Estimates of variance components due to parent-of-origin effects for body weight in Iran-Black sheep

Morpometric and molecular characterization of Surguli goat through CO1 gene in district Kohat

The present study was designed with the aim to study morphometric characterization as well as phylogeny and diversity of the local Surguli goat at their breeding tract district Kohat through mitochondrial DNA region, i.e., Cytochrome C Oxidase Subunit One (CO1) gene. Morphometric data and blood samples were collected from thirty (30) pure goats. Morphometric analysis showed that sex had significant effect (p < 0.05) on body weight, body length, hearth girth and horn length while no significant effect (p > 0.05) was observed for other characteristics. The results also indicated that age had significant effect (p < 0.05) on height at rump, ear length, horn length and tail length while no significant effect (p > 0.05) was observed for other characteristics. The phylogenetic analysis through CO1 nucleotide sequences within nucleotide range 1-767 showed nine polymorphic sites segregating into eight haplotypes. The mean intraspecific diversity and mean interspecific diversity were calculated as 0.23 and 2.36%, respectively. Phylogenetic tree revealed that Capra Ibex and native Surguli goat have common ancestors. The morphometric and molecular results obtained from the present study can be exploited as a selection tool for breeding and overall improvement.

Parent of origin genetic effects on milk production traits in a population of Iranian Holstein cows

The aim was to estimate the relative contribution of imprinting effects from both paternal and maternal sides to phenotypic variation in milk production traits including 305 days milk yield (MY), average daily milk production (ADM), fat percentage (F%), protein percentage (P%), 305 days fat yield (FY), 305 days protein yield (PY), ratio of fat percentage to protein percentage (F:P) and somatic cell score (SCS) in Iranian Holstein cows. To do this, each trait was analysed with a series of four animal models, which were identical for fixed and additive genetic effects but differed for combinations of paternal and maternal imprinting effects. The log-likelihood ratio test (LRT) and Akaike's information criteria (AIC) were used to select the best model for each trait. Correlations between traits due to additive and imprinting effects were estimated by bivariate analyses. For all traits studied, fitting the imprinting effect led to a better data fit. Also, it resulted in a noticeable decrease in additive genetic variance from 8% (SCS) to 28% (F:P). A significant maternal imprinting effect was detected on all traits studied. Estimates of maternal imprinting heritability (h mi 2 $$ {h}_{\mathrm{mi}}^2 $$ ) were 0.07 ± 0.02, 0.04 ± 0.01, 0.06 ± 0.01, 0.05 ± 0.01, 0.5 ± 0.01, 0.09 ± 0.02, 0.07 ± 0.02 and 0.06 ± 0.01 for MY, ADM, F%, P%, FY, PY, F:P and SCS, respectively. For F:P, in addition to the maternal imprinting effect, a significant paternal imprinting component was also detected with a 7% contribution to phenotypic variance of F:P. Estimates of direct heritability (h a 2 $$ {h}_{\mathrm{a}}^2 $$ ) were 0.29 ± 0.02, 0.17 ± 0.01, 0.22 ± 0.02, 0.11 ± 0.01, 0.18 ± 0.02, 0.22 ± 0.02, 0.15 ± 0.04 and 0.06 ± 0.01 for MY, ADM, F%, P%, FY, PY, F:P and SCS, respectively. Maternal imprinting correlations (rmi) were in a wide range between -0.75 ± 0.15 (P%-SCS) and 0.95 ± 0.11 (MY-ADM). Additive genetic correlations (ra) ranged between -0.54 ± 0.05 (MY-P%) and 0.99 ± 0.01 (MY-ADM) and phenotypic correlations (rp) ranged from -0.30 ± 0.01 (MY-F%) to 0.93 ± 0.01 (MY-ADM). The Spearman's correlation between additive breeding values including and excluding imprinting effects deviated from unity especially for top-ranked animals implying re-ranking of top animals following the inclusion of imprinting effects in the model. Since including imprinting effects in the model resulted in better data fit and re-ranking of top animals, including these effects in the genetic evaluation models for milk production traits was recommended.

Integrative Meta-Analysis: Unveiling Genetic Factors in Meat Sheep Growth and Muscular Development through QTL and Transcriptome Studies

OBJECTIVE

The study aimed to investigate the effects of castration on performance, carcass characteristics, and meat quality in sheep, as well as explore the expression of key genes related to metabolic pathways and muscle growth following castration.

METHODS

A meta-analysis approach was utilized to analyze data from multiple studies to compare the performance, carcass characteristics, and meat quality of castrated sheep (wethers) with intact rams. Additionally, protein-protein interaction (PPI) networks, differential gene expression (DEG) interactions, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were examined to identify molecular mechanisms associated with fat metabolism and muscle development in sheep tails.

RESULTS

The analysis revealed that castrated sheep (wethers) exhibited improved average daily gain, increased tenderness, lower backfat thickness, and a tendency for greater loin muscle area compared to intact rams. This suggests that castration promotes faster growth and results in leaner carcasses with potentially higher muscle content. Furthermore, the identification of downregulated DEGs like ACLY, SLC27A2, and COL1A1 and upregulated DEGs such as HOXA9, PGM2L1, and ABAT provides insights into the molecular mechanisms underlying fat deposition and muscle development in sheep.

