Attention module incorporated transfer learning empowered deep learning-based models for classification of phenotypically similar tropical cattle breeds (Bos indicus).

Accurate breed identification in dairy cattle is essential for optimizing herd management and improving genetic standards. A smart method for correctly identifying phenotypically similar breeds can empower farmers to enhance herd productivity. A convolutional neural network (CNN) based model was developed for the identification of Sahiwal and Red Sindhi cows. To increase the classification accuracy, first, cows's pixels were segmented from the background using CNN model. Using this segmented image, a masked image was produced by retaining cows' pixels from the original image while eliminating the background. To improve the classification accuracy, models were trained on four different images of each cow: front view, side view, grayscale front view, and grayscale side view. The masked images of these views were fed to the multi-input CNN model which predicts the class of input images. The segmentation model achieved intersection-over-union (IoU) and F1-score values of 81.75% and 85.26%, respectively with an inference time of 296 ms. For the classification task, multiple variants of MobileNet and EfficientNet models were used as the backbone along with pre-trained weights. The MobileNet model achieved 80.0% accuracy for both breeds, while MobileNetV2 and MobileNetV3 reached 82.0% accuracy. CNN models with EfficientNet as backbones outperformed MobileNet models, with accuracy ranging from 84.0% to 86.0%. The F1-scores for these models were found to be above 83.0%, indicating effective breed classification with fewer false positives and negatives. Thus, the present study demonstrates that deep learning models can be used effectively to identify phenotypically similar-looking cattle breeds. To accurately identify zebu breeds, this study will reduce the dependence of farmers on experts.

Deciphering the immune responses in late gestation Sahiwal cows under different microclimate and its carryover effect on progenies.

The current investigation aimed to comprehend the inflammatory and related immune responses in intrauterine calves subjected to heat stress (HS) during late gestation. For this purpose, 48 Sahiwal cows in late gestation were chosen and categorized into four equal groups: naturally heat stressed (NHS), cooling-treated (CLT), spring, and winter, and likewise their neonate calves born in summer (IUHS - intrauterine heat stressed and IUCL - intrauterine cooled), spring, and winter seasons. Environmental parameters were recorded, and the temperature-humidity index (THI) was calculated daily throughout the study period. The average THI values ranged between 84.18 (summer-NHS), 73.88 (summer-CLT), 78.92 (spring), and 64.91 (winter). NHS and spring groups exhibited thermal stress based on THI (> 76.00). Various treatments significantly (P < 0.01) impacted parameters like rectal temperature (RT), respiratory rate (RR), pulse rate (PR), and skin temperature (ST) in Sahiwal cows and their calves during the study, except for heart rate (HR). Blood samples collected during different seasons and from cows housed in a climatic chamber were used to extract plasma. Plasma cortisol, interleukin-6 (IL-6), tumour necrosis factor-α (TNF-α), and thiobarbituric acid reactive substances (TBARS) levels were notably higher (P < 0.05) in the NHS compared to the CLT group. Conversely, total antioxidant capacity (TAC) and immunoglobulin G (IgG) levels were higher (P < 0.05) in the CLT and winter groups. IUHS calves exhibited significantly (P < 0.05) lower overall mean plasma TAC and IgG levels but higher inflammatory and oxidative biomarkers, such as IL-6, TNF-α, and TBARS. Additionally, significant impacts on body weight were observed for factors such as interval (P < 0.01) and the interaction between treatment and interval (P < 0.05), exhibiting consistently lower body weight in IUHS calves throughout the study period. These findings suggest that late gestation heat stress may lead to physiological alterations in future calves. Strategies aimed at mitigating heat stress during late gestation should be considered not only for the productivity and well-being of the pregnant dam but also for the development and future performance of the calf.

Validation of Bos taurus SNPs for Milk Productivity of Sahiwal Breed (Bos indicus), Pakistan.

