed to evaluate the haplotype structure of Vrindavani cattle and explore the association of haplotypes with (re)production traits of economic interest. Genotyping array data of medium density (Bovine50KSNP BeadChip) on 96 randomly selected Vrindavani cows was used in the present study. Genotypes were called in GenomeStudio program while quality control was undertaken in PLINK using standard thresholds. The phenotypic traits used in the present study included age at first calving, dry days, lactation length, peak yield, total lactation milk yield, inter-calving period and service period. The haplotype structure of Vrindavani population was assessed, using a sliding window of 20 SNP with a shift of 5 SNPs at a time, in terms of the size of haplotype blocks regarding their length (in Kb) and frequency in chromosome-wise fashion. Haplotype blocks were assessed for possible association with important production and reproduction traits across three lactation cycles in Vrindavani cattle population. The first ten principal components were included in the model for haplotype-based association analysis to correct for stratification effects of assessed individuals. Multiple haplotypes were found to be associated with age at first calving, total lactation milk yield, peak yield, dry days, inter-calving period and service period. Various candidate genes were found to overlap haplotypes that were significantly associated with age at first calving (CDH18, MARCHF11, MYO10, FBXL7), total lactation milk yield (TGF, PDE1A, and COL8A1), peak yield (PPARGC1A, RCAN1, KCNE1, SMIM34 and MRPS6), dry days (CPNE4, ACAD11 and MRAS), inter-calving period (ABCG5, ABCG8 and COX7A2L) and service period (FOXL2 and PIK3CB). The putative candidate genes overlapping the significantly associated haplotypes revealed important pathways affecting the production and reproduction performance of animals. The identified genes and pathways may serve as good candidate markers to select animals for improved production and reproduction performance in future generations. [ABSTRACT FROM AUTHOR]

The oral lesions associated with foot-and-mouth disease (FMD) negatively affect animal behavior, which can adversely impact animal production and welfare. Physical form of a therapeutic diet (TD) can improve the feed intake and wellbeing during the acute phase of FMD. Accordingly, we tested the effect of two physical forms of a previously developed TD on the behavior of calves experimentally infected with FMD virus (FMDV). Crossbred Holstein Friesian male calves of 10–12 months (n = 12) were experimentally infected with a virulent strain of FMDV and were offered a TD enriched with 19% CP and 2.9 Mcal ME/kg for 11 days post-FMDV infection. One group received the TD in mash form (TD M) while the other (n = 6/group) received it in cooked form (TD C). A group of four calves served as uninfected control and were fed TD M. The time spent by the calves on certain behaviours was recorded in a pre-set form from 06:00–18:00 h for 10 days from day 2–11 post-FMDV infection. The data was divided into two sessions. Session 1 (06:00–13:00 h) represented after the offering of TD, while session 2 (13:01–18:00 h) represented the data after offering green fodder. Based on exploratory data analysis, data recorded from day 2–7 post-FMDV infection was included in the final analysis. Linear mixed model was used by fitting treatment, day and their interaction as fixed effects while calf as random effect. Orthogonal contrast was applied by comparing the infected TD M with other two groups. The results revealed that the cooked form of TD improved the ingestion time, resting time, sleeping time and licking time from day 2–7 post-FMDV infection as compared with the infected TD M group. Ingestive behaviour was better in the infected TD C than that of TD M group (p < 0.01). The sleeping time was significantly high in the infected groups as compared to the uninfected TD M group (p < 0.01) till day 6 post-FMDV infection. Daily activities such as licking, standing and resting differed significantly between the infected TD M and TD C groups in session 1, but not in session 2. Urination and defecation did not differ significantly between the infected TD M and TD C groups. It was concluded that cooked form of TD remediated the effects of infection with FMDV as evidenced by improvement in the behaviour of the calves. • Experimental FMDV infection adversely affected the behaviours, but not the daily activities in the calves. • Ingestive behaviour was better with cooked form of therapeutic diet (TD C) than that of mash form (TD M) in FMDV infected calves. • Licking, standing, and resting activities differed significantly between the infected TD M and TD C groups. [ABSTRACT FROM AUTHOR]

The assessment of productive and reproductive performances of pig breeds have been done in different countries of the world. However, the same study for indigenous or so called desi pigs in different parts of India is limited. It is now believed that the study of some productive and reproductive traits is most essential to evaluate the potentiality of these indigenous pigs. In India, only limited studies on productive and reproductive traits have been carried out on indigenous pigs that too detailed studies have been done only in three recognised pig breeds namely Ghungroo, Niang-Megha and Agonda Goan. The desi pigs are having very sound reproductive efficiency and medium production potential. These characteristics of desi pigs are very much suitable to the small pig farmers with low input production system for livelihood and sustainable pig farming. These productive and reproductive analyses will be useful in the selection of breeding stock for future parent generation. [ABSTRACT FROM AUTHOR]

