Shao, B., H. Sun, M. J. Ahmad, N. Ghanem, H. Abdel-Shafy, C. Du, T. Deng, S. Mansoor, Y. Zhou, Y. Yang, et al., Genetic Features of Reproductive Traits in Bovine and Buffalo: Lessons From Bovine to Buffalo, , vol. 12, pp. 366, 2021. AbstractWebsite

Bovine and buffalo are important livestock species that have contributed to human lives for more than 1000 years. Improving fertility is very important to reduce the cost of production. In the current review, we classified reproductive traits into three categories: ovulation, breeding, and calving related traits. We systematically summarized the heritability estimates, molecular markers, and genomic selection (GS) for reproductive traits of bovine and buffalo. This review aimed to compile the heritability and genome-wide association studies (GWASs) related to reproductive traits in both bovine and buffalos and tried to highlight the possible disciplines which should benefit buffalo breeding. The estimates of heritability of reproductive traits ranged were from 0 to 0.57 and there were wide differences between the populations. For some specific traits, such as age of puberty (AOP) and calving difficulty (CD), the majority beef population presents relatively higher heritability than dairy cattle. Compared to bovine, genetic studies for buffalo reproductive traits are limited for age at first calving and calving interval traits. Several quantitative trait loci (QTLs), candidate genes, and SNPs associated with bovine reproductive traits were screened and identified by candidate gene methods and/or GWASs. The IGF1 and LEP pathways in addition to non-coding RNAs are highlighted due to their crucial relevance with reproductive traits. The distribution of QTLs related to various traits showed a great differences. Few GWAS have been performed so far on buffalo age at first calving, calving interval, and days open traits. In addition, we summarized the GS studies on bovine and buffalo reproductive traits and compared the accuracy between different reports. Taken together, GWAS and candidate gene approaches can help to understand the molecular genetic mechanisms of complex traits. Recently, GS has been used extensively and can be performed on multiple traits to improve the accuracy of prediction even for traits with low heritability, and can be combined with multi-omics for further analysis.

Abdel-Shafy, H., M. A. A. Awad, H. El-Regalaty, S. E. - D. El-Assal, and S. Abou-Bakr, "Prospecting genomic regions associated with milk production traits in Egyptian buffalo", Journal of Dairy Research, 2020.
Awad, M. A. A., S. Abou-Bakr, H. El-Regalaty, S. E. - D. El-Assal, and H. Abdel-Shafy, "Determination of Potential Candidate Genes Associated with Milk Lactose in Egyptian Buffalo", World's Veterinary Journal, vol. 10, issue 1, pp. 35-42, 2020.
Lu, X. R., A. Q. Duan, W. Q. Li, H. Abdel-Shafy, H. E. Rushdi, S. S. Liang, X. Y. Ma, X. W. Liang, and T. X. Deng, "Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk production traits in Chinese buffalo breeds", Journal of Dairy Science: Elsevier, 2020. AbstractWebsite

The water buffalo is an important dual-purpose livestock that is widespread throughout central and southern China. However, there has been no characterization of the population genetics of Chinese buffalo. Using an Axiom buffalo genotyping array (Thermo Fisher Scientific, Wilmington, DE), we analyzed the genetic diversity, linkage disequilibrium pattern, and signature of selection in 176 Chinese buffaloes from 13 breeds. A total of 35,547 SNP passed quality control and were used for further analyses. Population genetic analysis revealed a clear separation between swamp and river types. Ten Chinese indigenous breeds were clustered into the swamp group, the Murrah and Nili-Ravi breeds were clustered into the river group, and the crossbred breed was closer to the river group. Genetic diversity analysis showed that the swamp group had a lower average expected heterozygosity. Linkage disequilibrium decay distance was much shorter in the swamp group compared with the river group, with an average square of correlation coefficient value of 0.2 of approximately 50 kb. Analysis of runs of homozygosity indicated extensive remote and recent inbreeding within swamp and river groups, respectively. Moreover, one genomic region under selection was detected between the river and swamp groups. Our findings contribute to our understanding of the characterization of population genetics in Chinese buffaloes, which in turn may be used in buffalo breeding programs.The water buffalo is an important dual-purpose livestock that is widespread throughout central and southern China. However, there has been no characterization of the population genetics of Chinese buffalo. Using an Axiom buffalo genotyping array (Thermo Fisher Scientific, Wilmington, DE), we analyzed the genetic diversity, linkage disequilibrium pattern, and signature of selection in 176 Chinese buffaloes from 13 breeds. A total of 35,547 SNP passed quality control and were used for further analyses. Population genetic analysis revealed a clear separation between swamp and river types. Ten Chinese indigenous breeds were clustered into the swamp group, the Murrah and Nili-Ravi breeds were clustered into the river group, and the crossbred breed was closer to the river group. Genetic diversity analysis showed that the swamp group had a lower average expected heterozygosity. Linkage disequilibrium decay distance was much shorter in the swamp group compared with the river group, with an average square of correlation coefficient value of 0.2 of approximately 50 kb. Analysis of runs of homozygosity indicated extensive remote and recent inbreeding within swamp and river groups, respectively. Moreover, one genomic region under selection was detected between the river and swamp groups. Our findings contribute to our understanding of the characterization of population genetics in Chinese buffaloes, which in turn may be used in buffalo breeding programs.

