hadeer aboshady

Identification of plasma biomarkers for feed efficiency in growing beef cattle offers a promising opportunity for developing prediction models to improve precision feeding strategies. However, these models must accurately predict feed efficiency at early stages of fattening. Our study aimed to evaluate the reliability of candidate biomarkers previously identified in late-fattening cattle when analysed during early fattening stages and to develop diet-specific prediction equations for residual feed intake (RFI). From a total of 364 Charolais bulls across seven cohorts, we selected 64 animals with extreme RFI values. The animals were fed either a corn‑ or grass-silage diets. These animals were chosen from four out of the available seven cohorts. Animals from three cohorts (24 high-RFI and 24 low-RFI, having a mean RFI difference of 1.48 kg/d) were used for biomarker confirmation and prediction model training. Animals from a fourth cohort (8 high-RFI and 8 low-RFI, having a mean RFI difference of 0.98 kg/d) were used for model external validation. Blood samples were collected at the beginning of the feed efficiency test (333 ± 20 days), and plasma underwent targeted metabolomic for 630 metabolites, natural abundance of N (δN), insulin, and IGF-1 analysis. Seven previously identified plasma biomarkers for RFI in late-fattening beef cattle still kept their capability for discriminating low and high RFI animals when analysed during early fattening stages (P < 0.05). Among these confirmed biomarkers, five were common for both grass- and corn-fed animals (creatinine, β-alanine, triglyceride TG18:0_34:2, symmetric dimethyl-arginine and phosphatidylcholine PC aa C30:2) while two were diet-specific (IGF-1 for grass silage-based diet, and isoleucine for corn silage-based diet. No new plasma biomarkers of RFI were identified at early-fattening stages (false discovery rate  > 0.05). Prediction models were developed based on seven confirmed RFI biomarkers analysed during early-fattening. Two logistic regression models incorporating creatinine and either IGF-1 (for grass silage-based diet) or PC aa C30:2 (for corn silage-based diet) effectively distinguished between high- and low-RFI animals with high sensitivity and specificity (area under the curve > 0.80). The biomarkers used in the models showed moderate to high repeatability between early and late fattening stages (0.45 < r < 0.65). The models were successfully externally validated, with more than 85% of animals from the fourth cohort correctly classified. Once validated in larger cohorts and utilising cost-effective and rapid analytical methods, these models could support precision feeding and breeding programmes, aiming to reduce the cost of raising beef cattle.

The animal gastrointestinal tract contains a complex microbiome whose composition ultimately reflects the co-evolution of microorganisms with their animal host and their host's environment. This study aimed to gain insights into the adaptation of the microbiota of local Egyptian cattle to three different ecosystems (Upper Egypt, Middle Egypt, and Lower Egypt) distributed across 11 governorates (with an average of 12 animals per governorate) using amplicon sequencing. We analyzed the microbiota from 136 fecal samples of local Egyptian cattle through a 16S rRNA gene sequencing approach to better understand the fecal microbial diversity of this breed which developed under different ecosystems. An alpha diversity analysis showed that the fecal microbiota of the Egyptian cattle was not significantly diverse across areas, seasons, sexes, or farm types. Meanwhile, microbiota data revealed significant differences in richness among age groups ( = 0.0018). The microbial community differed significantly in the distribution of its relative abundance rather than in richness across different ecosystems. The taxonomic analysis of the reads identified and as the dominant phyla, accounting for over 93% of the total bacterial community in Egyptian cattle. Middle Egypt exhibited a different microbial community composition compared to Upper and Lower Egypt, with a significantly higher abundance of and and a lower abundance of in this region than the other two ecosystems. Additionally, Middle Egypt had a significantly higher relative abundance of the family and the genera than Lower and Upper Egypt. These results suggest a difference in the adaptation of the fecal microbial communities of Egyptian cattle raised in Middle Egypt. At the genus level, eleven genera were significantly different among the three ecosystems including , , , , , , , , , , and . These significant differences in microbiota composition may impact the animal's adaptation to varied environments.

