The aim of this study was to assess the expression of some follicular genes and their association with fertility trait in goat using Qt-PCR. Two groups of Zaraibi goat breed; high (HFG) and low (LFG) fertility groups were used; each group has 15 animals. The animals from each group were sacrificed; all the ovarian follicles were mechanically collected, and the follicles were pulled together. RNA was extracted from ovarian follicles and cDNA was synthesized and subjected for QT-PCR using Sybr green and β-actin as House-Keeping genes. The expressions of twelve tested genes were increased in HFG comparing with LFG, which were MCPH1, DACT1, DKKL1, PLCZ1, GADD45A, CST3, FOS, FUCA1, LGALS1, PNPLA3, ID3 and TPM2. On the other hand, six genes were expressed at a lower level in HFG than those in LFG, including NEFM, INHBB, CD38, FST, APOE and RPS29. Two genes were identified with expressions nearly at the same level in both fertility groups which were LMX1A and STRBP. It is concluded that the expressions of new-reported follicular genes assessed in this study and their associations with ovulation rate and fertility trait can help for selection the animals entering in reproductive breeding programs depending on these new fertility markers.

Maintaining genetic diversity among native Egyptian breeds is important towards genetic resource conservation. Examining the mitochondrial genome in different or within breeds can be helpful in determining the genetic variety of populations. This study examined the mitochondrial COX-3 gene of Egyptian Camelus dromedaries using bioinformatics and phylogenetic analysis, revealing two distinct haplotypes based on single nucleotide polymorphisms at positions 280 and 325. These two haplotypes' amplified PCR products were uploaded to GenBank/NCBI with accession numbers OP994029 and OP994030 with protein id = WHO17331.1" and WHO17330.1, respectively. Comparison of nucleotide and amino acid sequences of the Egyptian camel populations' three-dimensional COX-3 structure showed how closely related these two haplotypes are genetically. Haplotype 1 was more predominant and found in Baldi and Sudani populations whereas haplotype 2 was more abundant in Maghrebi population. The two polymorphic sites have diversity and theta (per site): Theta (W: 0.00208); high variety of haplotypes (Hd: 0.667). These two haplotypes are the most genetically distant from camels in the Camelidae family, according to phylogenetic study. Based on the nucleotide sequences A + T and C + G have frequencies between 51.15% and 48.85%, respectively. The two non-synonymous SNPs caused the P94S amino acid substitution in the coiled region while I109V substitution located in the strand, which was neutral. Analysis of amino acid substitutions via protein prediction showed that the two amino acids were semi-conserved in which the resultant amino acid has different properties from the original amino acid and can affect the protein structure. The protein stability diminished according to the I-Mutant and MUpro tools. I109V nSNP and increased for P94S nSNP. This finding suggested that COX-3 gene variability in camels is important to preserve this genetic resource and creating future breeding programmes, conservation strategies that will increase camel production.

The objectives of the current study were to identify polymorphism in the prolactin receptor (PRLR) gene among three Egyptian goat breeds (Zaraibi, Damascus, and Barki) and to investigate the association between PRLR genotype, parity, season of kidding, and litter size factors with milk yield and reproductive traits of Zaraibi goats. One hundred and ninety blood samples were collected for DNA extraction, with 110 from Zaraibi, 40 from Barki, and 40 from Damascus breeds. Three genotypes, CC, CT and TT, for the prolactin receptor gene were identified in the 190 DNA samples using restriction fragment length polymorphism and were confirmed by direct sequencing technique. Milk yield during suckling and lactation periods in addition to age at first conception, gestation length, and litter size were determined in 110 Zaraibi goats. The Zaraibi goats recorded the highest heterozygosity (0.495) and the effective number of alleles (1.972). The g.62130C > T SNP showed a significant association (p < 0.01) with suckling, lactation, and total milk yield of Zaraibi goats with the highest values recorded at the third parity. Age at the first conception and gestation length traits were significantly influenced by the kidding season (p < 0.05) with younger age in autumn and shorter length in spring seasons. Milk yield during the suckling period was significantly (p < 0.01) higher in the case of triplets' litter size. The current study showed that litter size and parity played an important role in the amount of Zaraibi goats' milk yield. The g.62130C > T SNP of the PRLR gene may be a useful marker for assisted selection programs to improve goat milk yield during suckling and lactation periods with the heterozygous genotype CT recording the highest values.