The aim of the present study was the validation of the already reported Bos taurus SNPs in the Sahiwal breed. A total of nine SNPs of the casein gene were studied. Out of nine, seven Bos taurus SNPs of casein protein genes were found to be significantly associated with milk productivity traits. The genomic DNA was extracted from the mammary alveolar endothelial cells of a flock of 80 purebred Sahiwal lactating dams available at Khizrabad Farm near Sargodha. New allele-specific primers were designed from the NCBI annotated sequence database of Bos taurus to obtain 100 nt-long PCR products. Each dam was tested separately for all the SNPs investigated. Animals with genotype GG for the SNPs rs43703010, rs10500451, and 110323127, respectively, exhibited high milk yield. Similarly, animals with genotype AA for the SNPs rs11079521, rs43703016, and rs43703017 showed high milk yield consistently. For the SNP rs43703015, animals with genotype CC showed high milk productivity. These above-mentioned SNPs have previously been reported to significantly up-regulate casein protein contents in Bos taurus. Our results indicated SNPs that significantly affect the milk protein contents may also significantly increase per capita milk yield. These finding suggest that the above-mentioned reported SNPs can also be used as genetic markers of milk productivity in Sahiwal cattle.

Economic viability of using OvSynch and fixed timed artificial insemination protocol in breeding improvement of pastoral herds in the rangelands.

Though using Assisted Reproductive Technologies (ARTs) can improve oestrus detection, conception and pregnancy success, thus benefit breeding program implementation, empirical evidence of their economic viability is lacking to inform investment decisions in pastoral herds. This study assessed economic viability of using OvSynch and fixed Timed Artificial Insemination (TAI) protocol in Sahiwal upgrading breeding program under two hypothetical cases of best and worst in activity-based money allocations when pastoral herds deploy either optimal or low input husbandry practices. From herd owners' assessment of milk production, best-case scenarios attain on average 10 L/cow/day with optimal husbandry and 5 L/cow/day with low input husbandry. The worst-case scenarios attain 5 L/cow/day with optimal husbandry and 1 L/cow/day with low input husbandry. Benefit- Cost Analysis (BCA) estimated Net Present Value (NPV), Benefit-Cost ratio (BCR) and Internal Rate of Return (IRR) to establish economic viability of using OvSynch and TAI Protocol in pastoral breeding programs. Both best-case scenarios retuned positive NPVs (82,028 and 6,912), BCR values (1.68 and 1.08) and IRR (27.46% and 8.08%) while worst-case scenarios returned negative NPVs (-135,855 and -141,025), BCR values of below 1 (0.87 and 0.66) and IRR values below the minimum rate of returns. These economic parameters were sensitive to price changes in inputs and outputs, under both optimal and low input husbandry practices. Results indicate that using OvSynch and TAI Protocol is a profitable and economically viable investment under optimal husbandry practices but not under low input husbandry practices. By implications, use of OvSynch and TAI Protocol in Sahiwal upgrading breeding programs need be accompanied with improved husbandry practices and de-risking pastoral herd owners from price changes in input and output markets.

Genome-wide mining of diversity and evolutionary signatures revealed selective hotspots in Indian Sahiwal cattle.

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 (FHOM, FUNI, FROH, and FGROM), 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.

Seasonal assessment of mastitis using thermogram analysis in Sahiwal cows.

