Anti-Müllerian hormone as a promising novel biomarker for litter size in Romanov sheep.

Anti-Müllerian hormone (AMH) is a hormone produced by growing preantral and antral follicles of the ovary. AMH is accepted as an important biomarker for fertility and superovulation parameters in livestock species. This study aimed to evaluate changes in serum AMH level in the oestrous cycle, repeatability of AMH, the effect of age on serum AMH level and the effects of AMH on litter size in Romanov sheep. In the study, a total of 36 Romanov sheep were used as animal material. First blood samples (0th day) were collected from 36 ewes to evaluate AMH and progesterone levels. Second blood samples were collected randomly from 20 ewes 9 days after first sampling to compare AMH levels at two different periods of the oestrous cycle in Romanov ewes. The ewes were categorized into three groups as low, medium and high AMH based on their first AMH levels. Results indicated that serum AMH level did not change during the oestrous and dioestrous phases of the oestrous cycle and two random time points of the oestrous cycle (p > .05). Pearson correlation analysis revealed that there is a high (r = .95) and significant (p < .001) correlation between AMH levels at the 0th (AMH-1) and 9th (AMH-2) days. The effect of AMH level on litter size was found to be significant. Litter size was significantly higher in the high AMH group than in the low AMH group (p < .05). In addition, the age of ewes did not affect serum AMH levels (p > .05). ROC analysis indicates that AMH cut-off value >320 pg/mL with 70% sensitivity and 100% specificity can be used for litter size in Romanov ewes. In conclusion, AMH is highly repeatable and its serum AMH level did not change during the oestrous cycle in Romanov sheep. In addition, AMH affects litter size and can be reliably used as a marker for litter size in Romanov sheep.

ASReml-based estimation of early genetic parameters in hybrid mutton sheep populations.

The aim of this study was to analyze the effects of non-genetic factors on the estimation of genetic parameters of early growth traits in hybrid mutton sheep using ASReml software, in order to provide theoretical basis for screening the optimal hybriding combinations and accelerating the breeding process of new breeds of specialized housed-feeding mutton sheep. We selected the wellgrown hybrid Southhu (Southdown × Hu sheep) and Dorhu (Dorset × Hu sheep) sheep as the research objects, constructed weight correction formulae for SH and DH sheep at 60 and 180 days; and used ASReml software to investigate the effects of non-genetic factors on the estimation of genetic parameters of early growth traits in hybrid sheep. The results showed that the birth month and birth type were found significant for all traits (p < 0.001); the heritability of maternal effects ranged from 0.0709 to 0.1859. It was found that both SH and DH sheep emerged the potential for rapid early growth and development, early growth traits are significantly affected by maternal genetic effects, thereby the maternal effect should be taken into consideration for the purpose of improving accuracy in parameter estimations and therefore increasing the success of breeding programs.

Do forage production and ingestive behavior of locally adapted sheep differ from an irrigated silvopastoral system to an irrigated monoculture in the semi-arid region?

This study aimed to evaluate forage production and ingestive behavior of Morada Nova sheep in an intensive system with capim-tamani grass in both monoculture and silvopastoral irrigated systems in the Semi-arid region. Eighteen adult sheep, approximately 3 years old, with an average body weight of 26.8 ± 4.3 kg, were allocated to treatments with capim-tamani grass cultivated in monoculture and in silvopastoral systems with Caatinga trees. The experiment followed a completely randomized complete block design with two plots and three replications. Forage production, consumption, and behavioral activities were the assessed variables. The animals remained in the pasture daily between 6 am and 6 pm. No effects of the monoculture and silvopastoral systems were observed on the structural and productive characteristics of the capim-tamani grass pasture. There were also no observed effects on body condition score, consumption, and disappearance rate of dry matter (DM) and other nutrients in both systems. However, there was an interaction between the time animals spent under shade in monoculture and silvopastoral systems. In general, the animals spent more time under shade where there were trees, except during the period between 2 pm and 4 pm, when the times were similar. On average, the animals spent approximately 15.6% (equivalent to 1.87 h) of their total time in the artificial shade available in the monoculture system, whereas in the silvopastoral system, they remained under natural shade for approximately 40% (five and a half hours) of their time spent in the pasture during the day. The grazing frequency in both systems was approximately 70% (8.4 h) in relation to the total time spent in the pasture. The capim-tamani grass pasture managed intensively with sheep in the silvopastoral system showed similar forage production and consumption compared to the monoculture system. There was a positive influence of trees on the duration of solar radiation exposure to the animals throughout the day. The results support the need to provide shade for sheep, as well as to promote these sustainable systems in semi-arid regions.