Abdel-Shafy, H., M. A. A. Awad, H. El-Regalaty, A. Ismael, S. E. - D. El-Assal, and S. Abou-Bakr, "A single-step genomic evaluation for milk production in Egyptian buffalo", Livestock Science, vol. 234, pp. 103977, 2020.
El-Halawany, N., A. - E. - M. A. Shawky, S. M. Sherif, A. E. M. El-Wardany, M. A. Abdel-Latif, H. Abdel-Shafy, A. F. M. Al-Tohamy, and Y. El-Sayed, "Investigation of STAT5A, OLR1, LF and TLR4 Variants and Its Association With Milk Yield In Egyptian Buffalo", Research Journal of Pharmaceutical, Biological and Chemical Sciences, vol. 10, issue 3, pp. 179-187, 2019.
El-Halawany, N., A. El-Werdany, Y. A. El-Sayed, A. - E. - M. A. Shawky, A. F. Al-Tohamy, H. Abdel-Shafy, and F. M. Abd-El-Razek, "Characterization of growth hormone gene (GH) in three Egyptian goat breeds", Meta Gene, vol. 20, pp. 100556, 2019.
El-Halawany, N., A. - E. - M. A. Shawky, A. F. M. Al-Tohamy, M. A. Abdel-Latif, H. Abdel-Shafy, Y. A. S. S. E. R. A. GHAZI, C. Neuhoff, and K. Schellander, "Effect of complement component 5 polymorphisms on mastitis resistance in Egyptian buffalo and cattle.", Research in veterinary science, vol. 119, pp. 45-51, 2018 Aug. Abstract

Mastitis is one of the costliest diseases affecting the world's dairy industry. The important contribution of complement Component 5 (C5) to phagocytosis, which plays a major role in the defence of the bovine mammary gland against infection, makes this component of innate immunity a potential contributor in defending udder against mastitis. The objectives of this study were to sequence and analyse the whole coding region of the C5 gene in Egyptian buffalo and cattle, to detect any nucleotide variations (polymorphisms) and to investigate their associations with milk somatic cell score (SCS) as an indicator of mastitis in dairy animals. We sequenced a buffalo C5 cDNA fragment of 5336 bp (KP221293) and a cattle C5 cDNA fragment of 5303 bp (KP221294), which included the whole coding region and 3-UTR. Buffalo and cattle C5 cDNA shared sequence identity of 99%. The predicted complement C5 proteins consist of 1677 amino acid residues in both animals, one amino acid less than in humans and three amino acids more than in mouse C5 protein. Comparing cDNA sequences of different animals revealed nine novel SNPs in buffalo and seven SNPs in cattle, with two of them being novel. The association analysis revealed that five SNPs in buffalo are highly associated with SCS; indicating the contribution of complement C5 variants in buffalo mastitis resistance. No significant associations were detected between C5 variants and SCS in cattle. This is the first report about C5 variants in buffalo and its association with SCS.

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.

Abdel-Shafy, H., R. H. Bortfeldt, M. Reissmann, and G. A. Brockmann, "Validating genome-wide associated signals for clinical mastitis in German Holstein cattle.", Animal genetics, vol. 49, issue 1, pp. 82-85, 2018 Feb. Abstract

A validation study for six genomic regions previously identified by a genome-wide association study for somatic cell score was conducted with data of clinical mastitis in German Holstein cattle. Out of 10 tested SNPs, five on chromosomes 6, 13 and 19 were significantly associated with clinical mastitis (P < 0.05). Three SNPs on chromosomes 6 and 19 had the same direction of effect as those previously reported in the initial genome-wide association study for somatic cell score. The other two SNPs on chromosome 13 had opposite effects. As well as validating associations within known QTL from previous studies, e.g. chromosomes 6 and 19, novel loci on chromosome 13 were confirmed. Promising candidate genes are, for example: deoxycytidine kinase, immunoglobulin J chain, vitamin D binding protein, forkhead box K2, sodium/hydrogen exchanger 8 and cytoplasmic nuclear factor of activated T-cells 2. Our confirmation study provides additional evidence for the functional role of the linked genomic regions to immune response. This information can be used as a basis for further functional studies for those potential genes.