Deng, T., J. Wu, H. Abdel-Shafy, X. Wang, H. Lv, A. Shaukat, X. Zhou, Y. Zhou, H. Sun, P. Wei, et al., "Comparative Genomic Analysis of the Thiolase Family and Functional Characterization of the Acetyl-Coenzyme A Acyltransferase-1 Gene for Milk Biosynthesis and Production of Buffalo and Cattle.", Journal of agricultural and food chemistry, vol. 71, issue 7, pp. 3325-3337, 2023. Abstract

Cattle and buffalo served as the first and second largest dairy animals, respectively, providing 96% milk products worldwide. Understanding the mechanisms underlying milk synthesis is critical to develop the technique to improve milk production. Thiolases, also known as acetyl-coenzyme A acetyltransferases (ACAT), are an enzyme family that plays vital roles in lipid metabolism, including ACAT1, ACAT2, ACAA1, ACAA2, and HADHB. Our present study showed that these five members were orthologous in six livestock species including buffalo and cattle. Transcriptomic data analyses derived from different lactations stages showed that displayed different expression patterns between buffalo and cattle. Immunohistochemistry staining revealed that ACAA1 were dominantly located in the mammary epithelial cells of these two dairy animals. Knockdown of inhibited mammary epithelial cell proliferation and triglyceride and β-casein secretion by regulating related gene expressions in cattle and buffalo. In contrast, overexpression promoted cell proliferation and triglyceride secretion. Finally, three novel SNPs (g.-681A>T, g.-23117C>T, and g.-24348G>T) were detected and showed significant association with milk production traits of Mediterranean buffaloes. In addition, g.-681A>T mutation located in the promoter region changed transcriptional activity significantly. Our findings suggested that play a key role in regulating buffalo and cattle milk synthesis and provided basic information to further understand the dairy animal lactation physiology.

Ma, X. -ya, A. -qin Duan, X. -rong Lu, S. -sha Liang, P. -hao Sun, M. M. H. Sohel, H. Abdel-Shafy, A. Amin, A. -xin Liang, and T. -xian Deng, "Novel Insight into the Potential Role of Acylglycerophosphate Acyltransferases Family Members on Triacylglycerols Synthesis in Buffalo", International Journal of Molecular Sciences, vol. 23, no. 12, 2022. AbstractWebsite

Acylglycerophosphate acyltransferases (AGPATs) are the rate-limiting enzymes for the de novo pathway of triacylglycerols (TAG) synthesis. Although AGPATs have been extensively explored by evolution, expression and functional studies, little is known on functional characterization of how many members of the AGPAT family are involved in TAG synthesis and their impact on the cell proliferation and apoptosis. Here, 13 AGPAT genes in buffalo were identified, of which 12 AGPAT gene pairs were orthologous between buffalo and cattle. Comparative transcriptomic analysis and real-time quantitative reverse transcription PCR (qRT-PCR) further showed that both AGPAT1 and AGPAT6 were highly expressed in milk samples of buffalo and cattle during lactation. Knockdown of AGPAT1 or AGPAT6 significantly decreased the TAG content of buffalo mammary epithelial cells (BuMECs) and bovine mammary epithelial cells (BoMECs) by regulating lipogenic gene expression (p < 0.05). Knockdown of AGPAT1 or AGPAT6 inhibited proliferation and apoptosis of BuMECs through the expression of marker genes associated with the proliferation and apoptosis (p < 0.05). Our data confirmed that both AGPAT1 and AGPAT6 could regulate TAG synthesis and growth of mammary epithelial cells in buffalo. These findings will have important implications for understanding the role of the AGPAT gene in buffalo milk performance.

Lin, Y., H. Sun, A. Shaukat, T. Deng, H. Abdel-Shafy, Z. Che, Y. Zhou, C. Hu, H. Li, Q. Wu, et al., Novel Insight Into the Role of ACSL1 Gene in Milk Production Traits in Buffalo, , vol. 13, 2022. AbstractWebsite

