Deng, T., X. Ma, A. Duan, X. Lu, and H. Abdel-Shafy, "Multi-omics analysis provides insight into the genetic basis of proline-derived milk microbiota in buffalo", Food Bioscience, vol. 59, pp. 103942, 2024. AbstractWebsite

Understanding the intricate relationship between genetics, metabolites, and microbiota is paramount for unraveling the complexities that define buffalo milk composition. In this study, we employed a multi-omics approach to dissect the genetic and metabolic determinants of buffalo milk traits. Metabolomics analysis of 100 buffalo milk samples revealed a rich profile of 446 metabolites, with a particular emphasis on those associated with amino acid biosynthesis. Metabolite-based Genome-Wide Association Studies (mGWAS) uncovered 13 significant genetic variants, with a pronounced focus on l-Proline. Notably, single nucleotide polymorphisms (SNPs) within the ATG16L1 gene implicated its role in proline production. Concurrently, an in-depth exploration of milk microbiota dynamics highlighted marked differences between buffaloes with high and low proline groups. High proline abundance correlated with increased microbial diversity, dominated by Firmicutes and Proteobacteria. Distinct genera, such as Acinetobacter and Corynebacterium, characterized low and high proline groups, respectively. Functional changes in milk microbiota, especially in amino acid biosynthesis pathways, underscored proline's pivotal role in shaping microbial functions. Correlations between milk microbiota abundance and proline levels emphasized the intricate relationship between host physiology and microbial composition. These findings not only advance our understanding of the genetic basis of metabolic traits in buffalo milk but also present potential biomarkers for targeted breeding strategies. This integrated approach provides a nuanced perspective on milk composition, offering implications for dairy quality and nutritional enhancement.

Liu, Q., Z. Ni, B. Yu, H. Abdel-Shafy, L. Cheng, and H. Chen, "Comparative genomic and transcriptome analyses of transposable elements in buffalo identify key short interspersed element-derived genes for testicular and muscle development.", Journal of dairy science, vol. 108, issue 9, pp. 10325-10337, 2025. Abstract

Transposable elements (TE) are widespread genetic components that affect the structure and function of eukaryotic genomes. However, the comprehensive genomic and transcriptome characterization of buffalo TE remains unclear. Here, we first constructed a pan-TE library from 7 buffalo genomes representing both river and swamp buffalo breeds. We identified 46,389 unique TE comprising 15,975 cores and 30,414 variable elements. These TE span approximately 1.04 Gb and its length account for 33.53% of the buffalo reference genome. The core TE exhibited distinct chromosomal patterns, with the long-interspersed element (LINE), short interspersed element (SINE), and long-terminal repeats (LTR) superfamilies representing the most abundant groups, which varied across subspecies and individuals. Notably, these elements showed a preference for genic regions, with DNA and LTR transposons frequently located within gene introns. Transcriptomic analysis revealed that the TE-derived genes displayed tissue-specific expression, particularly in somatic and gametic tissues. Co-expression analysis identified several SINE-derived hub genes that played key roles in testicular and muscle tissue development. This study provides a comprehensive buffalo pan-TE library, offering an invaluable resource for exploring TE functions, and laying the foundation for future transposome studies in buffalo genetics.

Aboul-Naga, A. M., H. Abdel-Shafy, S. A. Mohamed, and R. M. Ahmed, "Genetic insights and prospects of Egyptian- Nubian (Zaraibi) goats.", Tropical animal health and production, vol. 57, issue 4, pp. 210, 2025. Abstract

The Egyptian Nubian (Zaraibi) goat has significant potential to contribute to animal production and rural livelihoods in Egypt. This article explores the breed's unique genetic makeup and potential for improvement through examining its genetic parameters, population structure, genetic diversity, and candidate genes associated with economically important traits. The reported potential candidate genes include caseins, alpha-lactalbumin (α-LA), beta-lactoglobulin (β-LG), prolactin receptor (PRLR), Fec gene, GDF9, and growth hormone. These genes are associated with milk yield and composition, litter size, and growth performance. Although most candidate gene studies on Zaraibi goats have limitations, their findings can be utilized in genomic evaluation to improve perdition accuracy. Despite challenges such as small herd size, experimental design constraints, epigenetic influence, and potential trade-off between productivity and heat tolerance, there are significant opportunities to enhance the breed's productivity and resilience. The studies highlight advantages such as high genetic diversity, positive genetic gain, adaptation to hot dry environment and clear genetic distinction from other local goat breeds. Prospects for improving Zaraibi goats include recognizing their socioeconomic role in rural communities, supporting selective breeding programs, integrating genomic information into selection strategies, implementing an open nucleus breeding scheme, and expanding the specialized goat cheese market. Like other promising subtropical breeds, utilizing their potential while addressing existing challenges is essential for ensuring sustainable production and continued contributions to the rural economy.