CONCLUSIONS

The findings support the practice of castration in sheep production as it enhances growth performance, leads to leaner carcasses with higher muscle content, and improves meat tenderness. The identified changes in gene expression offer valuable insights for further research into understanding the impact of castration on muscle development and fat metabolism in sheep. This meta-analysis contributes to the knowledge of molecular mechanisms involved in fat deposition in sheep, opening avenues for future investigations in livestock fat metabolism research.

Genomic diversity of the locally developed Latvian Darkheaded sheep breed

The Latvian Darkheaded is the only locally developed sheep breed. The breed was formed at the beginning of the 20th century by crossing local coarse-wooled sheep with the British Shropshire and Oxfordshire breeds. The breed was later improved by adding Ile-de-France, Texel, German blackheads, and Finnsheep to achieve higher prolificacy and better meat quality. Previous studies have reported the Latvian Darkheaded sheep to be closely related to Estonian and Lithuanian Blackface breeds, according to microsatellite data. To expand our knowledge of the genetic resources of the Latvian Darkheaded breed, we conducted a whole-genome resequencing analysis on 40 native sheep. The investigation showed that local sheep harbor genetic diversity levels similar to those observed among other improved breeds of European origin, including Charollais and Suffolk. Genome-wide nucleotide diversity (π) in Latvian Darkheaded sheep was 3.91 × 10-3, whereas the average observed heterozygosity among the 40 animals was 0.267 and 0.438 within the subsample of unrelated individuals. The Ne has rapidly decreased to 200 ten generations ago with a recent drop to Ne 73 four generations ago. However, inbreeding levels based on runs of homozygosity were, on average, low, with FROH ranging between 0.016 and 0.059. The analysis of the genomic composition of the breed confirmed shared ancestry with sheep of British origin, reflecting the history of the breed. Nevertheless, Latvian Darkheaded sheep were genetically separable. The contemporary Latvian Darkheaded sheep population is genetically diverse with a low inbreeding rate. However, further development of breed management programs is necessary to prevent an increase in inbreeding, loss of genetic diversity, and depletion of breed-specific genetic resources, ensuring the preservation of the native Latvian Darkheaded sheep.

Review on current status of Bonga, Afar, Menz, and Horro sheep breeds genetic improvement: Breeding program and progress

This working paper reviews the research and development in genetic improvement and breeding strategies of Bonga, Menz, Afar and Horro sheep in Ethiopia. This review aims to provide structured information regarding the Ethiopian indigenous sheep breeds (Bonga, Afar, Menz, and Horro) breeding programs and its progress. Genetic diversity is an essential element for genetic improvement, preserving populations, evaluation and adapting to variable environmental situations. Sustainable breeding techniques and sensible use of indigenous breed have been developed as result of recent research approaches to the conservation of sheep genetic resources. However, there is still growing interest of the government and of farmers in different breeding program to improve indigenous sheep breeds. There is no comprehensive study showing the performance of indigenous sheep breeds (Bonga, Afar, Menz, and Horro) genetic improvement under different breeding program and its progress, both biological and economic, to substantiate the argument on the benefit of different breeding programs for smallholders farmers. Programs for the sheep breeds Menz, Afar, Horro, and Bonga have now been developed at the community level. The idea behind the nucleus breeding program is to develop elite breeding animals by gathering the finest male and female breeding participants from the population in one central location. The first stage in creating a breeding program is defining the breeding goals. Planning breeding programs requires a thorough grasp of the farmers' (beneficiaries') breeding goals and production objectives. Therefore, this review makes it evident that numerous instruments and techniques, including choice experiments, participatory rural assessment procedures, and rating animals from flocks, have been used to define and ascertain the breeding aim of Afar, Horro, Bonga and Menz sheep breeds in Ethiopia.

Effect of Low Protein Diets Supplemented with Sodium Butyrate, Medium-Chain Fatty Acids, or n-3 Polyunsaturated Fatty Acids on the Growth Performance, Immune Function, and Microbiome of Weaned Piglets

This study aimed to investigate the effects of low-protein (LP) diets supplemented with sodium butyrate (SB), medium-chain fatty acids (MCT), or n-3 polyunsaturated fatty acids (n-3 PUFA) on the growth performance, immune function, and the microbiome of weaned piglets. A total of 120 healthy weaned piglets ((Landrace × Large White × Duroc); 7.93 ± 0.7 kg initial body weight), were randomly divided into five groups. Each group consisted of six replications with four piglets per replication. Dietary treatments included control diet (CON); LP diet (LP); LP + 0.2% SB diet (LP + SB); LP + 0.2% MCT diet (LP + MCT); and LP + PUFA diet (LP + PUFA). The experimental period lasted for 4 weeks. Compared with the CON diet, LP, LP + SB, LP + MCT, and LP + PUFA diets decreased the final weight and average daily gain (ADG) of piglets (p < 0.05). There were lower (p < 0.05) concentrations of IL-8 and higher (p < 0.05) Glutathione peroxidase (GSH-Px) activity in the plasma of piglets fed with LP + SB, LP + MCT, and LP + PUFA diets than those fed with the LP diet. The piglets in the LP + SB and LP + PUFA groups had lower IKK-alpha (IKKa) mRNA expression in the colonic mucosa compared with those in the CON and LP groups (p < 0.05). The mRNA expression of TLR4 in the colonic mucosa of piglets in the LP + SB, LP + MCT, and LP + PUFA groups was decreased when compared with the CON and LP groups (p < 0.05). The LP + MCT diets increased the gene expression of nuclear factor erythroid 2-related factor 2 (Nrf2) in the colonic mucosa of piglets compared with CON, LP, and LP + SB diets (p < 0.05). The abundance of Erysipelotrichaceae in the colonic microbiome of piglets in the LP group was higher than that in the other four groups (p < 0.05). Collectively, this study showed that LP diets supplemented with SB, MCT, or n-3 PUFA reduced plasma inflammatory factor levels, increased plasma GSH-Px activity, and declined mRNA expression of TLR4 and IKKa in the colonic epithelium, whereas it reduced the abundance of Erysipelotrichaceae in the colon of piglets.