Economic and financial viability of the production of Brazilian somalis sheep fed with different nutritional plans.

The objective of this study was to evaluate the economic and financial viability of finishing of two sexes of Brazilian Somalis sheep in feedlot receiving diets with 0 and 15% reduction in the total digestible nutrients and crude protein contents. A completely randomized design was adopted, in a 2 × 2 factorial arrangement, with treatments consisting of two sexes (non-castrated males (21.13 ± 5.00 kg) and females (17.99 ± 3.79 kg) and two diets (0 and 15% reduction in the levels of total digestible nutrients and crude protein). Four simulations of productive scenarios were carried out: non-castrated males receiving the diet with 0% reduction; non-castrated males receiving the diet with 15% reduction; females receiving the diet with 0% reduction and females receiving the diet with 0% reduction, for a period of 70 days in feedlot. The highest costs of the system were with feeding and other costs, mainly the acquisition of animals. For both sexes, the 0% reduction diet showed the highest total cost, total revenue, break-even point. Non-castrated males fed a non-reduced diet and females fed a 15% reduction diet had higher net income, rate of return, total productivity, net present value, internal rate of return, profitability index and profitability rate. Less favorable situations were not profitable for any scenario. However, the increase in sales price favorability makes the activity viable. The reduction of total digestible nutrients and crude protein affects the economic and financial viability of Brazilian Somalis sheep. For non-castrated males it is recommended the diet without reduction and for females the diet with 15% reduction of nutrients.

Right parasternal echocardiographic reference values in the healthy male Iranian Shall sheep.

BACKGROUND: Among the large animals, the heart of sheep is functionally and structurally very similar to the human heart. In research, sheep are used as an animal model to study the process of cardiac disease pathogenesis and treatment. Therefore, determining the normal values of the heart structures of sheep with echocardiography is of particular emphasis. The purpose of the present research is to define the normal echocardiography values of heart in Iranian Shall breed sheep. MATERIALS AND METHODS: In 20 healthy Iranian Shall male sheep weighing 30-35 kg and aged 4-6 months, standing echocardiography was done from the right parasternal approach concentrated on the 3rd to 5th intercostal spaces by 2.5-5 MHz phased array transducer in the longitudinal and transverse views by B-mode, M-mode and Doppler systems. In M-mode echocardiographic, the parameters of interventricular septal, left ventricular internal diameter, left ventricular free wall, right ventricular free wall and right ventricular internal diameter in diastole and systole as well as end point septal separation, ejection fraction (EF) slope, aortic root diameter, left atrial appendage, left atrial diameter/aortic valve diameter, left ventricular ejection time, fractional shortening, end-diastolic volume, end-systolic volume, EF, stroke volume and cardiac output and in pulsed-wave spectral Doppler echocardiographic, the parameters of mitral valve maximum velocity (Vmax), mitral valve mean velocity (Vmean), mitral valve maximum pressure gradient (PGmax), mitral valve mean pressure gradient (PGmean), mitral valve velocity time integral (VTI), mitral valve E-wave (MV-E), MV-E pressure gradient, mitral valve A-wave (MV-A), MV-A pressure gradient, aortic Vmax, aortic valve Vmean, aortic valve PGmax, aortic valve PGmean, aortic valve VTI, left ventricular outflow tract (LVOT)-Vmax, LVOT-Vmean were measured. RESULTS: All the sheep in this study were healthy and had no signs of heart disease. In this study, the parameters of M-mode and spectral Doppler echocardiographic were assessed and recognized in Iranian Shall sheep. The results demonstrated the parameters of echocardiographic could be dependably determined in Shall sheep which, established normal reference values for these parameters and left ventricular function indices in healthy Shall sheep. These results can be beneficial in appropriate imagination, recognition and measuring cardiac structures. CONCLUSION: This study can be exerted as a reference for the assessment and diagnosis of heart diseases in sheep medicine and human cardiovascular research in sheep experimental models.

