El-Halawany, N., A. A. Shawky, A. F. M. Al-Tohamy, L. Hegazy, H. Abdel-Shafy, M. A. Abdel-Latif, Y. A. S. S. E. R. A. GHAZI, C. Neuhoff, D. Salilew-Wondim, and K. Schellander, "Complement component 3: characterization and association with mastitis resistance in Egyptian water buffalo and cattle", Journal of Genetics, vol. 96, pp. 1 - 9, 2017. AbstractWebsite

Mastitis is an infectious disease of the mammary gland that leads to reduced milk production and change in milk composition. Complement component C3 plays a major role as a central molecule of the complement cascade involving in killing of microorganisms, either directly or in cooperation with phagocytic cells. C3 cDNA were isolated, from Egyptian buffalo and cattle, sequenced and characterized. The C3 cDNA sequences of buffalo and cattle consist of 5025 and 5019 bp, respectively. Buffalo and cattle C3 cDNAs share 99% of sequence identity with each other. The 4986 bp open reading frame in buffalo encodes a putative protein of 1661 amino acids—as in cattle—and includes all the functional domains. Further, analysis of the C3 cDNA sequences detected six novel single-nucleotide polymorphisms (SNPs) in buffalo and three novel SNPs in cattle. The association analysis of the detected SNPs with milk somatic cell score as an indicator of mastitis revealed that the most significant association in buffalo was found in the C >A substitution (ss: 1752816097) in exon 27, whereas in cattle it was in the C >T substitution (ss: 1752816085) in exon 12. Our findings provide preliminary information about the contribution of C3 polymorphisms to mastitis resistance in buffalo and cattle.

El-Halawany, N., H. Abdel-Shafy, A. A. Shawky, M. A. Abdel-Latif, A. F. M. Al-Tohamy, and O. M. Abd El-Moneim, "Genome-wide association study for milk production in Egyptian buffalo", Livestock Science, vol. 198: Elsevier, pp. 10 - 16, 2017. AbstractWebsite

With the aim of characterizing the genetic background of Egyptian buffalo and identifying genomic regions and potential causative mutations associated with milk yield, we performed a Genome-Wide Association Study (GWAS) in Egyptian buffalo using Axiom Buffalo Genotyping Array 90K. This study was carried out with 250 buffalo cows using 89,069 daily milk records. After quality control, a total of 42,269 single nucleotide polymorphisms (SNPs) remained for further analysis. Genome-wide analysis was performed in the way of SNP-by-SNP, through regressing the observations of an average daily milk yield deviations on SNP alleles. Several genomic regions were detected with suggestive signals of association on chromosomes BTA1, BTA5, BTA6, and BTA27. The most significant SNP (Affx-79526274) was located on chromosome BTA27. The convincingly associated SNPs were located within or close to several candidate genes. A GO analysis ranked immune response at the top of all biological process associated with those genes.This is the first GWAS in Egyptian buffalo. Although a small sample size was used in this study, several suggestive genomic loci associated with daily milk production were detected. Further work is required on a larger sample size with fine mapping of identified QTL to detect potential candidate regions.With the aim of characterizing the genetic background of Egyptian buffalo and identifying genomic regions and potential causative mutations associated with milk yield, we performed a Genome-Wide Association Study (GWAS) in Egyptian buffalo using Axiom Buffalo Genotyping Array 90K. This study was carried out with 250 buffalo cows using 89,069 daily milk records. After quality control, a total of 42,269 single nucleotide polymorphisms (SNPs) remained for further analysis. Genome-wide analysis was performed in the way of SNP-by-SNP, through regressing the observations of an average daily milk yield deviations on SNP alleles. Several genomic regions were detected with suggestive signals of association on chromosomes BTA1, BTA5, BTA6, and BTA27. The most significant SNP (Affx-79526274) was located on chromosome BTA27. The convincingly associated SNPs were located within or close to several candidate genes. A GO analysis ranked immune response at the top of all biological process associated with those genes.This is the first GWAS in Egyptian buffalo. Although a small sample size was used in this study, several suggestive genomic loci associated with daily milk production were detected. Further work is required on a larger sample size with fine mapping of identified QTL to detect potential candidate regions.