Expression profile of FASN gene and association of its polymorphisms with intramuscular fat content in Hu sheep

The content of intramuscular fat (IMF) is one of the most important factors that has a large impact on meat quality, and it is an effective way to improve IMF according to marker-assisted selection (MAS). Fatty-acid synthase (FASN) is a key gene in meat lipid deposition and fatty acid composition. Thus, this study was conducted to investigate the expression profile of FASN in mRNA and protein levels using real-time quantitative PCR (RT-qPCR) and western-blot methods. In addition, single nucleotide polymorphisms (SNPs) within FASN in 921 Hu rams with IMF content records were investigated using DNA-pooling sequencing and improved multiple ligase detection reaction (iMLDR) methods. Consequently, the highest mRNA expression level of FASN was observed in the perinephric fat, and the lowest in the liver among the 11 tissues analyzed, while no significant difference was found in mRNA and protein expression levels in longissimus dorsi among individuals with different IMF contents. A total of 10 putative SNPs were identified within FASN, and 9 of them can be genotyped by iMLDR method. Notably, two SNPs were significantly associated with IMF content, including NC_040262.1: g.5157 A > G in intron 5 (p = 0.046) and NC_040262.1: g.9413 T > C in intron 16 (p = 0.041), which supply molecular markers for improving meat quality in sheep breeding.

Impact of inclusion non-additive effects on genome-wide association and variance's components in Scottish black sheep

CONTEXT

It's well-documented that most economic traits have a complex genetic structure that is controlled by additive and non-additive gene actions. Hence, knowledge of the underlying genetic architecture of such complex traits could aid in understanding how these traits respond to the selection in breeding and mating programs. Computing and having estimates of the non-additive effect for economic traits in sheep using genome-wide information can be important because; non-additive genes play an important role in the prediction accuracy of genomic breeding values and the genetic response to the selection.

AIM

This study aimed to assess the impact of non-additive effects (dominance and epistasis) on the estimation of genetic parameters for body weight traits in sheep.

METHODS

This study used phenotypic and genotypic belonging to 752 Scottish Blackface lambs. Three live weight traits considered in this study were included in body weight at 16, 20, and 24 weeks). Three genetic models including additive (AM), additive + dominance (ADM), and additive + dominance + epistasis (ADEM), were used.

KEY RESULTS

The narrow sense heritability for weight at 16 weeks of age (BW16) were 0.39, 0.35, and 0.23, for 20 weeks of age (BW20) were 0.55, 0.54, and 0.42, and finally for 24 weeks of age (BW24) were 0.16, 0.12, and 0.02, using the AM, ADM, and ADEM models, respectively. The additive genetic model significantly outperformed the non-additive genetic model (p < 0.01). The dominance variance of the BW16, BW20, and BW24 accounted for 38, 6, and 30% of the total phenotypic, respectively. Moreover, the epistatic variance accounted for 39, 0.39, and 47% of the total phenotypic variances of these traits, respectively. In addition, our results indicated that the most important SNPs for live weight traits are on chromosomes 3 (three SNPS including s12606.1, OAR3_221188082.1, and OAR3_4106875.1), 8 (OAR8_16468019.1, OAR8_18067475.1, and OAR8_18043643.1), and 19 (OAR19_18010247.1), according to the genome-wide association analysis using additive and non-additive genetic model.

CONCLUSIONS

The results emphasized that the non-additive genetic effects play an important role in controlling body weight variation at the age of 16-24 weeks in Scottish Blackface lambs.

IMPLICATIONS

It is expected that using a high-density SNP panel and the joint modeling of both additive and non-additive effects can lead to better estimation and prediction of genetic parameters.

Candidate genes for litter size in Xinjiang sheep identified by Specific Locus Amplified Fragment (SLAF) sequencing

The aim of this study was to investigate the selection signatures at a genome-wide level in 'Pishan' sheep using Specific Locus Amplified Fragment (SLAF)-seq. Blood samples from 126 ewes were sequenced using SLAF tags, and the ovarian tissues from 8 ewes (Bashbay sheep, a single litter size group (SG group); 'Pishan' sheep, double litter size group (DG group)) were collected to detect expression levels by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Selection signature analysis was performed using global fixation index (Fst) and nucleotide diversity (π) ratio. A total of 1,192,168 high-quality SLAFs were identified. Notably, 2380 candidate regions under selection using two approaches were identified. A total of 2069 genes were identified, which were involved in dopaminergic synapses, thyroid hormone synthesis, ovarian steroidogenesis and thyroid hormone signalling pathways. Furthermore, Growth Differentiation Factor 9 (GDF9), Period Circadian Regulator 2 (PER2), Thyroid Stimulating Hormone Receptor (TSHR), and Nuclear Receptor Coactivator 1 (NCOA1) reside within these regions and pathways. The expression levels of GDF9 and PER2 genes in sheep tissue of the DG group were significantly higher than those in the SG group. These genes are interesting candidates for litter size and provide a starting point for further identification of conservation strategies for 'Pishan' sheep.