Camels are considered an important food source in North Africa. Trypanosomiasis in camels is a life-threatening disease that causes severe economic losses in milk and meat production. Therefore, the objective of this study was to determine the trypanosome genotypes in the North African region. Trypanosome infection rates were determined by microscopic examination of blood smears and polymerase chain reaction (PCR). In addition, total antioxidant capacity (TAC), lipid peroxides (MDA), reduced glutathione (GSH), superoxide dismutase (SOD) and catalase (CAT) were determined in erythrocyte lysate. Furthermore, 18S amplicon sequencing was used to barcode and characterizes the genetic diversity of trypanosome genotypes in camel blood. In addition to Trypanosoma, Babesia and Thelieria were also detected in the blood samples. PCR showed that the trypanosome infection rate was higher in Algerian samples (25.7%) than in Egyptian samples (7.2%). Parameters such as MDA, GSH, SOD and CAT had significantly increased in camels infected with trypanosomes compared to uninfected control animals, while TAC level was not significantly changed. The results of relative amplicon abundance showed that the range of trypanosome infection was higher in Egypt than in Algeria. Moreover, phylogenetic analysis showed that the Trypanosoma sequences of Egyptian and Algerian camels are related to Trypanosoma evansi. Unexpectedly, diversity within T. evansi was higher in Egyptian camels than in Algerian camels. We present here the first molecular report providing a picture of trypanosomiasis in camels, covering wide geographical areas in Egypt and Algeria.

Background and Aim: Toll-like receptors (TLRs) are important for the recognition of pathogen-associated molecular patterns. Single nucleotide polymorphisms (SNPs) within TLRs have a potential impact on the alteration of susceptibility or resistance to inflammatory diseases. This work focused on a case-control study for the distribution of SNPs in TLR2 gene to test their role for endometritis occurrence in river buffalo. Materials and Methods: Egyptian buffaloes from the slaughterhouse were tested, where forty samples divided into apparently healthy uteri (20n) and clinically infected ones (20n) were used to detect the genetic association between TLR2 gene SNPs and endometritis disease. Results: Nineteen novel polymorphic sites were identified. Three SNPs were found to be statistically significant. AA genotype at 5`UTR and CC genotype at the coding region had significant association with susceptibility to endometritis, while GG genotype at 5`UTR had significant association with resistance to endometritis. Polyphen 2 analysis revealed three amino acids substitutions in TLR2 protein having potential functional significance. Haplotype reconstruction revealed the statistical significance of haplotype frequencies between cases and controls indicating its association with the occurrence of endometritis. Conclusions: It is to be concluded that the innate immune activation response may be interfered by the effect of polymorphisms and mutations of TLRs due to the reduction of the protein ability to recognize Pathogen associated Molecular pattern (PAMPs).

Background and Aim: Despite the economic importance of buffalo as a main source of milk and meat, only little attention has been directed to its immune and reproductive performance. The early diagnosis of subclinical endometritis may reduce the economic loss of buffalo’s production. The difference in expression profiles of immunity-related genes has an important role in the early detection of subclinical endometritis. This study aimed to assess the expression of five immunity-related genes: TGFBR1, PTGER2, PTGER4, HP and CXCL5 in endometritis-infected buffaloes. Materials and Methods: Total RNA was extracted from 120 buffalo uterine samples; 60 infected with endometritis and 60 healthy ones. Qt-PCR was performed on cDNA synthesized from extracted RNA using Sybr green and GAPDH as a house-keeping gene. Results: The results showed the up-regulation of two tested genes; TGFBR1 and CXCL5 in endometritis-infected buffalo compared to healthy animals by 7.9 and 4.3 folds, respectively at a significance level of p<0.05. The other three tested genes; PTGER2, PTGER4 and HP were down-regulated in buffalo during endometritis infection at different levels; PTGER2 and HP (0.6 folds, p<0.05) and PTGER4 (0.4 fold, p= 0.2). Conclusions: It is to be concluded that the assessment of expression of inflammation-related immunity genes may have an effective role on the detection of endometritis infection in buffalo during its early stages and this early diagnosis can reduce the economic loss of buffalo production and reproduction.