Linear body measurements and real-time ultrasound may serve as crucial factors in cost-effective carcass prediction, thereby facilitating value-based marketing of living animals. The current study aimed to evaluate carcass components and cuts of male Damascus kids from body and ultrasound measurements. Besides investigate the effect of presence of horns and type of birth (single or twins) on body measurements and carcass characteristics. Thirteen male Damascus kids aged 12 months were used in the study. Ultrasound measurements were taken with probe (7.5 MHZ) between the 12th and 13th thoracic vertebra on live kids.
Body measurements, carcass components and cuts of horned kids were higher than those of hornless ones. The birth type showed no significant influence on body weight and measurements at 12 months and on carcass components and cuts. Body length was entered in all prediction equations to predict carcass cuts and measurements. Afterward, heart girth and chest width were the most variables used in prediction equations. Ultrasound measurements (depth, area, width) of rib-eye muscle on live kids led to accurate prediction for weights of hot carcass, leg, flank, shoulder, neck, best end of neck, middle neck in their carcasses. Accurate prediction equations were obtained to predict real eye muscle width, depth and area using ultrasound measurements of rib-eye muscle width, depth, area, respectively. R2 accounted 33% to predict width of rib-eye muscle (P<0.05). Moreover, ultrasound depth and area of rib-eye muscle contributed 51% and 61%, respectively of the total variation in real depth and area of eye muscle (P<0.01).

Haemonchus contortus is one of the most detrimental gastrointestinal nematode parasites for small ruminants, especially in tropics and subtropics. Gastrointestinal nematode and microbiota share the same microhabitat; thus they interact with each other and their host. Metagenomics tools provide a promising way to examine the alterations in the gastric microbial composition induces by gastrointestinal parasites. In this study, we used metagenomics tools to characterize the impact of H. contortus infection on the caprine abomasal microbiota at early and late stage of infection and compared it with non-infected control. Our results showed that H. contortus infection caused a significant increase in abomasal pH at early (7 days post-infection) and late stage of infection (56 days post-infection). The analysis of alpha and beta diversity showed that the microbiota diversity both in number and in proportion was significantly affected at early and late stage of infection. All microbiota classes are impacted by H. contortus infection but Clostridia and Bacteroidia are more concerned. In infected animals, the genera Prevotella decreased at 7 and 56 days post-infection. Here we showed that the abomasal microbiota was significantly affected early after H. contortus infection, and these changes persist at late stage of the infection.

In small ruminant production, gastrointestinal nematode (GIN) infection is one of the major causes of economic losses. The aim of this study was to compare the abomasal mucosa transcriptome of naïve and pre-infected goats at early time points after infection, in order to identify different pathways and upstream regulators involved in the host immune response. Naïve and pre-infected Creole kids were orally infected with 10,000 infective larvae (L3), and abomasal mucosa was sampled at 0, 4, and 6 days post-infection (dpi). At 6 dpi, all the animals were slaughtered to perform parasite burden counts. The mean number of L4 recovered in naïve kids was more than twice as high as that recovered in the pre-infected ones (5,860 and 2,474 respectively, < 0.001). RNA-seq analysis showed a number of differentially expressed genes (DEGs) very low for both naïve and pre-infected animals when comparing day 0 vs. day 4 post-infection. A total of 2,237 and 3,206 DEGs were identified comparing 0 vs. 6 dpi in naïve and pre-infected animals, respectively. Interestingly, only 18 DEGs were found for the comparison of pre-infected vs. naïve animals at 6 dpi. Ingenuity pathway analysis (IPA) showed that several immune responses were activated in pre-infected compared with naïve animals at 0 and 4 dpi such as Th2 and Th1 pathways, natural killer cell, B cell receptor, IL-2, and IL-15 signaling. On the other hand, both naïve and pre-infected animals showed activation for those pathways comparing 6 vs. 0 dpi, with no difference between them. A similar pattern was recorded for upstream regulator genes which were related to immunity like TNF, IL-1β, IL-2, IL-5, TGFβ1, IFNγ, TCR, IL-18, IL-6, and IL-4. Our results showed that at 0 and 4 dpi the immune response was activated toward Th1 and Th2 pathways in pre-infected kids compared to the naïve ones, however, the same immune response was developed in naïve kids as earlier as 6 dpi. We conclude that repeated infection in kid goats induced a concomitant early activation of a Th1 and Th2 immune response resulting in the regulation of worm establishment.