"India is the world's leading producer of milk" and demands a non-invasive diagnostic tool like infrared thermography (IRT) to identify the costliest production disease, mastitis. It can form the basis of precision dairy farming. Therefore, the present study focuses on thermal imaging of the udder and teat quarters of Sahiwal cows during different seasons to identify subclinical (SCM) and clinical mastitis (CM) cases using the Darvi DTL007 camera. A total of 24-69 lactating Sahiwal cows were screened out using IRT regularly throughout the year. The intramammary infection status was further assessed using the CMT. The receiver operating characteristic analysis was carried out to develop the current study's cut-off for various thermographic parameters. The incidence for SCM and CM ranged from 26.47 to 38.75% and 17.83-22.79%, respectively during different seasons in Sahiwal udder quarters. The thermogram analysis revealed a significant difference (p < 0.01) in the mean values of the udder and teat surface temperature of Sahiwal cows between healthy, SCM, and CM during different seasons. The mean values of udder skin surface temperature (USST) during different seasons ranged between 29.07 and 36.91 °C, 31.51 to 37.88 °C and 32.42 to 38.79 °C among healthy, SCM, and CM-affected quarters, and correspondingly, the mean values of teat skin surface temperature (TSST) were 28.28 to 36.77 °C, 30.68 to 37.88 °C and 31.70 to 38.73 °C, respectively. Further results revealed an increase (p < 0.01) in the mean values of USST during winter, summer, rainy, and autumn as 2.44, 3.35; 0.97, 1.88; 1.06, 1.83; 1.29, 2.39 °C and TSST as 2.4, 3.42; 1.11, 1.96; 1.21, 2.19, 1.3, 2.4 °C of SCM, CM-affected quarters to healthy quarters, respectively, in Sahiwal cows. Thermograms showed a strong positive correlation with the CMT scores of SCM, CM cases, and healthy samples. Henceforth, irrespective of the seasons studied in the present work, IRT is an efficient, supportive tool for the early identification of subclinical mastitis.

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.

Comparative RNA isolation methods from fresh ejaculated spermatozoa in Sahiwal cattle (Bos indicus) and Murrah buffalo (Bubalus bubalis) bulls for high quality and enhanced RNA yield.

Sperm mRNA transcriptional profiling can be used to evaluate the fertility of breeding bulls. The aim of the study was to compare the modified RNA isolation methods for higher RNA yield and quality from freshly ejaculated sperm of cattle and buffalo bulls. Ten fresh ejaculates from each Sahiwal (n = 10 bulls × 10 ejaculates) and Murrah bulls (n = 10 bulls x 10 ejaculates) were used for RNA isolation. From the recovered live sperm, total sperm RNA was isolated by conventional methods (TRIzol, Double TRIzol), membrane-based methods combined with TRIzol (RNeasy + TRIzol) with the addition of ß-mercaptoethanol (BME) and Kit (RNeasy mini) methods in fresh semen. Among different isolation methods; the membrane-based modified methods combined with TRIzol (RNeasy + TRIzol) with the addition of ß-mercaptoethanol (BME) resulted significantly (p < .05) higher total RNA quantity (300-340 ng/µL) and better purity in different concentrations of spermatozoa viz., 30-40 million, 70-80 million and 300-400 million sperm. The study concluded that the inclusion of BME to the combined membrane-based methods with somatic cell lysis buffer solution was best for constant increased yield and purity of RNA isolation from Sahiwal cattle and Murrah buffalo bull sperm.

Moringa oleifera leaf meal supplementation improves nutrient digestibility, milk yield, and reproductive performances in dairy cows during early lactation.

The study aimed to evaluate the effects of Moringa oleifera leaf meal (MOLM) supplementation on nutrient utilization, milk yield, and reproductive performance of early lactating Sahiwal cows. Control cows (GC) received a basal diet, while the treatment cows (GM) were supplemented with concentrate comprising 12% MOLM. Ovarian activity and uterine involution were monitored by trans-rectal ultrasonography on the 21st, 28th, 35th, and 42nd days postpartum. The result indicated that MOLM-supplemented cows required fewer days (P ≤ 0.05) to complete uterine involution. As lactation progresses, there was a significant reduction (P ≤ 0.05) in the diameter of the cervix and uterine horns in GM than GC. There was a significant increase in the number of follicles on the 21st day and average milk yield in GM than GC. The incidence of endometritis and cystic ovarian disease was less in MOLM supplemented group. The use of MOLM in the diet reduced the total cost per cow per successful service. It is concluded that MOLM can be safely included at 12% in the diet of early lactating cows to modulate the reproductive performances of dairy cows. Dairy farmers can use moringa leaf meal to feed their dairy cows, which is cheaper and improves production and reproduction performance.

Investigation of milk microbiota of healthy and mastitic Sahiwal cattle.