D NA methylation is explained as attachment of me- thyl group to DNA especially to the carbon atom of cytosine base C at 5 th position (Blow e al., 2016).Also, the addition of the methyl group may be occurred to the adenine nucleotide (Greer et al., 2015).The C methylation in CpG context is the extensively examined one compared to other contexts; CHG or CHH (An et al., 2018).DNA methylation is considered an important epigenetic factor which can transmit through successive generations (Ming et al., 2021) and it has different important physiological and biological activities such as gene expression and cellular differentiation (Vento-Tormo et al., 2016; Adamkova et al., 2017) and can affect the phenotypes characters in domestic animals (Fan et al., 2020).DNA methylation can be studied using different sequenc-research

Amira M. Nowier1, Hassan R. Darwish2, Sherif I. Ramadan3, Nadia A. Abo El-Maaty2 and Othman E. Othman2* 1Biotechnology Research Department, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza, Egypt. 2Cell Biology Department, National Research Centre, Dokki, Egypt. 3Animal Wealth Development Department, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt. Article Information Received 06 July 2020 Revised 29 August 2020 Accepted 26 September 2020 Available online 12 August 2021

(1) Background: It has been recognized that the origin of fat-tailed sheep occurred within coarse wool breeds and that this character was introgressed several times into thin-tailed populations. However, no study has investigated this idea for Egyptian breeds using mtDNA analyses. (2) Methods: Using new sequences of the control region, we constructed a database of 467 sequences representing 37 breeds including fat- and thin-tailed ones with 80 Egyptian individuals belonging to six local breeds (Barki, Fallahi, Ossimi, Rahmani, Saidi, Sohagi). The phylogenetic tree obtained with the maximum likelihood method was submitted to the Newick Extra program to count the direct and indirect links between the individuals of each breed. (3) Results: Several Egyptian breeds were strongly connected to "primitive" thin-tailed breeds from Europe, indicating a clear genetic background of the "thin tail" breed type that supports the view of archeologists. In several cases, we suspected Western Asian breeds to be involved in the introgression of the fat tail character. In contrast, the Ossimi breed showed a high affinity to a fat-tailed breed of Western Asia, suggesting a direct migration and no thin tail ancestors. The Saidi is unique as our analyses revealed its strong connection with thin-tailed Sudanese breeds.

To understand the molecular and genetic mechanisms related to the litter size in one species of two different populations (high litter size and low litter size), we performed RNA-seq for the oocytes and granulosa cells (GCs) at different developmental stages of follicle, and identified the interaction of genes from both sides of follicle (oocyte and GCs) and the ligand-receptor pairs from these two sides. Our data were very comprehensive to uncover the difference between these two populations regarding the folliculogenesis. First, we identified a set of potential genes in oocyte and GCs as the marker genes which can be used to determine the goat fertility capability and ovarian reserve ability. The data showed that GRHPR, GPR84, CYB5A and ERAL1 were highly expressed in oocyte while JUNB, SCN2A, MEGE8, ZEB2, EGR1and PRRC2A were highly expressed in GCs. We found more functional genes were expressed in oocytes and GCs in high fertility group (HL) than that in low fertility group (LL). We uncovered that ligand-receptor pairs in Notch signaling pathway and transforming growth factor-β (TGF-β) superfamily pathways played important roles in goat folliculogenesis for the different fertility population. Moreover, we discovered that the correlations of the gene expression in oocytes and GCs at different stages in the two populations HL and LL were different, too. All the data reflected the gene expression landscape in oocytes and GCs which was correlated well with the fertility capability.