Understanding the genetic mechanisms underlying milk production traits contribute to improving the production potential of dairy animals. Long-chain acyl-CoA synthetase 1 (ACSL1) plays a key role in fatty acid metabolism and was highly expressed in the lactating mammary gland epithelial cells (MGECs). The objectives of the present study were to detect the polymorphisms within ACSL1 in Mediterranean buffalo, the genetic effects of these mutations on milk production traits, and understand the gene regulatory effects on MGECs. A total of twelve SNPs were identified by sequencing, including nine SNPs in the intronic region and three in the exonic region. Association analysis showed that nine SNPs were associated with one or more traits. Two haplotype blocks were identified, and among these haplotypes, the individuals carrying the H2H2 haplotype in block 1 and H5H1 in block 2 were superior to those of other haplotypes in milk production traits. Immunohistological staining of ACSL1 in buffalo mammary gland tissue indicated its expression and localization in MGECs. Knockdown of ACSL1 inhibited cell growth, diminished MGEC lipid synthesis and triglyceride secretion, and downregulated CCND1, PPARγ, and FABP3 expression. The overexpression of ACSL1 promoted cell growth, enhanced the triglyceride secretion, and upregulated CCND1, PPARγ, SREBP1, and FABP3. ACSL1 was also involved in milk protein regulation as indicated by the decreased or increased β-casein concentration and CSN3 expression in the knockdown or overexpression group, respectively. In summary, our present study depicted that ACSL1 mutations were associated with buffalo milk production performance. This may be related to its positive regulation roles on MGEC growth, milk fat, and milk protein synthesis. The current study showed the potential of the ACSL1 gene as a candidate for milk production traits and provides a new understanding of the physiological mechanisms underlying milk production regulation.

Hua, G., H. Abdel-Shafy, T. Deng, Y. Zhou, and W. Y. Low, Buffalo Genetics and Genomics, , Lausanne, Frontiers Media SA, 2022.
Almarzook, S., H. Abdel-Shafy, A. Said Ahmed, M. Reissmann, and G. Brockmann, "Genetic diversity of Arabian horses using microsatellite markers", Egyptian Journal of Animal Production, vol. 59, issue 1, pp. 19 - 27, 2022. AbstractWebsite

The horse strains designation system was shaped in the 7th century in the Arabian Peninsula and spread to the neighboring oriental empires and it is still used. The aim of the present study was to investigate genetic diversity among three Arabian horse strains using twelve equine microsatellite markers. The study included 84 Arabian horses comprising Arabian horses from the major Syrian strains Hamdani, Kahlawi and Saglawi. The studied horses represented five geographical regions in Syria. To determine genetic population structure within and between the three strains, we applied different methods. The selected panel of microsatellite markers confirmed a general genetic feature of the three main strains of Syrian Arabian horses suggesting low level of population differentiation. To ascertain the results, it will be necessary to collate our findings with the historical pedigrees. Furthermore, we need a genome-wide investigation of microsatellites or an analysis of strain/breed specific SNPs across the Syrian Arabian horse populations for better insight into the genetic diversity.

Abdel-Shafy, H., T. Deng, Y. Zhou, W. Y. Low, and G. Hua, "Editorial: Buffalo Genetics and Genomics", Frontiers in Genetics, vol. 12, pp. 820627, 2022. AbstractWebsite


Abdel-Shafy, H., "Genomic Selection: Towards Meeting Challenge of Food Security", Annals of Agricultural Science, Moshtohor, vol. 59, issue 2, pp. 1 - 8, 2021. AbstractWebsite

Breeding is a powerful science and remains a core component of most agriculture production. Although traditional selection has proven to be a successful approach for improving animal and plant production in the last decades, several studies have reported a worrying shortage between the current rates of production and expected global future demands for food. These challenges, coupled with a constant loss of suitable land for agricultural production, needs to implement new breeding strategies to significantly increase the genetic gain and meet the future requirements. Recent advances in genotyping capacity with affordable costs have allowed selection based on genomic information. These technologies would reshape the breeding programs, accelerate the genetic gain and maximize the productivity per unit. Although this concept was suggested many decades ago, the applications of marker-assisted selection were limited due to the low number of genotyped markers and low number of identified QTL. In contrast, genomic selection (GS) utilizes the dense genetic markers across the whole genome to predict the effect of all QTL that are assumed to be in linkage disequilibrium with at least one genetic marker. Nowadays, GS is widely implemented in several species for breeding purposes and attracted attention for human disease risk predictions. It has been proven for many traits to double the rate of the genetic gain and reduce the generation interval, which would efficiently contribute to more food security. Here, we introduce the general concept of GS, and briefly describe the GS models along with the recent progress in some farm animal species.

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.