Gastrointestinal nematodes (GIN) are an important constraint in small ruminant production. Genetic selection for resistant animals is a potential sustainable control strategy. Advances in molecular genetics have led to the identification of several molecular genetic markers associated with genes affecting economic relevant traits. In this study, the variants in the genome of Creole goats resistant or susceptible to GIN were discovered from RNA-sequencing. We identified SNPs, insertions and deletions that distinguish the two genotypes, resistant and susceptible and we characterized these variants through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible genotype with 78% of the genes involved in this pathway showing genomic variants. These genomic variants are expected to provide useful resources especially for molecular breeding for GIN resistance in goats.

Gastrointestinal nematode (GIN) infections are one of the major constraints for grazing sheep and goat production worldwide. Genetic selection for resistant animals is a promising control strategy. Whole-transcriptome analysis via RNA-sequencing (RNA-seq) provides knowledge of the mechanisms responsible for complex traits such as resistance to GIN infections. In this study, we used RNA-seq to monitor the dynamics of the response of the abomasal mucosa of Creole goat kids infected with Haemonchus contortus by comparing resistant and susceptible genotypes. A total of 8 cannulated kids, 4 susceptible and 4 resistant to GIN, were infected twice with 10 000 L3 H. contortus. During the second infection, abomasal mucosal biopsies were collected at 0, 8, 15 and 35 days post-infection (dpi) from all kids for RNA-seq analysis. The resistant animals showed early activation of biological processes related to the immune response. The top 20 canonical pathways of differentially expressed genes for different comparison showed activation of the immune response through many relevant pathways including the Th1 response. Interestingly, our results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids.

The rise of anthelmintic resistance worldwide has led to the development of alternative control strategies for gastrointestinal nematodes (GIN) infections, which are one of the main constraints on the health of grazing small ruminants. Presently, breeding schemes rely mainly on fecal egg count (FEC) measurements on infected animals which are time-consuming and requires expertise in parasitology. Identifying and understanding the role of immunoglobulins in the mechanisms of resistance could provide a more efficient and sustainable method of identifying nematode-resistant animals for selection. In this study we review the findings on immunoglobulin response to GIN in the literature published to date (june 2019) and discuss the potential to use immunoglobulins as biomarkers. The literature review revealed 41 studies which measured at least one immunoglobulin: 35 focused on lamb immune response (18 used non-naïve lambs) and 7 on yearlings. In this review we propose a conceptual model summarizing the role of immunoglobulins in resistance to GIN. We highlight the need for more carefully designed and documented studies to allow comparisons across different populations on the immunoglobulin response to GIN infection.

A total of 49918/1176670 test-day records belonging to 8231/177605 lactating goats/ewes were used to study heat stress in Spanish dairy goats (Florida breed) and sheep (Manchega breed). The productive traits investigated were daily milk, fat and protein yield. The tolerance threshold and the slope of the response of these traits to heat stress have been calculated. Test day records from each herd were merged with maximum and average daily temperature and a temperature-humidity index (THI) registered in weather stations the day of milk recording. Two sets of data were analysed: data from high milk yielding animals and data from low milk yielding animals. Two thresholds were found, one for low temperatures and the other for high temperatures. Climatic effects on yields were less marked in the case of ewes. No very important differences were found between high and low productive animals in respect to thresholds and slopes, except for the decay of fat and protein yields due to heat stress.