The new technology of high-throughput single-cell RNA sequencing (10 x scRNA-seq) was developed recently with many advantages. However, it was not commonly used in farm animal research. There are few reports for the gene expression of goat ovarian follicle granulosa cells (GCs) during different developmental stages. In the current investigation, the gene expression of follicle GCs at different stages from two populations of Ji'ning grey goats: high litter size (HL; >= 3/L; 2 L) and low litter size (LL; <= 2 /L; 2 L) were analysed by scRNA-seq. Many GC marker genes were identified, and the pseudo-time showed that GCs developed during the time course which reflected the follicular development and differentiation trajectory. Moreover, the gene expression difference between the two populations HL versus LL was very clear at different developmental stages. Many marker genes differentially expressed at different developmental stages. ASIP and ASPN were found to be highly expressed in the early stage of GCs, INHA, INHBA, MFGE8 and HSD17B1 were identified to be highly expressed in the growing stage of GCs, while IGFBP2, IGFBP5 and CYP11A1 were found to be highly expressed in late stage. These marker genes could be used as reference genes of goat follicle GC development. This investigation for the first time discovered the gene expression patterns in goat follicle GCs in high- or low-fertility populations (based on litter size) by scRNA-seq which may be useful for uncovering the oocyte development potential.

Although some studies have investigated the DNA methylation modification in goat ovaries, it is not understood DNA methylation related to goat litter size. This investigation was designed to explore the DNA methylation status in the ovaries of high litter size and low litter size groups using whole-genome bisulfite sequencing (WGBS). We found that there was global difference on DNA methylation in high litter size and low litter size goat ovaries. Many differentially methylated region-related genes (DMGs) were found in the ovaries of these two different goat populations. Moreover, enrichment analysis discovered that many DMGs were involved in gamete development, reproductive system development, wingless-type MMTV integration site family (WNT) signalling pathways and mitogen-activated protein kinase 1 (MAPK) signalling pathways. The data indicated that DNA methylation in goat ovaries may play important roles in the folliculogenesis, the oocyte ovulation rate and finally the litter size. This study provides a comprehensive analysis of genome-wide DNA methylation patterns in ovaries of high and low litter size goat which helps the understanding of ovarian DNA methylation in relation to goat fertility capability.

Background and Aim: Uterine lumen contamination with bacteria is ubiquitous in buffalo after parturition. Nearly one-third of these infected animals develop endometritis which leads to reduced fertility. The present study aimed to evaluate the expressions of IFN-γ and NOS2 genes in uterine tissue of buffaloes with endometritis and comparing them with those in healthy animals using RT-qPCR Materials and Methods: Uterine samples were collected from 50 apparently healthy and 50 clinically infected buffaloes. RNA was extracted from the collected buffalo's uteri and cDNA was synthesized from extracted RNA. Quantitative Real Time PCR technique was performed using this synthesized cDNA. Results: Apparent up-regulation of both genes mRNA expression was recorded in endometritis-infected animals with 8.3-folds for IFN-γ and 9.99-folds for NOS2 (P<0.001). Conclusion: The upregulation of IFN-γ and NOS2 expression in the uterine tissue of endometritis-infected buffaloes can be used as a scale for measuring the efficiency of drugs used for endometritis treatment.

Contamination of the uterine lumen with bacteria occurred in bovid within the first week after parturition. The bacterial infection causes the persistent inflammation in the endometrium leading to the infertility and huge economical loss in animal production. TGF-β and IL-1R2 genes are involved in innate immune recognition of pathogens and the inflammatory response. This study aimed to compare the expression of these two genes in uteri samples of endometritis-infected and apparently healthy buffaloes using QT-PCR. The uteri samples were collected from endometritis-infected and normal buffaloes. Bacterial examination of uteri from endometritis-infected buffaloes showed the presence of bacterial contamination with E. coli, P. Klebsiella pneumonia and/or P. vulgaris. RNA was extracted from uteri of infected and normal animal, and cDNA was synthesized for QT-PCR. Using GAPDH as a housekeeping gene, the gene expression of two tested genes was assessed and the results showed that the expression of TGF-β and IL-1R2 genes was up-regulated in infected animals compared to control by 11.39 and 12.99 folds, respectively and this increase of gene expressions was highly significant. In conclusion, the gene expression assessment of important innate immune genes—like TGF-β and IL-1R2 genes can help to establish new approaches for the improvement of the immune response of buffalo through marker-assisted selection of animals characterized by superior innate immunity system.