The effect of exogenous melatonin administration before superovulation on embryo yield in Assaf ewes.

The aim of this study was to determine the effect of exogenous melatonin administration on transferable embryos by increasing total antioxidant status before superovulation in Assaf ewes. Selected ewes were randomly divided into two equal groups: melatonin (n = 9) and control (n = 9). In the melatonin group, a melatonin implant (18 mg melatonin, Regulin®, Ceva, Turkey) was placed under the skin of the ear 7 days prior to insertion of the progesterone-containing sponge. In the control group, a physiological saline solution was injected under the skin of the ear on the same day. The same superovulation protocol was used in both groups. In addition, blood samples for determination of Glutathione peroxidase, superoxide dismutase, total antioxidant status and total oxidant status concentrations were collected on five different days, including the day of melatonin implant placement (Day-7), vaginal sponge insertion (Day 0), vaginal sponge removal (Day 11), mating (Day 12-13) and uterine flushing (Day 19). Embryos were collected by laparotomy on the 7th day after mating. Uterine flushing taken into petri dishes were scanned under a stereomicroscope, and the quality and developmental stages of the embryos were recorded. In the study, total corpus luteum count and total cell count were found to be higher in the control group than in the melatonin group (p < .05). When the results were evaluated in terms of oxidative stress index, a negative correlation was found between the total number of corpus luteum, number of cells obtained, count of transferable embryos and number of Grade 1 embryos on Day 0. There was also a positive correlation oxidative stress index and the number of unfertilized oocytes on Day-7. As a result, exogenous melatonin administration prior to superovulation during the breeding season is thought to have a negative effect on embryo yield and quality. Therefore, the use of exogenous melatonin in MOET studies during the breeding season is recommended to be investigated in new studies.

Clinico-histopathological and molecular detection of small ruminants' papillomaviruses in Iran.

BACKGROUND: Papilloma DNA viruses are one of the viruses that cause skin lesions in ruminants. OBJECTIVES: The clinical, histopathological and molecular characteristics of cutaneous papilloma in ruminants in Iran are to be investigated in this study. METHODS: Samples were collected from 19 small ruminants (5 sheep and 14 goats) with various papillomatosis lesions. The samples taken were studied with histopathological and molecular techniques. RESULTS: In clinical terms, the lesions appeared in different sizes, ranging from 0.5 to 11 cm, and the cauliflower exophytic masses appeared in other parts of the animal's body. In the limbs, most papilloma lesions have been seen (42.1%). In histopathological examination, perinuclear vacuolation epidermal granule layer with various degrees of hypergranulosis, hyperkeratosis, acanthosis, orthokeratosis and parakeratosis were seen. Moreover, all the suspected samples were positive for papillomavirus using the polymerase chain reaction technique. CONCLUSIONS: Although the prevalence of papillomaviruses in Iranian sheep and goats is low, it seems necessary to distinguish them from other viral skin diseases, such as cutaneous contagious ecthyma, using molecular techniques and histopathology.

Discovery and characterization of BRBV-sheep virus in nasal swabs from domestic sheep in China.

Introduction: The escalating occurrence of infectious disease outbreaks in humans and animals necessitates innovative, effective, and integrated research to better comprehend their transmission and dynamics. Viral infection in livestock has led to profound economic losses globally. Pneumonia is the prevalent cause of death in sheep. However, very few studies exist regarding virus-related pathogens in sheep. Metagenomics sequencing technologies in livestock research hold significant potential to elucidate these contingencies and enhance our understanding. Methods: Therefore, this study aims to characterize respiratory viromes in paired nasal swabs from Inner Mongolian feedlot sheep in China using metaviromic sequencing. Through deep sequencing, de novo assembly, and similarity searches using translated protein sequences, several previously uncharacterized and known viruses were identified in this study. Results: Among these discoveries, a novel Bovine Rhinitis B Virus (BRBV) (BRBV-sheep) strain was serendipitously detected in the nasal swabs of domestic sheep (Ovis aries). To facilitate further molecular epidemiological studies, the entire genome of BRBV-sheep was also determined. Owing to the unique sequence characteristics and phylogenetic position of BRBV-sheep, genetically distinct lineages of BRBV in sheep may exist. A TaqMan-based qRT-PCR assay targeting the 3D polymerase gene was developed and used to screen 592 clinical sheep specimens. The results showed that 44.59% of the samples (264/592) were positive. These findings suggest that BRBV sheep are widespread among Inner Mongolian herds. Conclusion: This discovery marks the initial identification of BRBV in sheep within Inner Mongolia, China. These findings contribute to our understanding of the epidemiology and genetic evolution of BRBV. Recognizing the presence of BRBV in sheep informs strategies for disease management and surveillance and the potential development of targeted interventions to control its spread.