Increasing global temperatures might affect negatively the availability of food resources. Therefore, selecting animals adapted to climate change could be a way to guarantee the continuous production of food. With this motivation, genome wide association analysis (GWAS) for susceptibility/tolerance to heat stress was carried out in Spanish Florida dairy goats (n = 538). Several significant SNPs at whole genome level, located in different chromosomes, were identified. Gene annotation and functional classification analysis carried out with BioMart and DAVID online tools showed significant SNP located in genes involved in milk composition such as kappa casein (CSN3), acetyl-coenzyme A carboxylase alpha (ACACA) and malic enzyme 1 (ME1) and a significant SNP (snp39045-scaffold-3419) mapped at the heat shock 27 kDa associated protein 1 (HSPBAP1) which inhibits the antiapoptotic and thermotolerance function of heat shock protein 27 kDa (HSP27) at cell level

The model initially proposed for dairy cattle to evaluate the impact of heat stress (HS) on milk yield assumes a comfort zone and a zone above a threshold (To) with a linear decrease of production. Studies with this or other models are scarce for small dairy ruminants. Our aim was to examine the shape of response on production associated with increasing values of temperature and a temperature and humidity index (THI) in two breeds. A total of 1,675,886 and 116,258 daily fat and protein yields from the official milk recording of 191,641 Manchega ewes and 11,259 Florida goats, respectively, were used. Average (Tave) and maximum daily values for temperature and THI at the test day were obtained from the Spanish Meteorological Agency. Two data sets, all and only high producing animals (above 1.5 SD) were analyzed per breed. Two types of models were used, one fitting splines (SP) with one knot at To and a linear slope b afterwards, and another fitting Legendre polynomials (LP) of varying order (up to cubic). Models included herd-year of test day, number and stage of lactation, age of the animal at recording, prolificacy, milking time and animal apart from the temperature/THI functions. For Tave, To was found at 29ºC for sheep and at unexpectedly small values around 10 ºC for goats. Values of b were low in general, but larger for highly productive ewes, with declines of up 16g/ºC of protein. LP models resulted in better fits in both species, lower HS thresholds for sheep and similar for goats. It was also interesting the assessment of thresholds for cold stress in sheep. The latter might suggest the existence of a zone of comfort with two thresholds, outside of which yields decrease.

In the present thesis the effect of heat stress on milk, fat, and protein yields and fat and protein contents has been studied in the Spanish Florida breed of dairy goats. It comprises three chapters: The first one is a bibliographic review of the state of the art. The second one is a phenotypic analysis carried out to determine the climatic variables most correlated to the production traits and to estimate the tolerance thresholds and slopes of the responses of the dairy traits studied to heat stress. The third chapter is a genetic analysis of formerly cited responses, undertaken with the objective to estimate the environmental and genetic (co)variance components of heat stress tolerance. A total of 185,675 test-day records belonging to 13,481 lactating goats distributed in 20 flocks, collected between 2006 and 2012, combined with maximum and average temperatures and the values of an index of temperature and relative humidity (THI), registered the day of milk recording and one and two days before in meteorological stations located less than 22 Km from the farms, were used for the phenotypic and genetic analysis. For the first study, a Ridge regression analysis and a GLM select analysis were carried out in order to select the climatic variables and dates that were recorded, having the highest correlations with the dairy traits under study. Then, tolerance thresholds and slopes of the regressions of these traits with the selected climatic variables were estimated with spline and polynomial models by means of Bayesian methods. Results shows that the maximum and average temperatures (mean of maximum and minimum temperatures) explain the change in dairy traits caused by climatic effects better than the THI. Temperatures registered the day of milk recording or one day before have more effect on the traits studied than those registered two days before. Generally, yields and contents of milk components decrease when temperature increases. However, milk yield seem to be less affected by high temperatures, being more affected by cold temperatures. Climatic variables have a higher effect on milk composition in high productive animals in respect to the rest. For the genetic analysis, a reaction norm animal model (RNM) was used to estimate the genetic and permanent environmental (co)variance components of the relation of dairy traits with THI, maximum and average temperature, modeling this relation by means of Legendre polynomials. Results show that the heritability of dairy traits tends to decrease for increasing values of the climatic variables. Genetic correlations between the intercept and the slope of each model, and between the first and the subsequent points in the scales of the climatic variables, provide evidences that selection for better milk performance will reduce heat stress tolerance. The genetic variation of the response to heat stress found in this analyses could be used to select animals according to their response to heat stress (robust, tolerant and non-tolerant).