El-Halawany, N. K., H. Abdel-Shafy, A. A. Shawky, and A. F. M. Al-Tohamy, "A genome-wide association study for daily milk production in Egyptian buffalo", The 6th International Symposium on Animal Functional Genomics, Italy, 2015. isafg2015_proceedings_13.pdf
Abdel-Shafy, H., R. H. Bortfeldt, M. Reissmann, and G. A. Brockmann, "Short communication: Validation of somatic cell score-associated loci identified in a genome-wide association study in German Holstein cattle.", Journal of dairy science, vol. 97, issue 4, pp. 2481-6, 2014 Apr. AbstractWebsite

Recently, we identified 6 genomic loci affecting daughter yield deviations (DYD) for somatic cell score (SCS) in a genome-wide association study (GWAS) performed with German Holstein bulls. In the current study, we tested if these loci were associated with SCS in cows using their own performance data. The study was performed with 1,412 German Holstein cows, of which 483 were daughters of 71 bulls that had been used in the GWAS. We tested 10 single nucleotide polymorphisms (SNP) representing 6 genomic regions that were associated with DYD for SCS in bulls. All tested SNP were significant in cows. Seven of them, located on Bos taurus autosomes (BTA) 6, 13, and 19, had the same direction of effect as those previously reported in the bull population. The most significant associations were detected on BTA6 and BTA19, accounting for 1.8% of the total genetic variance. The major allele of the 2 SNP on BTA6 and the minor allele of the 2 SNP on BTA19 were favorable for lower SCS. The differences between the homozygous genotype classes were up to 15,000 cells/mL. The verification of SNP associated with SCS in this study provides further evidence for the functional role of the linked genomic regions for immune response and contributes to identification of causative mutations. In particular, SNP with minor frequency of the favorable allele possess high potential to reduce SCS in German Holstein cattle by selection.

Abdel-Shafy, H., R. H. Bortfeldt, J. Tetens, and G. A. Brockmann, "Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle", Genetics Selection Evolution, vol. 46: BioMed central, pp. 35, 2014. AbstractWebsite

Background
To better understand the genetic determination of udder health, we performed a genome-wide association study (GWAS) on a population of 2354 German Holstein bulls for which daughter yield deviations (DYD) for somatic cell score (SCS) were available. For this study, we used genetic information of 44 576 informative single nucleotide polymorphisms (SNPs) and 11 725 inferred haplotype blocks.
Results
When accounting for the sub-structure of the analyzed population, 16 SNPs and 10 haplotypes in six genomic regions were significant at the Bonferroni threshold of P <= 1.14 x 10-6. The size of the identified regions ranged from 0.05 to 5.62 Mb. Genomic regions on chromosomes 5, 6, 18 and 19 coincided with known QTL affecting SCS, while additional genomic regions were found on chromosomes 13 and X. Of particular interest is the region on chromosome 6 between 85 and 88 Mb, where QTL for mastitis traits and significant SNPs for SCS in different Holstein populations coincide with our results. In all identified regions, except for the region on chromosome X, significant SNPs were present in significant haplotypes. The minor alleles of identified SNPs on chromosomes 18 and 19, and the major alleles of SNPs on chromosomes 6 and X were favorable for a lower SCS. Differences in somatic cell count (SCC) between alternative SNP alleles reached 14 000 cells/mL.
Conclusions
The results support the polygenic nature of the genetic determination of SCS, confirm the importance of previously reported QTL, and provide evidence for the segregation of additional QTL for SCS in Holstein cattle. The small size of the regions identified here will facilitate the search for causal genetic variations that affect gene functions.

Abde-Shafy, H., Y. M. Hafez, A. M. El-Borady, and N. A. Ahmed, "Can Early Heat Exposure and rbST Alleviate Heat Stress in Rabbits?", The 14th Scientific Conference of Egyptian Society of Animal Production (ESAP) & the 3rd Scientific Conference of Animal Production Research Institute (APRI), 2008. Abstract
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Abdel-Shafy, H., R. Bortfeldt, and G. Brockmann, "Identification of SNPs and chromosomal regions in chromosome 5 associated with somatic cell score (SCS) in German Holstein", Physiology and Genomics of Mastitis: Tutzing, Germany, 2011. Abstract
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Abdel-Shafy, H., and G. Brockmann, "Identification of chromosomal regions associated with somatic cell score in German Holstein cattle", Dairy Cattle Symposium: Humboldt-Universität zu Berlin, Germany, 2012. Abstract
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Abdel-Shafy, H., R. Bortfeldt, J. Tetens, and G. Brockmann, "Genome-wide association study for somatic cell score in German Holstein cattle", 25th International conference - Genetic Days: Wroclaw University of Environmental, Poland, 2012. Abstract
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Hafez, Y. M., A. M. El-Borady, N. A. Ahmed, and H. Abdel-Shafy, "Productive performance and meat quality of rabbits treated with recombinant bovine somatotropin (rbST) as growth enhancer. Egyptian Journal of Rabbit Science", Egyptian Journal of Rabbit Science, vol. 16, no. 2, pp. 263–275, 2006. Abstract
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