BACKGROUND: Sahiwal cattle is an indigenous cattle breed of Pakistan and mastitis is one of the major problems faced by Sahiwal cattle which hinders its production potential. The study was designed to investigate the milk microbiota of healthy and mastitic Sahiwal cattle as part of a multistep project to develop probiotics for the mitigation and control of mastitis. Milk samples of Sahiwal cattle (healthy clinical mastitis and subclinical mastitis) reared under similar husbandry and management practices were processed for 16S rRNA gene base metagenomics analysis. RESULTS: Results revealed that Proteobacteria were dominant in the healthy group and subclinical mastitis group (56.48% and 48.77%, respectively) as compared to the clinical mastitis group (2.68%). In contrast, Firmicutes were abundant in the clinical mastitis group (64%) as compared to the healthy and subclinical mastitis groups (15.87% and 38.98%, respectively). Dominant species assigned in the healthy group were Ignavibacterium album, Novosphingobium capsulatum, Akkermansia muciniphila and Lactobacillus fermentum.The clinical mastitis group was dominated by Streptococcus dysgalactiae and Corynebacterium bovis, while subclinical mastitis group included Lactobacillus fermentum and uncultured acidobacteriales and Akkermansia muciniphila as dominant species. Alpha diversity indices showed higher microbial diversity in the healthy group compared to the clinical and sub-clinical mastitis groups. CONCLUSION: It is concluded that the milk microbiota of healthy sahiwal cattle has higher diversity and dominant taxa in the different groups may be used as signature microbes for mastitis susceptibility. Akkermansia muciniphila is one of candidate specie that was identified and may be used for development of probiotics.

Short-milking-tube thermograms: An alternative to udder thermograms for mastitis detection in Sahiwal cows.

Mastitis is a multi-etiological production disease that causes substantial financial loss to dairy farmers. In this context, early detection of mastitis using thermograms can aid the dairy sector in managing mastitis efficiently, and this technology could be a supportive tool in precision dairy farming. Infrared cameras can detect minor temperature changes on the udder surface by taking multiple images of the udder and teat. In the current study, a thermogram of the short milking tube (SMT) of the milking machine, as well as the udder and teat of lactating Sahiwal cow (n = 100 quarters of 25 Sahiwal cows), was captured using a hand-held digital infrared thermal camera (DarviDTL007) during morning milking to assess the mastitis status. CMT and SCC of milk samples were carried out for further confirmatory diagnosis of healthy, sub-clinical (SCM), and clinical mastitis (CM). Cut-offs for short milking tube temperature were developed using the receiver operating characteristics analysis. Results of thermal image analysis revealed that the pre-milking, milking, and post-milking parameters of the udder and the teat skin surface temperatures showed a significant difference in the healthy, SCM, and CM-affected quarters. The thermogram analysis showed a significant increase (p < 0.05) of 1.11 and 2.04°C in the mean values of SMT surface temperature among SCM and CM quarters compared to healthy quarters, respectively. In addition, the values of CMT and SCC revealed a significant increase (p < 0.05) in SCM and CM samples and a positive correlation to SMT surface temperatures. Short milking tube thermograms can be a useful assessment tool for detecting sub-clinical mastitis in dairy animals.

Genome wide mining of SNPs and INDELs through ddRAD sequencing in Sahiwal cattle.

The study was conducted in Sahiwal cattle for genome wide identification and annotation of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) in Sahiwal cattle. The double digest restriction-site associated DNA (ddRAD) sequencing, a reduced representation method was used for the identification of variants at nucleotide level. A total of 1,615,211 variants were identified at RD10 and Q30 consisting of 1,480,930 SNPs and 134,281 INDELs with respect to the Bos taurus reference genome. The SNPs were annotated for their location, impact and functional class. The SNPs identified in Sahiwal cattle were found to be associated with a total of 26,229 genes. A total of 1819 SNPs were annotated for 209 candidate genes associated with different production and reproduction traits. The variants identified in the present study may be useful to strengthen the existing bovine SNP chips for reducing the biasness over the taurine cattle breeds. The diversity analysis provides the insight of the genetic architecture of the Sahiwal population Studied. The large genetic variations identified at the nucleotide level provide ample scope for implementing an effective and efficient breed improvement programme for increasing the productivity of Sahiwal cattle.