Dietary supplementing South African indigenous rams with flaxseed oil and ascorbic acid improves cryopreserved semen quality and in vitro fertility.

The purpose of this study was to evaluate how ascorbic acid with dietary flaxseed oil affects the quality and fertility of cryopreserved ram sperm in South African indigenous rams. Treatment diets were supplemented 60 days before semen collection to afford proper spermatogenesis, adaptation to the feed formulated and fed throughout the study. Semen was collected with the use of artificial vagina following dietary supplementation with five treatment diets (neg. cont. - negative control, pos. cont. - positive control, FLO - 5% Flaxseed oil, ASA - 4% Ascorbic acid, and FLO + ASA). Semen was then extended using tris-based extender and cryopreserved using the programmable freezer (CBS Freezer 2100 series, Laboratory consumables & chemical suppliers, America). Ovaries were collected from a neighbouring slaughter house and conveyed to the lab in 0.9% saline at 37 °C. Data (sperm parameters and in vitro fertility) was then exposed to the GLM (General Linear Model) in Minitab 17. Pearson's correlation coefficient was utilized to investigate the relationship between cryopreserved sperm quality and in vitro fertility. The student Least Significant Difference Test was used to separate the treatment means, and differences were accepted when the p-value was less than 0.05. The FLO + ASA group had higher (p < 0.05) progressive (36.33 ± 1.87), total (88.24 ± 2.24), rapid motility (27.52 ± 1.74), intact plasma membrane (75.67 ± 2.08), total fertilization (65.98 ± 7.39), and total cleavage (66.19 ± 6.50) when compared to other treatment groups. Total fertilization rate had a medium significant (p < 0.001) medium correlation with the progressive motility (r2 = 0.435), total motility (r2 = 0.447) and rapid motility (r2 = 0.409). In conclusion, dietary flaxseed and ascorbic acid (FLO + ASA) improves cryopreserved semen quality, in vitro fertilization rate, and the total cleavage rate. Noteworthy, the progressive, total and rapid motility play a crucial in the in vitro fertilization rate.

Chromosome-level genome assembly of Guide Black-Fur sheep (Ovis aries).

Guide Black-Fur sheep (GD) is a breed of Tibetan sheep (Ovis aries) that lives in the Qinghai-Tibetan plateau region at an altitude of over 4,000 m. However, a lack of genomic information has made it difficult to understand the high-altitude adaptation of these sheep. We sequenced and assembled the GD reference genome using PacBio, Hi-C, and Illumina sequencing technologies. The final assembled genome size was 2.73 Gb, with a contig N50 of 20.30 Mb and a scaffold N50 of 107.63 Mb. The genome is predicted to contain 20,759 protein-coding genes, of which 98.42 have functional annotations. Repeat elements account for approximately 52.2% of the genomic landscape. The completeness of the GD genome assembly is highlighted by a BUSCO score of 93.1%. This high-quality genome assembly provides a critical resource for future molecular breeding and genetic improvement of Tibetan sheep.

The effects of supplementation of vitamin D to the egg-yolk extender on cryopreservation of ram semen.