The prion protein is coded by the PRP gene which is active in the brain and several other tissues. The functions of normal PrPs are related to energy production, protein degradation and DNA replication. Prions are the essential factor for the transmissible spongiform encephalopathies (TSEs) in different mammalian species. The present study aimed to identify the nucleotide characterization of the PRP gene in six camel breeds reared in Egypt. Genomic DNA which was extracted from 80 camels belonging to six breeds reared in Egypt was used to amplify fragments at 725-bp using a specific primer for PRP gene. Alignment of Egyptian camel PRP nucleotide sequences with those of other mammalian species declared the similarity 100% between PRP sequences of Egyptian and Iranian camels and 99.7% similarity with English, German and Chinese camel populations. The nucleotide sequence of Egyptian camel was submitted to GenBank under the accession no.: MF685344. The comparison between PRP amino acids of Camelus species with other mammalian species showed two missing amino acids in Camelus and Lama glama species; Glycine at position 83 and Leucine at position 229 whereas there is a unique amino acid addition - Glycine at position 89 - in Camelus species.

The objectives of this study were to identify polymorphisms in the lactoferrin gene among three Egyptian goat breeds (Barki, Zaraibi, and Damascus) and to investigate the effect of LF genotype, parity, and lactation stage on milk composition traits of Zaraibi goats. One hundred and thirty-two blood samples were collected for DNA extraction, with 53 from Zaraibi, 40 from Damascus, and 39 from Barki breeds. Fat, protein, total solids, solids-not-fat, and lactose percentages were determined in Zaraibi goat milk using an automatic milk analyzer. Two genotypes, GG and GA, in the lactoferrin gene were identified using single-strand conformation polymorphism and were confirmed by direct sequencing technique. The Zaraibi breed recorded the highest heterozygosity (0.272) and effective number of alleles (1.369), while the Damascus breed recorded the lowest values. The G/A SNP showed a significant association with protein, solids-not-fat, and total solid content of Zaraibi goat milk. Protein, solids-not-fat, and total solid content in our study were significantly higher at early and late parities. Lactose percentage decreased significantly from early to late parity. Fat, protein, solids-not-fat, and total solid content were significantly higher at early and late stages of lactation, and our results encourage the utilization of Zaraibi goat milk in cheese and butter processing at these stages. Moreover, the G/A SNP of the LF gene may be a useful marker for assisted selection programs to improve goat milk composition.

Bone morphogenetic protein 15 (BMP15/FecX) gene is considered one of the major genes and a candidate marker for the reproduction in farm animals, especially sheep. The present study aimed to detect the genetic polymorphisms of BMP15 gene in sheep using PCR-RFLP technique. In the present study, 115 ewes were assigned into high and low prolificacy categories according to their reproductive history. In high prolific group (n = 20), ewes produced twins more than single births. In the low prolific type (n = 95), the ewes produced single births more than twins. DNA was extracted from blood samples of all ewes, subjected to PCR-RFLP analysis and confirmed by sequence analysis. The PCR products of 356 bp size were cut with HinƒI restriction enzyme. Three digested fragments of 70, 117 and 169 bp were obtained in both types of sheep. All animals were homozygous with CC genotype. In conclusion, the accessible findings did not detect any mutation in FecX gene in sheep, regardless their prolificacy. Therefore, further attempts are necessary to detect other SNP for BMP-15 gene in Egyptian sheep breeds.