The growth curve determination and economic trait correlation for Qinchuan bull population

Carcass weight, as a measure of meat yield, and body measurements are directly correlated traits in livestock. However, longitudinally collected phenotype records of local breeds are not comprehensive. The research was performed on Qinchuan bull population to understand their growth and development, and data from Qinchuan bull that was weighed and measured at birth, 6, 12, 18, and 24 months of age was analyzed. Furthermore, Logistic, Brody, Gompertz, and Bertallanffy were used to fit the growth curves for weight and body size traits. The results showed that the four curve models have good fitting degrees for the weight and body size (R2 > 0.99), and the Bertallanffy model exhibited a good fit to the measured data of body weight, and the model estimated the inflection point of body weight as (5.43 months of age, 122.01 kg). Particularly, the limited mature body weight can reach 557.8 kg by the Brody model. Body weight was significantly positively correlated with body height, hip height, body length, chest circumference, abdominal girth, and calf girth (p < 0.0001), and the correlation between body weight and body length was the highest (r = 0.975). The regression equation predicting body weight was Y = -275.691 + 3.28 X3 + 1.311 X4 - 0.397 X5.

Polymorphism and expression level of the FADS3 gene and associated with the growth traits in Hu sheep

Growth traits are the economically important traits of sheep, and screening for genes related to growth and development is helpful for the genetic improvement of ovine growth traits. The fatty acid desaturase 3 (FADS3) is one of the important genes affecting the synthesis and accumulation of polyunsaturated fatty acids in animals. In this study, the expression levels of the FADS3 gene and polymorphism of the FADS3 gene associated with growth traits in Hu sheep were detected using quantitative real-time PCR (qRT-PCR), Sanger sequencing, and KAspar assay. The result showed that the expression levels of the FADS3 gene were widely expressed in all tissues, and the expression level of FADS3 in the lung was significantly higher than in other tissues (p < .05). Then, the polymorphism locus g. 2918 A > C was detected in intron 2 of the FADS3 gene, and associated analysis showed that the mutation in the FADS3 gene was associated significantly with growth traits (including body weight, body height, body length, and chest circumference, p < .05). Therefore, individuals with AA genotype showed significantly better growth traits than those with CC genotype, and FADS3 gene could be a candidate gene for improving growth traits in Hu sheep.

Single-cell sequencing reveals the reproductive variations between primiparous and multiparous Hu ewes

BACKGROUND

In the modern sheep production systems, the reproductive performance of ewes determines the economic profitability of farming. Revealing the genetic mechanisms underlying differences in the litter size is important for the selection and breeding of highly prolific ewes. Hu sheep, a high-quality Chinese sheep breed, is known for its high fecundity and is often used as a model to study prolificacy traits. In the current study, animals were divided into two groups according to their delivery rates in three consecutive lambing seasons (namely, the high and low reproductive groups with ≥ 3 lambs and one lamb per season, n = 3, respectively). The ewes were slaughtered within 12 h of estrus, and unilateral ovarian tissues were collected and analyzed by 10× Genomics single-cell RNA sequencing.

RESULTS

A total of 5 types of somatic cells were identified and corresponding expression profiles were mapped in the ovaries of each group. Noticeably, the differences in the ovary somatic cell expression profiles between the high and low reproductive groups were mainly clustered in the granulosa cells. Furthermore, four granulosa cell subtypes were identified. GeneSwitches analysis revealed that the abundance of JPH1 expression and the reduction of LOC101112291 expression could lead to different evolutionary directions of the granulosa cells. Additionally, the expression levels of FTH1 and FTL in mural granulosa cells of the highly reproductive group were significantly higher. These genes inhibit necroptosis and ferroptosis of mural granulosa cells, which helps prevent follicular atresia.

CONCLUSIONS

This study provides insights into the molecular mechanisms underlying the high fecundity of Hu sheep. The differences in gene expression profiles, particularly in the granulosa cells, suggest that these cells play a critical role in female prolificacy. The findings also highlight the importance of genes such as JPH1, LOC101112291, FTH1, and FTL in regulating granulosa cell function and follicular development.

Polymorphism and expression of the HMGA1 gene and association with tail fat deposition in Hu sheep

Hu sheep is an excellent short fat-tailed breed in China. Fat deposition in Hu sheep tail affects carcass quality and consumes a lot of energy, leading to an increase in feed cost. The objective of this study was to analyze the effects of HMGA1 polymorphism on tail fat weight in Hu sheep. Partial coding and non-coding sequences of HMGA1 were amplified with PCR and single nucleotide polymorphisms (SNP) of HMGA1 in 1163 Hu sheep were detected using DNA sequencing and KASPar technology. RT-qPCR analysis was performed to test HMGA1 expression in different tissues. The results showed that the expression of HMGA1 was higher in the duodenum, liver, spleen, kidney, and lung than in the heart, muscle, rumen, tail fat, and lymph. A mutation, g.5312 C > T, was detected in HMGA1; g.5312 C > T was significantly associated with tail fat weight, relative weight of tail fat (body weight), and relative weight of tail fat (carcass) (p < 0.05). The tail fat weight of the TT genotype was remarkably higher than that of the CC and TC genotypes. Therefore, HMGA1 can be used as a genetic marker for marker-assisted selection of tail fat weight in Hu sheep.