OBJECTIVES: This study aimed to examine the effects of supplementation of vitamin D to the egg-yolk extender on characteristics of frozen-thawed ram semen. METHODS: Semen samples obtained from adult rams were pooled and divided into five equal volumes. It was reconstituted with extenders containing different concentrations of vitamin D: 0 (control), 12.5 (VITD 12.5), 25 (VITD 25), 50 (VITD 50), and 100 ng/mL (VITD 100), and then they were frozen. Sperm motility parameters, plasma membrane functional integrity, acrosomal integrity, DNA fragmentation, and mitochondrial membrane potential of the groups were evaluated after sperm thawing. RESULTS: Total motility and progressive motility were higher in VITD 50 than in all other groups (p < 0.05). Higher sperm straightness, linearity, and wooble were higher in VITD 50 than in the control group (p < 0.05). A similar pattern of VITD 50 was observed for plasma membrane integrity and mitochondrial membrane potential (p > 0.05). CONCLUSIONS: In the study, it was observed that adding vitamin D to the extender had a beneficial effect on ram spermatological parameters. In addition, it was concluded that the use of the 50 ng/mL vitamin D in the extender provided more effective protection than the other doses.

The comparisons of non-linear models to describe the growth performance of Lori-Bakhtiari sheep.

BACKGROUND: The study of growth traits is of interest to many animal scientists, regardless of specialization, due to the economic importance of growth rate, mature weight and other related traits. OBJECTIVE: This study aimed to compare six non-linear models for describing the growth of Lori-Bakhtiari sheep. METHODS: In order to collect weight data, 85 lambs (41 males and 44 females) were reared from birth to 140 days of age, and their growth patterns were recorded by measuring their body weight at 10-day intervals. Various mathematical functions, including the negative exponential, Brody, Gompertz, Logistic, Morgan-Mercer-Flodin (MMF) and Weibull, were used to model the relationship between body weight records and age. RESULTS: The results showed that the MMF and Gompertz models provided the best fit to the body weight data, whereas the negative exponential model exhibited the worst fit. In all models, the asymptotic weight of male lambs was higher than females. The research also revealed differences in growth patterns between male and female lambs. Overall, females had a lower absolute growth rate than males, but they reached their peak growth at an earlier period, and their growth rate declined faster. CONCLUSIONS: The differences in growth patterns between males and females indicate the importance of analysing male and female data separately when describing growth. As a result, Gompertz model can be recommended to Lori-Bakhtiari female and male lamb breeders to determine more accurate growth traits. In addition, it should be considered that feeding male and female lambs separately according to absolute growth rate values may increase growth performance.

Effects of dietary arginine supplementation on muscle structure, meat characteristics and lipid oxidation products in lambs and its potential mechanisms of action.

This study aimed to assess the effect of dietary arginine supplementation on muscle structure and meat characteristics of lambs also considering lipid oxidation products and to contribute to reveal its mechanisms of action using tandem mass tagging (TMT) proteomics. Eighteen lambs were allocated to two dietary treatment groups: control diet or control diet with the addition of 1% L-arginine. The results revealed that dietary arginine supplementation increased muscle fibre diameter and cross-sectional area (P < 0.05), which was attributable to protein deposition, as evidenced by increased RNA content, RNA/DNA ratio, inhibition of apoptotic enzyme activity, and alterations in the IGF-1/Akt signaling pathway (P < 0.05). In addition, dietary arginine elevated pH24h, a* values, and IMF content, decreased shear force value and backfat thickness (P < 0.05), as well as decreased the formation of lipid oxidation products involved in meat flavor including hexanal, heptanal, octanal, nonanal and 1-octen-3-ol by increasing the antioxidant capacity of the muscle (P < 0.05). The proteomics results suggested that seven enrichment pathways may be potential mechanisms by which arginine affected the muscle structure and meat characteristics of lambs. In summary, arginine supplementation in lamb diets provides a safe and effective way to improve meat quality, and antioxidant capacity of muscle of lamb.

Do sheep (Ovis aries) discriminate human emotional odors?