Fat and protein production from 191.768 ewes and 11.259 goats, together with climatic variables were used to determine the threshold and response to heat stress (HS) in dairy sheep (Manchega) and goat (Florida) Spanish local populations. Models including the effects of herd-year of test day, number and stage of lactation, age of the animal at recording, prolificacy, milking time, animal and a regression (b) on the climatic variable that operates only after a certain threshold (To) were used. Average (Tave) and maximum temperature (Tmax) plus an index combining both temperature and humidity (THI) were used as climatic variables. The analyses were carried out for the whole population and for the highly producing (AP) animals (1.5 sd above average). To was lower for goats than for sheep around 10°C vs. 29 °C for Tmedia and Tmax, respectively. Small b values were observed for the whole sheep population, but a larger impact of HS was found for the AP animals. For these, b ranged between 6 (fat) and 16 (protein)g/°C. For the goat population, declines were similar for the global and AP data, but larger for fat%, ranging between 0.05 and 0.09% per unit of climatic variable.

Genetic (co)variance components of daily fat plus protein yields (FPY) along the trajectory of a heat stress index (THI) were estimated by means of a Reaction Norm Model (RNM). FPY data were provided by the corresponding breeders associations and consisted of 126,825 and 154,240 test day (TD) from Florida and Malagueña goats, respectively. Climatic records register each TD were provided by the Spanish Meteorological Agency from weather stations located less than 20 Km away from the farms. Daily maximum temperature and relative humidity were use to obtain a composite index of temperature and humidity (THI). The model included age at kidding, number of milking per day, a combination of flock-date of TD and a second order Legendre polynomial of THI on FPY as fixed effects, and a second order Legendre polynomial for the animal, a single individual permanent environmental effect and a residual as random effects. Results showed a comfort zone (THI from 6 to 21) where the heat stress effect was very small and a sensitive zone (THI from 21 to 31) having a significantly negative effect on FPY. Heritability estimated within the comfort zone ranged from 0.368 to 0.198 for Florida and from 0.294 to 0.159 for Malagueña. These ranges dropped from 0.185 to 0.112 and from 0.156 to 0.159, respectively, within the sensitive zone. Results also showed heterogeneity of genetic (co)variance and estimated breeding values across the trajectory of THI values in both breeds. Therefore, daily fat plus protein yield can not be considered to be the same all over this trajectory. The RNM also allows for the identification of animals showing a robust response to high temperatures.

Twenty three Zaraibi and sixteen Damascus does were used to investigate the influence of tactile, olfactory and auditory stimuli of bucks on sexual behavior and LH secretion. Does of each breed were randomly allotted into four groups. Does of the first group served as a control. In the second group, does were joined by an intact male of the same breed (tactile group). Does of the third group were exposed to buck hair (olfactory group). The fourth group was subjected to recorded buck voice (auditory group). Tests were carried out for 30 min. twice a day for three days. Behavioral displays of does were recorded for each doe in the four groups. Blood samples were collected immediately before treatment then every 12 hour for 72 hours to assay LH and estradiol concentrations. Does of both breeds responded significantly to the different stimuli. Tactile and olfactory stimuli resulted in estrus of 67% and 50% of Zaraibi and Damascus does, respectively. Relatively lower response due to vocalization was observed in Zaraibi and Damascus does (50% and 25%, respectively). Response to vocalization in Damascus does was not significantly different from that of the non-stimulated (control) group. Reaction time in both breeds was similar and generally ranged from 36 to 60 h regarding behavioral displays. Results showed no significant differences due to breed or stimulus in search for male or urination. Meanwhile, vocalization percentage, tailing, degree of isolation and degree of restlessness displays were significantly (P<0.05) affected between groups tested. No vaginal changes (edema of the vulva and mucous discharge) were observed in both breeds in response to any stimulus. The only exception was that 33% of Zaraibi does (2/6) responded to tactile stimulus. Results showed that Zaraibi does subjected to buck hair had the highest LH concentration at 36 h and at 72 h after treatment (0.75 IU/L) compared with other treatments as well as Damascus breed. The highest concentration of LH was that of Zaraibi does exposed to buck voice at 48 h after treatment (0.87 IU/L). Exposure of Zaraibi does to buck’s odour and voice may induce sexual behavior and ovulation within 1.5 – 3 days.