Quantitative analysis of parent-of-origin effect in reproductive and morphological selection criteria in the Pura Raza Española horse

It is generally assumed that parents make a genetically equal contribution to their offspring, but this assumption might not always hold. This is because the expression of a gene can be blocked by methylation during gametogenesis, and the degree of methylation can depend on the origin of the parental gene (imprinting) or by preferential management associated with genetic merit. The first consequences of this for quantitative genetics is that the mean phenotypes of reciprocal heterozygotes need no longer be the same, as would be expected according to Mendelian heritage. We analysed three mare reproductive traits (reproductive efficiency, age at first foaling and foaling number) and three morphological traits (height at withers, thoracic circumference, and scapula-ischial length) in the Pura Raza Española (PRE) horse population, which possesses a deep and reliable pedigree, making it a perfect breed for analysing the quantitative effect of parent-of-origin. The number of animals analysed ranged from 44,038 to 144,191, all of them with both parents known. The model comparison between a model without parent-of-origin effects and three different models with parent-of-origin effects revealed that both maternal and paternal gametic effects influence all the analysed traits. The maternal gametic effect had a higher influence on most traits, accounting for between 3% and 11% of the total phenotypic variance, while the paternal gametic effect accounted for a higher proportion of variance in one trait, age at first foaling (4%). As expected, the Pearson's correlations between additive breeding values of models that consider parent-of-origin and that do not consider parent-of-origin were very high; however, the percentage of coincident animals slightly decreases when comparing animals with the highest estimated breeding values. Ultimately, this work demonstrates that parent-of-origin effects exist in horse gene transmission from a quantitative point of view. Additionally, including an estimate of the parent-of-origin effect within the PRE horse breeding program could be a great tool for a better parent's selection and that could be of interest for breeders, as this value will determine whether the animals acquire genetic categories and are much more highly valued.

Effects of starter feeding and early weaning on developmental expressions of IGF-I gene in liver and IGF-IR gene in rumen of lambs from birth to eighty-four days of age

The early weaning and starter feeding have significant effects on lamb growth and digestive tract development. However, it is not clear whether the expression of IGF-1/IGF-1R genes could be affected by feeding starter and weaning. Therefore, a total of 102 Hu male neonatal lambs were randomly divided into 3 groups: fed with starter at 42d + weaned at 56d (group A), fed with starter at 7d + weaned at 28d (group B) and fed with starter at 7d + weaned at 56d (group C), to explore the effects of starter feeding and weaning age on developmental expressions of IGF-I gene in liver and IGF-IR gene in rumen of Hu sheep. The results showed that IGF-I and IGF-IR genes were expressed extensively in various tissues of lambs, the expression of IGF-I was significantly higher in liver (p < 0.01), while the expression of IGF-IR was higher in rumen among gastrointestinal tissues. The mRNA level of IGF-I of group C was strikingly higher than that of group A at 28, 70, and 84d (p < 0.01) in liver, respectively. Rumen mRNA level of IGF-IR of group C was prominently higher than that of group A at 70d and 84d (p < 0.05), respectively. However, IGF-IR expression of group A was higher than that of group C at 14 and 42d (p < 0.05). The mRNA level of IGF-I of group B was significantly higher than that of group C at 42, 56, 70, and 84d (p < 0.01) in liver, while IGF-IR expression of group B was higher than that of group C at 70d (p < 0.01). In conclusion, early weaning and starter feeding affected liver IGF-I mRNA and rumen IGF-IR mRNA expression.

Pulse wave Doppler ultrasound of umbilical cord in experimentally induced pregnancy toxemia in sheep

Contrary to its widespread use in human cases, the use of Doppler ultrasonography is only recently becoming prevalent in farm animals. This study aimed to determine the effects of maternal metabolic and clinical changes on fetal hemodynamics during pregnancy toxemia with the doppler examination of umbilical cord. In the study twenty ewes with a single healthy fetus were included in the study. At the end of the 120th day of pregnancy, 20 single-bearing pregnant ewes were randomly categorized into two groups. Ewes in the control group were fed to meet all nutritional requirements. On the other contrary, the experimental ewes were fed to meet equivalent to 50 % of the daily needs and then fasted for 96 h. Doppler ultrasonographic examinations of umbilical cord were performed once every two days and once a day during fasting. Beta hydroxybutyric acid (BHBA) concentration was measured by taking blood from sheep on examination days. Pulse systolic velocity (PSV), end diastolic velocity (EDV), PSV/EDV, pulsatility index (PI), resistance index (RI), and fetal heart rate (FHR) as well as BHBA values and how those parameters has changed over time (time by treatment effect) due to energy deprivation during pregnancy were evaluated using repeated measure analysis of variance. No clinical signs were observed in both toxemia and control groups during restricted feeding. BHBA concentration increased and there was a significant time, time by treatment and main effect of treatment effect between groups. No significant main effect of treatment and time by treatment interaction was observed in the changes of PI, RI, FHR, and systolic/diastolic velocity values over time in both groups. FHR was reduced over time, and there was a significant time effect in FHR in both groups. Although doppler indices didn't increase, both PSV and EDV values increased significantly in the pregnancy toxemia group compared with the controls (Time P = 0.03, time by treatment interaction P < 0.05) and the main effect of treatment P < 0.05). The marked increase in blood velocities (PSV and EDV) in the umbilical cord is probably due to the compensatory functioning for excessive energy deprivation of the fetus. Therefore, PSV and EDV might be a valuable indicator for evaluating the fetus's health status during the management of the PT.