While sheep can detect and discriminate human emotions through visual and vocal cues, their reaction to human body odors remains unknown. The present study aimed to determine whether sheep (Ovis aries) can detect human odors, olfactorily discriminate stressed from non-stressed individuals, and behave accordingly based on the emotional valence of the odors. Axillary secretions from 34 students were collected following an oral examination (stress odor) or a regular class (non-stress odor). Fourteen female and 15 male lambs were then exposed to these odors through a habituation-dishabituation procedure. The habituation stimulus was presented four times for one minute, followed by the dishabituation stimulus presented once for one minute. Behavioral variables included spatiality relative to target odors, approach/withdrawal, ear positioning, sniffing, ingestion, and vocalization. Both female and male lambs more often positioned their ears backwards/forwards, and asymmetrically when exposed to the dishabituation stimulus, but regardless of their stress or non-stress value. They also changed their approach behavior when exposed to the dishabituation stimuli. Lambs displayed some behavioral signs of discrimination between the habituation and dishabituation odors, but regardless of their relation to stress or non-stress of human donors. In sum, this exploratory study suggests that young sheep respond negatively to the odor of unfamiliar humans, without showing any specific emotional contagion related to the stress odor. This exploratory study suggests young ovines can detect human body odor, a further step toward understanding the human-sheep relationship.

Comparative assessment of growth curves in Brazilian white Morada Nova hair sheep breed.

The Morada Nova sheep breed is essential for the economy of the semi-arid region of Northeast Brazil, standing out for its adaptability, resistance to parasites and reproductive ability. However, the white variant is endangered, highlighting the importance of studies on its productivity to support conservation efforts. This study focuses on the growth curve of the Morada Nova sheep breed, using nonlinear models and analyzing flock profiles. Total of 764 observations of 165 animals from four farms in Ceará and Rio Grande do Norte, Brazil, were analyzed. Canonical discriminant analysis (CDA) was used for the exploratory analysis and four nonlinear models were used to study the growth curve. Weight from birth to 270 days of age, absolute growth rate (AGR), and the impact of sex on growth curves were assessed. Sex and farm are significant discriminating variables (P < 0.05) for the studied effects (weight and age). Weight was the primary phenotypic biomarker that discriminated between the two indicators, while age was a discriminating indicator only for the core effect. The Gompertz model was the most efficient, presenting the lowest residuals and greatest convergence. The study reveals new information about the growth of Morada Nova sheep, the white variety, including weight differences between the sexes at all analyzed ages and an inflection point before 90 days of age. These discoveries contribute to the understanding of the breed's growth and help in the formulation of conservation strategies.

Inclusion of cocoa bran in the diet of lambs and its effect on reproductive parameters.

The objective of the study was to evaluate the effect of the inclusion of cocoa bran in the diet of lambs and its effect on reproductive parameters. For this, 40 lambs were randomly assigned to four treatments, and including 0, 10, 20 and 30% levels of cocoa bran in the concentrate. Blood was collected to measure cholesterol and testosterone and semen for physical and morphological evaluation; testicular biometry and morphometry were also evaluated. There was significant difference (P < 0.05) in body weight and tubulosomatic index between the lambs in the control treatment and those in the 30% cocoa bran treatment. There was no difference in testicular biometry, physical and morphological parameters of fresh semen, testicular morphometry, and volumetric ratio between lambs in all the treatments (P < 0.05). In addition, there was no difference in plasma cholesterol or testosterone concentration (P > 0.05). Thus, it is possible to include up to 30% of cocoa bran in diet without affecting the reproductive parameters of lambs.

The benefits of flushing with Lemuru fish oil as a source of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) on the performance of reproductive parameters in Garut ewes.

This study aimed to evaluate and analyze the effects of a flushing diet containing Docosahexaenoic acid (DHA) and Eicosapentaenoic acid (EPA) from Lemuru (Sardinella sp) fish oil on the reproductive performance parameters of Garut ewes. Forty (n = 40) primiparous Garut ewes aged 12-14 months with an average body weight of 28.92 ± 4.94 kg were assigned into four experimental treatment groups. The experimental diets contained roughage: concentrate (30:70%) designated as control concentrate (CNT), flushing concentrate with 6% palm oil (PO), flushing concentrate with 3% palm oil mixed with 3% lemuru oil as DHA and EPA sources (PFO), and flushing concentrate with the addition of 6% lemuru oil (FO). Treatment animals were fed two weeks before and after conception and parturition (8 weeks of total flushing treatment). The addition of fish oil at either 3% (PFO) or 6% (FO) resulted in significantly higher reproductive performance of ewes by increasing the litter size, as reflected by the birth of multiple kids (P < 0.05) compared to CNT and PO. Adding fish oil (PFO and FO) also maintains gestation, resulting in increased lamb yield, especially in the FO treatment, which yields the highest lamb yield (0% single lamb birth). The lamb male ratio was also higher with fish oil supplementation (PFO and PO) (P < 0.05). This research revealed a positive effect of 6% Lemuru oil on decreasing embryo loss and increasing the proportion of twin births. These findings thus support the hypothesis that ration flushing with double the required DHA and EPA from 6% Lemuru fish oil (FO) resulted in significantly higher reproductive performance in Garut sheep.