Genome-wide in silico analysis leads to identification of deleterious L290V mutation in RBBP5 gene in Bos indicus.

Genome-wide deleterious mutations were identified in zebu cattle (Bos indicus) using in silico approach. The ddRAD sequence data of Sahiwal cattle were annotated and aligned with the cattle reference genome (ARS-UCD1.2). A total of 279,383 SNPs were identified at Read Depth10, which were further filtered to 692 missense SNPs. These SNPs were further analyzed, for functional consequences, by using Variant Effect Predictor, PolyPhen, PROVEAN, and PANTHER tools. A total of 18 SNPs, were finally identified as deleterious, and among these, 12 SNPs were mapped on nine different genes. ERRAT, ProSA-web, Project HOPE, TM-Align, and YASSARA tools, further confirmed the protein malfunctioning of one missense (L290V) mutation of Retinoblastoma binding protein-5 (RBBP5) gene, transcribing a cell cycle regulatory protein and associated with Retinoblastoma in human. This derived bioinformatics pipeline may be useful for preliminarily identifying the deleterious DNA mutations in livestock, specifically in absence of any genetic disease records.

Tinospora cordifolia modulates the seminal parameters, leakage of intracellular enzymes and seminal antioxidants in equilibrated and cryopreserved semen of Sahiwal bulls.

The present study was undertaken to assess the effects of stem extract of Tinospora cordifolia (Giloy or Guduchi) in the semen extender on seminal parameters, leakage of intracellular enzymes and antioxidants in semen of Sahiwal bull. A total of 48 ejaculates from four bulls were selected for the study. Spermatozoa of 25 × 106 were incubated in 100, 300 and 500 µg of stem extract of Guduchi as Gr II, III and IV, respectively, and pre-freeze and post-thaw semen samples were analysed for seminal parameters [motility, viability, total sperm abnormality (TSA), plasma membrane integrity (PMI) and acrosomal integrity (AcI)], intracellular enzymes [aspartate aminotransferase (AST) and lactate dehydrogenase (LDH)] and seminal antioxidants [superoxide dismutase (SOD) and catalase] in comparison with an untreated control group (Gr I). The results revealed that stem extract-treated semen had significantly (p < .05) higher motility, viability, PMI, AcI, SOD and catalase and had significantly (p < .05) lower TSA, AST and LDH compared to those in untreated control group at pre-freeze and post-thaw stages. Semen treated with 100 µg stem extract/25 × 106 spermatozoa had significantly (p < .05) higher motility, viability, PMI, AcI, SOD and catalase and had significantly (p < .05) lower TSA, AST and LDH compared to those in control, 300- and 500-µg-treated groups at pre-freeze and post-thaw stages. Further, these seminal parameters and antioxidants were showing decreasing trend and TSA and leakage of intracellular enzymes were showing increasing trend from Gr II to Gr IV at pre-freeze and post-thaw stages. Thus, 100 µg/25 × 106 spermatozoa were optimum or suitable dose for cryopreservation of Sahiwal bull semen. The study concluded that T. cordifolia stem extract 100 µg/25 × 106 spermatozoa in the semen extender can be effectively utilized to reduce the oxidative stress and improve the pre-freeze and post-thaw seminal parameters in Sahiwal bull. However, further studies on effects of different concentrations of stem extract on in vitro or in vivo fertility trials are to be conducted to assess the impact of the stem extract supplementation in the semen extender on field pregnancy outcomes in bovine species.

Response to hormonal treatment and conception rates of Sahiwal cows subjected to fixed time artificial insemination in pastoral dairy systems.