The growth hormone gene polymorphism and its relationship to performance and carcass features in Egyptian Awassi lambs

The main purpose of the existing experiment was to assess the allelic and genotypic polymorphisms of the Growth hormone (GH) gene and its correlation with growth indices, efficiency of consumed feed, some body indices and carcass traits of the Egyptian Awassi sheep. Forty Egyptian Awassi male lambs were selected for their growing indices (post-weaning daily gain, marketing weight, and weaning weight), feed efficiency (consumed feed and of consumed feed), body conformational indicators (skeletal muscle index, relative body index, body mass index, and body index), and carcass features (dressing %, hot carcass weight, fore-legs %, neck %, loin %, ribs %, abdominal fat %, Tail % and hind-legs %). The polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP) tool was applied to detect the genotypic and allelic GH gene polymorphisms properties. The PCR-RFLP analysis identified three main genotypes (AA, AB and BB) and two main alleles (A and B). The GH genotype (AA or AB) exhibited moderate significant influence (P < 0.05) on marketing weight, Loin% and Tail%. Also, genotype (AB or BB) of expressed GH gene significantly (P < 0.01) influence on consumed feed, post-weaning daily gain, neck% and body mass index, whereas, it had no influence on the phenotypic values of the other characteristics investigated. The presence of the A allele in the genotype was markedly associated (P < 0.01) with consumed feed, body mass index and post-weaning daily growth; conversely, the presence of the B allele in the genotype was significantly related (P < 0.05) with marketing weight, loin %, and tail %. While, GH gene expression was revealed to be highly significant (P < 0.01) in relation to post-weaning daily growth, feed intake, and neck %. According to the findings, determining the associations between GH gene variation and growth, efficiency of consumed feed, body measurements, and carcass features of Egyptian Awassi sheep and applying marker assisted selection with the GH gene to improve these traits is warranted and will be of significant economic value to sheep production.

Meta-analysis of genetic parameters for growth traits in meat, wool and dual-purpose sheep breeds in the world using a random-effects model

BACKGROUND

There is large variation in genetic parameters in literature for growth traits in sheep. Reliable estimation of genetic parameters is required for developing breeding programmes.

OBJECTIVES

The aim of this study was to aggregate results of different studies by meta-analysis to improve reliability of estimated parameters.

METHODS

In the current study, 221 papers that have been published between 1995 and 2021 were reviewed. Using a random-effects model in the Comprehensive Meta-Analysis software, direct and maternal heritabilities, as well as, genetic and phenotypic correlations between growth traits were estimated in meat (M), wool (W) and dual-purpose (D) sheep breeds. The growth traits in this study were birth weight, 3-month weight, 6-month weight, 9-month weight and yearling weight.

RESULTS

The combined direct heritability was the lowest for birth weight (0.190 ± 0.004, 0.198 ± 0.003 and 0.196 ± 0.004 for M, W and D breeds, respectively) and the highest for yearling weight (0.264 ± 0.010, 0.304 ± 0.005 and 0.285 ± 0.020 for M, W and D breeds, respectively). The maternal heritability was the lowest for yearling weight (0.085 ± 0.003, 0.055 ± 0.002 and 0.052 ± 0.005 for M, W and D breeds, respectively) and the highest for 6-month weight (0.240 ± 0.088, 0.164 ± 0.001 and 0.162 ± 0.006 for M, W and D breeds, respectively). The phenotypic and genetic correlations were lower between the weights measured at more distant intervals. The lowest genetic correlation was observed between birth weight and yearling weight (0.290 ± 0.051 for W breeds).

CONCLUSIONS

The small standard errors could indicate that the aggregation of results from different studies improved the reliability of estimated parameters and reduced range of 95% confidence intervals. Hence, the results could be used with greater level of confidence in sheep breeding programmes.

Influence of genetic and non-genetic factors on growth performance in Black Bengal goats under field condition in West Bengal

Data on 10148 Black Bengal kids recorded from 2008 to 2019 and maintained at farmer’s fields at different agroclimatic clusters of West Bengal under the project “AICRP on Goat Improvement, Black Bengal Field Unit- Kolkata” were used to study the effect of non-genetic factors on body weight from birth to 12 months of age. The data were analysed using least squares analysis technique. The average birth weights of Black Bengal goats obtained under four different agro-climatic clusters revealed that there was a significant variation in body weight (kg) of all ages. The effect of year of kidding, influence of season and parity of the dam on body weight of Black Bengal kids at different ages were significant. But a non-significant result was found at the body weight in all the seasons as well as in all the parities at 9 and 12 months of age. Sex of the kid and type of birth had significant effect on body weights from birth to 12 months of age. Significantly higher body weight at birth was recorded in single born kid, followed by twin and triplets. The study concluded that it is possible to improve non-genetic elements in the field, particularly by providing excellent housing, reducing stress, having access to grazing pasture, and doing routine deworming and vaccinations. The findings supported the need for environmental changes that can aid in the development of management strategies and decision making regarding the selection.