Insights into the genomic homogeneity of Moroccan indigenous sheep breeds though the lens of runs of homozygosity.

Numerous studies have indicated that Morocco's indigenous sheep breeds are genetically homogenous, posing a risk to their survival in the challenging harsh climate conditions where they predominantly inhabit. To understand the genetic behind genetic homogeneity through the lens of runs of homozygosity (ROH), we analyzed the whole genome sequences of five indigenous sheep breeds (Beni Guil, Ouled Djellal, D'man, Sardi, Timahdite and Admixed).The results from principal component, admixture, Fst, and neighbour joining tree analyses consistently showed a homogenous genetic structure. This structure was characterized by an average length of 1.83 Mb for runs of homozygosity (ROH) segments, with a limited number of long ROH segments (24-48 Mb and > 48 Mb). The most common ROH segments were those ranging from 1-6 Mb. The most significant regions of homozygosity (ROH Islands) were mostly observed in two chromosomes, namely Chr1 and Chr5. Specifically, ROH Islands were exclusively discovered in the Ouled Djellal breed on Chr1, whereas Chr5 exhibited ROH Islands in all breeds. The analysis of ROH Island and iHS technique was employed to detect signatures of selection on Chr1 and Chr5. The results indicate that Chr5 had a high level of homogeneity, with the same genes being discovered across all breeds. In contrast, Chr1 displays some genetic variances between breeds. Genes identified on Chr5 included SLC39A1, IL23A, CAST, IL5, IL13, and IL4 which are responsible for immune response while genes identified on Chr1 include SOD1, SLAMF9, RTP4, CLDN1, and PRKAA2. ROH segment profile and effective population sizes patterns suggests that the genetic uniformity of studied breeds is the outcome of events that transpired between 250 and 300 generations ago. This research not only contributes to the understanding of ROH distribution across breeds but helps design and implement native sheep breeding and conservation strategies in Morocco. Future research, incorporating a broader sample size and utilizing the pangenome for reference, is recommended to further elucidate these breeds' genomic landscapes and adaptive mechanisms.

Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep.

BACKGROUND: Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs). RESULTS: Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms. CONCLUSIONS: In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.

Sheep litter size heredity basis using genome-wide selective analysis.

Sheep are important herbivorous domestic animal globally, and the Chinese indigenous sheep breed has a multitude of economically significant variations due to the diverse geographical and ecological conditions. In particular, certain native breeds exhibit a visible high litter size phenotype due to the selection pressure of natural and artificial for thousands of years, offering an ideal animal model for investigating sheep's fecundity. In this study, selective signal analysis was performed on public whole-genome sequencing data from 60 sheep across eight breeds to identify candidate genes related to litter size. Results revealed that a total of 34,065,017 single-nucleotide polymorphisms (SNPs) were identified from all sheep, and 65 candidate genes (CDGs) were pinpointed from the top 1% of interacted windows and SNPs between the pairwise fixation index (FST, >0.149543) and cross-population extended haplotype homozygosity (XP-EHH, >0.701551). A total of 41 CDGs (e.g. VRTN, EYA2 and MCPH1) were annotated to 576 GO terms, of which seven terms were directly linked to follicular and embryonic development (e.g. TBXT, BMPR1B, and BMP2). In addition, 73 KEGG pathways were enriched by 21 CDGs (e.g. ENTPD5, ABCD4 and RXFP2), mainly related to Hippo (TCF4, BMPR1B and BMP2), TGF-ß (BMPR1B and BMP2), PI3K-Akt (ITGB4, IL4R and PPP2R5A) and Jak-STAT signalling pathways (IL20RA and IL4R). Notably, a series of CDGs was under strong selection in sheep with high litter size traits. These findings result could improve the comprehension of the genetic underpinnings of sheep litter size. Furthermore, it provides valuable CDGS for future molecular breeding.