This study aimed at determining factors influencing response of Sahiwal cows/heifers to fixed time artificial insemination protocol in pastoral systems in Kenya. Available cows/heifers were inspected for conformity to Sahiwal breed characteristics, parity, body condition score, and subsequently rectal palpation to determine pregnancy status, ovarian structures, and estimated ovarian diameter. Consequently, these animals were injected with 100 µg of gonadotrophin-releasing hormone. On days 7 and 9, only responsive cows/heifers were injected with 500 µg of cloprostenol and 100 µg of gonadorelin Acetate, respectively. On day 10, animals were inseminated and separated from bulls for 45 days and pregnancy diagnosis done after 90 days. Analysis of variance was performed to determine the effects of production system, parity, and ovarian structures on ovary diameters pre- and post-hormonal treatment. Logistic regression was used fitting a logit function to account for the binomial distribution of conception. Overall, 56.2%, 23.1%, and 20.7% of the animals had follicles (F), corpus luteum (CL), and corpus albicans (CA), respectively, at day 0, and 16.6%, 68.6%, and 14.8%, respectively, at day 7. Human and environmental factors had no influence on conception. Among the animal factors, only the ovarian structures at day 7 had a significant effect on conception. Ovaries with CL at this time were about 6 times significantly more likely to conceive than those with F. For higher conception rates, animals with ovaries with CL should be recruited into the FTAI program as they are significantly more likely to conceive than those with other ovarian structures.

Influence of endometritis on the follicular dynamics, recovery, quality, gene expression, nuclear maturation and in-vitro developmental competence of oocytes in Sahiwal cattle.

Uterine infections often lead to culling of valuable animals from a herd, resulting in genetic drain. The genetic potential of problematic females could be harvested by in-vitro embryo production. The objective of this study was to evaluate the effect of clinical endometritis on follicular dynamics, recovery, quality, gene expression, nuclear maturation and in-vitro developmental competence of oocytes in Sahiwal cattle. The B-mode ultrasonography was performed to examine the uterus for the presence of pus. Based on the history and reproductive examination of cows, a total of twelve (n = 12) Sahiwal cattle were selected for the experiment: (1) healthy group (n = 6) and (2) clinical endometritis group (n = 6). The 1st ovum pick-up (OPU) was conducted on day 165 postpartum. The collected cumulus oocytes complexes (COCs) were graded into A, B, C and D grades depending on the number of layers of cumulus cells and homogeneous nature of cytoplasm. Nuclear maturation was assessed by staining the oocytes with Hoechst 33,342. The results revealed that the number of medium-sized follicle (1.3 ± 0.1 versus 0.6 ± 0.1) and total number of follicles (9.1 ± 0.7 versus 6.6 ± 0.7) were higher (p < .05) in the healthy group as compared to clinical endometritis group, respectively. Similarly, the number of oocytes recovered (5.0 ± 0.4 versus 2.8 ± 0.4), oocytes with grade A, B and C (2.9 ± 0.3 versus 1.5 ± 0.3), proportion of oocytes with grade A or B (33 ± 0.0 versus 20 ± 0.1) and nuclear maturation (68 ± 0.1 versus 55 ± 0.1) were also higher (p < .05) in the healthy group as compared to clinical endometritis group, respectively. Perhaps, cleavage rate (55.1 ± 0.1 versus 46.2 ± 0.1) and blastocyst rate (29.7 ± 0.0 versus 26.3 ± 0.1) did not differ (p > .05) between the groups. Likewise, the expression level of growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) in immature oocytes did not differ (p > .05) between both the groups. In conclusion, clinical endometritis has a negative effect on follicular dynamics, oocyte recovery, oocyte quality and nuclear maturation; furthermore, the developmental competence of COCs is not compromised by it.

Effect of non-genetic factors on linear type traits in Karan fries (Bos taurus × Bos indicus) and Sahiwal (Bos indicus) cows in sub-tropical climatic conditions of India.