• The review covers livestock genomics of South Asian cattle, buffalo, sheep, goat, pig, camel, horse, yak, mithun, and poultry. • Advancements in next-generation sequencing (NGS) technologies led to the discovery of numerous SNP arrays for different livestock species. • The application of genomics in animal breeding has had the biggest economic impact on livestock production. Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements. [ABSTRACT FROM AUTHOR]

• CU CPT 4a inhibited TLR3 expression resulted in decreased clinical signs, pathological lesions, and increased survival time in SRABV-infected mice. • Decreased expression of pro-inflammatory cytokines during TLR3-inhibition indicated anti-inflammatory effect of CU CPT 4a. • TLR3-inhibited group revealed normal CD4+/CD8+ T - cells ratio with less TUNEL-positive apoptotic cells in SRABV-infected mice. • SRABV-infected and mock-treated mice showed severe clinical signs and histopathological lesions, more NBs formation, viral load and TLR3 expression. Rabies is a zoonotic viral disease with inevitably fatal outcome. Toll-like receptor 3 (TLR3) could sense dsRNA viral infections, and implicated in pathogenesis of rabies and Negri bodies (NBs) formation. Present study was undertaken to elucidate the role of TLR3 in pathogenesis, NBs formation, and therapeutic potential of blocking TLR3/dsRNA interaction in rabies infection. Young Swiss albino mice were infected with 100 LD 50 of street rabies virus (SRABV) intracerebrally (i/c) on day 0 and treated with 30 μg of CU CPT 4a (selective TLR3 inhibitor) i/c on 0, 3 and 5 days post-infection (DPI). Three mice each were sacrificed at 1, 3, 5, 7, 9, 11, and 13 DPI to study sequential pathological consequences through histopathology, Seller's staining, immunofluorescence, immunohistochemistry, TUNEL assay, flow cytometry, and viral and cytokine genes quantification by real-time PCR. CU CPT 4a inhibited TLR3 expression resulted in delayed development and decreased intensity of clinical signs and pathological lesions, low viral load, significantly reduced NBs formation, and increased survival time in SRABV-infected mice. These parameters suggested that TLR3 did influence the SRABV replication and NBs formation. Inhibition of TLR3 led to decreased expression of pro-inflammatory cytokines and interferons indicated an anti-inflammatory effect of CU CPT 4a during SRABV infection. Further, TLR3-inhibited group revealed normal CD4+/CD8+ T - cells ratio with less TUNEL-positive apoptotic cells indicated that immune cell kinetics are not affected during TLR3-inhibition. SRABV-infected and mock-treated mice were developed severe clinical signs and histopathological lesions, more NBs formation, high viral load, increased pro-inflammatory cytokines expression in brain, which were correlated with higher expression levels of TLR3. In conclusion, these data suggested that TLR3/dsRNA signaling pathway could play critical role in pathogenesis of SRABV infection in vivo and opens up new avenues of therapeutics. [ABSTRACT FROM AUTHOR]

Peste-des-Petits-Ruminants (PPR) or goat plague is an important viral disease of sheep and goats caused by the small ruminant morbilli virus or PPR virus (PPRV). Long non coding RNAs (lncRNA) and circular RNAs (circRNA) play a pivotal role in several biological processes including regulation of virus-host interactions. The present study explored the expression of lncRNA, circRNA and their functions in PPRV infected B-lymphocyte (B95a) cells. The results revealed a total of 4531 lncRNA and 2348 circRNA expression in both mock and PPRV infected samples. Analysis of differentially expressed (DE) RNA identified 123 DE-lncRNA and 39 DE-circRNA as significantly dysregulated. Functional analysis of cis -target genes of DE-lncRNA indicated activation of TCF dependent WNT signaling and PKN1 stimulated transcription process. Interactions (sponging) of microRNA (miRNA) revealed 344 DE-lncRNA-miRNA and 93 DE-circRNA-miRNA pairs. The competing endogenous RNA (ceRNA) network of lncRNA/circRNA-miRNA-mRNA in PPRV infected B95a cells was represented by 69 ceRNA pairs. We validated the DE-circRNA by targeted amplification and sequencing of back spliced junctions (BSJs). The present study revealed a profile of lncRNA, circRNA and their potential ceRNA network in PPRV infection. The results provide insight for better understanding of PPRV-host interactions. • Peste-des-Petits-Ruminants Virus (PPRV) infection altered the lncRNA and circRNA expression in the host cells. • Dysregulated lncRNA and circRNA affected different cellular functions through their cis -target genes. • A competing endogenous RNA (ceRNA) network represent potential PPRV-host interactions. [ABSTRACT FROM AUTHOR]