Identification of the key proteins associated with different hair types in sheep and goats

Animal-derived fiber has the characteristics of being light, soft, strong, elastic and a good thermal insulator, and it is widely used in many industries and traditional products, so it plays an important role in the economy of some countries. Variations in phenotypes of wool fibers among different species and breeds are important for industry. We found that the mean fiber diameter of cashmere was significantly smaller than that of sheep wool (p < 0.01), and sheep wool was significantly smaller than goat wool (p < 0.01). Compared with traditional proteomics technology, we analyzed cashmere, guard hair, and wool by Laber-free proteomics technology and detected 159, 204, and 70 proteins, respectively. Through the sequential windowed acquisition of all theoretical fragmentations (SWATH), 41 and 54 differentially expressed proteins were successfully detected in the cashmere vs. wool group and guard hair vs. wool group. Protein‒protein interaction network analysis of differentially expressed proteins revealed many strong interactions related to KRT85, KRTAP15-1 and KRTAP3-1. The final analysis showed that the proportion of KRT85, KRTAP15-1 and KRTAP3-1 might be the key to the difference in fiber diameter and could be used as a potential molecular marker for distinguishing different fiber types.

Relative contribution of Imprinting, X chromosome and Litter effects to phenotypic variation in economic traits of sheep

Data on Zandi sheep were analysed to quantify maternal and paternal imprinting, X chromosome and litter effects' contribution to phenotypic variation in birth weight (BW), weaning weight (WW), growth rate (GR), Kleiber ratio (KR), efficiency of growth (EF) and relative growth rate (RGR). To this end, a two-step approach was adopted. In the first step, each trait was analysed with a series of 16 animal models, which were identical for fixed and autosomal additive genetic effects but differed for combinations of maternal permanent environmental, maternal genetic, X chromosome and litter effects. For each trait, the best model was selected by the Akaike information criterion (AIC) and likelihood ratio tests (LRTs). In the second step, three additional models were fitted by adding maternal imprinting, paternal imprinting or both (models 17, 18 and 19) to the best model selected in the first step. Estimators of bias, dispersion and accuracy of breeding values estimated within 19 models with whole, and partial data were used to evaluate how well were the 19 models in estimating breeding values for the animals when their records were masked. For all traits studied, fitting the litter effect led to a better data fit. Also, it resulted in noticeable decreases in residual variance and other maternal variances. For growth traits, models containing the X-linked effects fitted the data substantially better than corresponding models without the X-linked effects. For BW, WW and GR, estimates of X-linked heritability ( h s 2 $$ {h}_s^2 $$ ) ranged between 0.09 (GR) and 0.14 (BW). Ignoring X-linked effects from the genetic evaluation model resulted in significant inflated autosomal additive genetic variance. For BW, WW, EF and RGR, models containing the imprinting effects provided a better fit of the data than otherwise identical models. Imprinting effects contributed significantly to the phenotypic variation of these traits in a range between 5% (RGR) and 8% (BW, WW). A sharp decline was observed in autosomal additive genetic variance following including imprinting effects in the model (27% to 40% depending on the trait). The least bias and dispersion, as well as greater accuracies for breeding values of focal animals, were for a model which included imprinting, X-linked and litter effects. It was concluded that imprinting, X-linked and litter effects need to be included in the genetic evaluation models for growth and efficiency-related traits of Zandi lambs.

Analysis of genetic parameters and genetic trends for early growth and reproductive traits of Doyogena sheep managed under community-based breeding program

This study aims to estimate genetic parameters and genetic trends for early growth and reproductive traits of Doyogena sheep. Data used in the study were collected over 6 years (2013–2018). Studied traits were birth weight (BWT), weaning weight (WWT), 6-month weight (SMWT), average daily gains from birth to weaning (ADG0-3), average daily gains from weaning to 6-month age (ADG3-6), average daily gain from birth to 6-month age (ADG0-6), litter size (LS), lambing interval (LI), age at first lambing (AFL), and annual reproductive rate (ARR). (Co) variance components and genetic parameters were estimated using restricted maximum likelihood (REML). The analyses were carried out using WOMBAT program. Univariate analysis was applied to estimate genetic parameters. Six different animal models were fitted by including or excluding maternal effects. The direct heritability estimates for BWT, WWT, SMWT, ADG0-3, ADG3-6 and ADG0-6 were 0.33 ± 0.06, 0.31 ± 0.06, 0.14 ± 0.06, 0.13 ± 0.04, 0.11 ± 0.07, and 0.02 ± 0.05 respectively. Direct heritability for LS, LI, and AFL were 0.28 ± 0.12, 0.20 ± 0.5, and 0.001 ± 0.3, respectively. The maternal heritability estimates for BWT, WWT, and LS were 0.24 ± 0.12, 0.60 ± 0.07, and 0.24 ± 0.08, respectively. The genetic correlation between BWT with WWT and BWT with SMWT were 0.21 ± 0.07 and 0.21 ± 0.09, respectively. Genetic progress for most of the studied traits has shown promising improvements. Thus, continuation of selection, therefore, suggested for more improvements in the performance of Doyogena sheep. Direct heritability estimates decrease as lamb age increases and selection based on earlier body weight will be more efficient.