The focus of present study was to find out the effect of non-genetic factors on linear type traits in Karan Fries and Sahiwal cows reared at an organized farm of northern India. The present study was conducted on Lactating Karan Fries (N = 123) and Sahiwal (N = 133) cows maintained at Livestock Research Center of ICAR- National Dairy Research Institute, Karnal, India during the period of 2017-2019. Total eight udder morphometric traits and seven teat morphometric traits were measured. The linear model including fixed effects of season, parity and stage of lactation was used for the analysis. In Karan Fries cows, linear type traits were significantly affected by parity and stage of lactation, while in Sahiwal cows linear type traits were significantly affected by season, parity and stage of lactation. Udder depth (UD) and udder circumference (UC) were significantly (p < 0.05) affected by season, parity and stage of lactation in Sahiwal cattle, while in Karan Fries cattle udder length (UL) and shortest distance from rear teat ends to floor (SDR) were significantly (p < 0.01) affected by parity and stage of lactation. The results pertaining to present study indicated that season, parity and stages of lactation were important sources of variation for most of linear type traits. Adjustment of data for these effects is necessary to reduce known differences between animals and to obtain reliable estimates of the traits.

Nano Copper Supplementation Increases Superoxide Dismutase and Catalase Gene Expression Profiles and Concentration of Antioxidants and Immune Variables in Sahiwal Heifers.

This study was conducted to evaluate the effect of inorganic and nano copper (nanoCu) supplementation on superoxide dismutase (SOD) and catalase (CAT) gene expression, antioxidant status, and immune response in growing Sahiwal heifers. Twenty-four Sahiwal heifers were allocated at random into four groups of six heifers in each groups and fed for 120 days. Feeding regimen was similar in all the groups except that treatment groups were supplemented with 0.0 mg Cu, 10.0 mg inorganic copper (inCu), and 5.0 and 10.0 mg of nanoCu per kg dry matter (DM) in four respective groups. Feed intake and growth performance were similar in growing Sahiwal heifers fed on basal diet with or without supplemental Cu. Antioxidative variables like SOD, CAT, ceruloplasmin (Cp), total antioxidant status (TAS), and glutathione peroxidase (GSH-Px) were found higher in Cu-supplemented groups than control. Variables like malondialdehyde (MDA) and lipid peroxidation (LPO) were found lower in treatment groups than control. Total immunoglobulins (total Ig) and immunoglobulin G (IgG) were higher in treatment groups than control, although interleukin-6 (IL-6) was similar in all groups. There were upregulation of mRNA expression of SOD and CAT genes in experimental animals fed on Cu-supplemented diet while mRNA expression of interleukin-6 (IL-6) and interleukin-10 (IL-10) genes was not altered by dietary treatment. The results suggest that the level of 5-ppm nanoCu can be selected for feeding in growing cattle as it exerts similar effects as showed by 10-ppm inorganic Cu.

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.

Effect of BsaA I genotyped intronic SNP of leptin gene on production and reproduction traits in Indian dairy cattle.

In the present study, candidate single nucleotide polymorphism (SNP) g.92450765 G > A of leptin gene was explored for Bos indicus cattle with an aim to explore its possible effect on production and reproduction traits. The genotypic and allelic frequencies of BsaA 1 genotyped SNP g.92450765 G > A indicated the predominance of AG (0.65) genotyped Sahiwal cows in our studied population. The least-squares analysis showed a significant association (p < 0.05) of identified genetic variants with total milk yield (TMY) and 305 days milk yield (MY) (p < 0.05). The GG genotyped cows were found to be associated with higher milk yields. However, for reproduction traits under study AA genotype was found to be more favorable with respect to service period and calving interval (p < 0.05). Computational analysis was also performed to predict changes if any in the transcription factor binding sites (TFBS) caused due to the identified SNP in the intronic region of the leptin gene. TFBS analysis predicted that the targeted SNP at g.92450765G > A may lead to the disappearance of TFBS such as Hypermethylated in cancer 2 protein (HIC2), Max-binding protein MNT (MNT), Cyclic AMP-dependent transcription factor -3 (ATF3), Myc-associated factor X (MAX) and Microphthalmia-associated transcription factor (MITF). It may lead to changes in transcriptional regulation.