Foot and Mouth disease (FMD) is a contagious disease leads to economically loss in livestock production all over the world. This serious disease is caused due to the infection of the animal with a single-stranded RNA virus (FMDV). This study aimed to investigate the genetic polymorphism of BoLA-DRB3 gene in Egyptian buffalo as a candidate genetic marker included in multi-factorial process of FMD resistance/susceptibility. Also this work aimed to genetically characterization and serotyping of circulating FMD virus in Egypt during 2016. For serotyping of FMDV, RT-PCR was used for FMDV-positive samples and the results declared the presence of serotype O in all tested animals. The sequence analysis of FMDV samples revealed five different patterns for the detected serotype O which were submitted to GenBank under the accession Nos.: MG017361-MG017365. The 302-bp amplified fragments from BoLA-DRB3 exon 2 were digested with HaeIII endonuclease and the results showed that the presence of five BoLA-DRB3 genotypes, among them the genotype AA might be associated with FMD-resistance (P < 0.01). On the other hand, genotype AC could be correlated with susceptibility (P < 0.01) to FMD in Egyptian buffaloes where it was absent in resistant group. The five detected genotypes of BoLA-DRB3 exon 2 were submitted to GenBank with the accession Nos.: MF977316-MF977320. In conclusion, our findings suggested that the detection of different BoLA-DRB3 genotypes may be has a promising role for raising the resistance of Egyptian buffalo against FMDV especially serotype O which is prevalent in Egypt with preferring genotype AA.

One of the effective approaches for genetic improvement of productivity traits in farm animals is markerassisted selection (MAS) depending on the genetic markers that are associated with superior productivity traits. The improvement of fertility trait is one of the main targets in small ruminant breeding programs. This work aimed to identify RFLPs and SNPs variations among three fertility genes in Egyptian sheep and goat breeds. RFLP analysis of the amplified fragments at 462-bp from exon 1 of GDF9 using HpaII endonuclease showed the presence of two genotypes GG and AG. Depending on the presence of the restriction site of TaqI endonuclease (T^CGA) in the 348-bp amplified fragment from exon 5 of GPR54 gene, the results showed the presence of two alleles, C and T with three genotypes, viz. CC, TT and CT. The PCR amplified fragments of 190-bp from FecB gene were digested with AvaII restriction enzyme and the results showed that all tested animals had the same homozygous non-carrier genotype (++). It was concluded that the identification of genetic structure and nucleotide sequences of GDF9, GPR54 and FecB genes is considered the first step towards the genetic improvements of fertility trait in Egyptian small ruminants where these genes are associated with different fertility traits parameter like ovulation rate, ovarian follicular development, puberty and litter size in small ruminant breeds.

This work was carried out in collaboration between all authors. Author OEO designed the study, performed the data analysis, wrote the protocol and wrote the first draft of the manuscript. Author AAE performed the practical work and followed the publication process. Author AEED managed the analyses of the study and the literature searches. All authors read and approved the ABSTRACT Aim: The present work was carried out to study the genetic characteristics of the IGFBP-3 gene in buffaloes reared in Egypt, where it is considered as one at three The genetic character of the IGFBP-3 gene studied by using PCR-RFLP and nucleotide sequencing. The PCR products after the digestion with those restriction enzymes revealed that the presence of the following fragments: two fragments at 506- and 145-bp with Msp I two fragments at 240- and 411-bp with Taq I; and eight fragments at 199-, 164-, 154-, 56-, 36-, 18-, 16- and 8-bp with Hae III. The restriction digestion of the amplified fragments of the IGFBP-3 gene did not show a genetic polymorphism or nucleotide substitution where all restricted fragments yielded from the digestion with three restriction enzymes were of the same sizes. Conclusion: Our findings indicated that the absence of the genetic polymorphism of the IGFBP-3 gene in Egyptian buffalo. Based on our results in addition to the significant effect of this gene on different productivity traits, the crossing between Egyptian buffalo with other breeds, particularly the Italian breed, is needed for more improvements of Egyptian buffalo's productivity where the Italian buffaloes characterized by high growth and fertility phenomena.