Polymorphisms in the ovine GP5 gene associated with blood physiological indices

This study aimed to analyze the effects of polymorphisms in GP5 on blood physiological indices of 1065 sheep. The coefficients of variation of the red blood cell count (RBC), hemoglobin concentration (HGB), mean platelet volume (MPV), mean erythrocyte hemoglobin content (MCH), and red blood cell distribution-coefficient of variation (RDW-CV) were greater than 10%, and there was a very significant correlation between the main indices such as RBC, white blood cell, and platelet count (PLT) and most other indices (p < 0.01). qRT-PCR showed that GP5 was expressed in the heart, liver, spleen, lung, kidney, rumen, duodenum, muscle, tail fat, and lymph tissue, with significantly higher expression in the lymph. Subsequently, we detected single nucleotide polymorphisms (SNPs) in GP5 from group, which identified synonymous mutation g.657 T > C in the first exon of GP5. Association analysis showed significant correlations between the SNP and the physiological traits (p < 0.05), in which the RBC, neutrophilic granulocyte (NEUT) and RDW-CV values in sheep with the TC genotype and TT genotype were markedly lower than those in the CC genotype (p < 0.05). Thus, GP5 polymorphisms could be candidate biomarkers to screen blood physiological indices.

Transcriptome profiling of LncRNAs in sheep tail fat deposition

LncRNAs have recently received special attention due to their critical role in many important biological processes. There are few reports on its regulatory function in sheep fat deposition. In this study, two sheep populations with different tail types in Xinjiang, Bashibai sheep (fat-tailed) and the hybrid population of Bashibai sheep and wild argali (small-tailed) were selected for whole transcriptome sequencing from their tail tissues. First, 728 differentially expressed LncRNAs of tail fat between Bashibai and F2 sheep were identified by RNA-seq. Second, the tissue expression profile and relative expression difference between Bashibai and F2 sheep of 2 of 728 DE LncRNAs were analyzed by RT-PCR. LncRNA-MSTRG.24995 was highly expressed in tail fat, while lncRNA-MSTRG.36913 was highly expressed in subcutaneous fat. In addition, the expressions of LncRNA-MSTRG.24995 and LncRNA-MSTRG.36913 in tail fat of F2 sheep were significantly lower than that of Bashibai sheep, while those patterns in longissimus dorsi, quadriceps femoris and rumen were reversed. Third, the expression pattern of target genes FASN and THRSP in each tissue was similar with that of corresponding LncRNAs. The LncRNA-MSTRG.24995 directly affects tail fat deposition by FASN gene, while the LncRNA-MSTRG.36913 indirectly affects that by THRSP gene. This will help us to understand molecular mechanism of fat tail deposition from transcriptomic perspectives.

Identification of polymorphisms in the MSTN and ADRB3 genes associated with growth and ultrasound carcass traits in Kajli sheep

The aim of this investigation was to find single nucleotide polymorphisms (SNPs) in the myostatin (MSTN) and the beta-3 adrenergic receptor (ADRB3) genes associated with growth and ultrasound carcass traits in Kajli sheep. The five growth traits were birth weight (BWT-EBV), 120-day weight (120DWT-EBV), 180-day weight (180DWT-EBV), 270-day weight (270DWT-EBV), and 365-day weight (365DWT-EBV). The three ultrasound carcass traits were width (WLD) and depth of longissimus dorsi (DLD) and back fat thickness (BFT). The analysis of the MSTN sequence revealed one non-synonymous substitution (c.197T > A) in exon 1, one single nucleotide substitution (c.373 + 18G > T) in intron 1, and one synonymous substitution (c.861T > A) in exon 3. However, there were four single nucleotide synonymous substitutions (c.130C > T, c.294C > G, c.579G > T, and c.654C > G) in exon 1 of the ADRB3 gene. All the SNPs in the MSTN gene, except for c.373 + 18G > T, were in Hardy-Weinberg Equilibrium (HWE). Conversely, none of the SNPs found in ADRB3 were in HWE. Two of the MSTN SNPs (c.197T > A and c.373 + 18G > T) had significant associations with all evaluated growth and ultrasound carcass traits. The SNPs c.130C > T and c.294C > G in ADRB3 were significantly associated with 180DWT-EBV. Collectively, these findings indicate that several SNPs in the studied genes were significantly related to growth and carcass traits in Kajli sheep.

Variation in the ovine FOXP3 gene and its effect on growth traits in Egyptian Barki sheep

The aim of the present study was to detect the FOXP3 gene polymorphisms in Barki sheep at a variable region covering exon 13, intron 13 and the coding sequence in exon 14 and to test the association of these polymorphisms with growth traits. 122 Barki lambs were phenotyped for various growth traits, viz., birth weight (BW), weaning weight (WW), pre-weaning daily gain in weight (ADG1), post-weaning daily gain in weight (ADG2) and marketing bodyweight (MW). The polymerase chain reaction - single-strand conformational polymorphisms (PCR-SSCP) and DNA sequencing methods were used to identify the genetic variants in the FOXP3 gene. The associations between the variation in FOXP3 gene and growth traits were tested using a general linear model. Two variants (F1 and F2 with gene frequencies of 0.64 and 0.36, respectively), and three genotypes (F1F1, F1F2 and F2F2 with frequencies of 0.37, 0.53 and 0.10, respectively) were detected. The association of FOXP3 genotype was significant (p < 0.05) with ADG2 and MW. It is concluded that FOXP3 genotype might be helpful for sheep breeders to produce fast-growing lambs. However, further studies are needed in a large population to confirm the association we found.