Shi, Z., W. Wang, B. Shokrollahi, W. Wang, H. Abdel-Shafy, and T. Deng, "Role of Quercetin in Modulating Inflammation and Epigenetic Regulation of -Induced Bovine Mastitis.", Journal of agricultural and food chemistry, vol. 73, issue 15, pp. 8784-8797, 2025. Abstract

Mastitis is a prevalent inflammatory disease in dairy herds and presents substantial economic and welfare challenges. Although antibiotics are the most widely used and effective treatment for mastitis, research into alternative antibiotics with plant-derived compounds has gained increasing attention due to the high side effects of antibiotics. Quercetin is known to play a crucial role in regulating inflammation, yet its role in preventing and treating mastitis requires further investigation. To fill this gap, we construct a bovine mastitis model using () as the pathogen and bovine mammary epithelial cells (BMECs) as the cell model. Based on this, our study further investigated the therapeutic potential of quercetin by using assays and murine models. Our results demonstrated that quercetin inhibited the inflammatory response and reduced morphological damage in -induced BMECs by disrupting cell adhesion. Direct RNA sequencing revealed that multiple genes enriched in the TNF/IL-17 pathway were pivotal in the ability of quercetin to mitigate inflammation, which was influenced by N6-methyladenosine (m6A) methylation. Quercetin effectively modulated CCL5 expression, a key chemokine in inflammatory responses in -induced BMECs, through m6A methylation mediated by YTHDF2, revealing a novel epigenetic mechanism in mastitis. RNA-seq analysis showed that quercetin significantly altered genes related to inflammation, extracellular matrix regulation, and matrix metalloproteinase activity, including MMP3, MMP1, MMP1A, and IGFBP3, indicating its impact on tissue remodeling and inflammation. Additionally, quercetin disrupted adhesion to BMECs, inhibited biofilm formation, and reduced the severity of infection. The assay supported the notion that quercetin regulates CCL5 activity to alleviate the inflammatory response in an m6A-YTHDF2-dependent manner. This study demonstrated the dual role of quercetin in inflammation suppression and epigenetic modulation via m6A, positioning quercetin as a promising therapeutic for bovine mastitis and suggesting new treatment strategies targeting CCL5- and m6A-related pathways.

Deng, T. X., X. Y. Ma, A. Q. Duan, X. R. Lu, and H. Abdel-Shafy, "Genomic insights into selection signatures and candidate genes for milk production traits in buffalo population.", Animal : an international journal of animal bioscience, vol. 19, issue 4, pp. 101427, 2025. Abstract

Genetic variability in livestock driven by selection leaves distinct signatures within the genome. However, the comprehensive landscape of the selection responses for milk production traits in the Chinese buffalo population remains elusive. This study employed an integrated haplotype score (iHS) and runs of homozygosity (ROH) analyses of whole-genome sequence data from 100 Chinese buffaloes to decipher selection signatures. Using iHS and ROH, we identified 1 046 and 1 045 significant genomic regions, containing 717 and 263 candidate genes, respectively. The integration of iHS and ROH revealed 258 candidate regions and 108 overlapping genes, representing true selection signatures. Additionally, 94 candidate regions overlapped with 672 previously reported quantitative trait loci associated with key economically important traits. Annotation of the genomic regions highlighted candidate genes linked to milk production traits, including SNORD42, COX18, ANKRD17, ALB, RASSF6, CXCL8, TMEM232, ARHGAP26, and NR3C1. Transcriptome-wide association analysis supported ANKRD17 and CEP41 as potential candidates for affecting milk traits. This study unveils a comprehensive selection signature profile for the Chinese buffalo population by integrating iHS and ROH methods. The findings have broad implications for improving milk production traits in buffalo populations globally, contributing to more sustainable livestock systems. The identified candidate genes shed light on the selection response for milk production traits, offering crucial insights into optimising the breeding strategies for Chinese buffaloes.

Lv, H., X. Xu, Z. Wu, Y. Lin, Y. Liu, M. Liu, L. Xu, X. Wang, N. Sun, H. Abdel-Shafy, et al., "Yes-associated protein 1 is essential for maintaining lactation via regulating mammary epithelial cell dynamics and secretion capacity.", International journal of biological macromolecules, vol. 293, pp. 139290, 2025. Abstract

Understanding the physiology and molecular mechanisms of lactogenesis is crucial for enhancing mammalian milk production. Yes-associated protein 1 (YAP1) regulated mammary epithelial cell survival during pregnancy, but its role in lactation maintenance remains unclear. We found that YAP1 was highly expressed in mammary gland across specie, with elevated expression levels during murine gestation and lactation, particularly localized in alveoli epithelial cells. In vivo administration of a YAP1 inhibitor impaired murine milk yield, mammary gland weight, alveolar structure, and mammary epithelial cell dynamics. In vitro, YAP1 positively affected mammary epithelial cell growth and the synthesis of triglyceride and α-casein. Notably, the primary lactogenesis hormone Prolactin induced cell growth and triglyceride secretion while enhancing YAP1 expression and activity. In contrast, Melatonin inhibited cell growth and triglyceride synthesis, decreasing YAP1 expression and activity. YAP1 knockdown compromised prolactin induced effects, whereas YAP1 overexpression partially rescued cell functions inhibited by melatonin. Finally, Bioinformatics analyses revealed that YAP1 regulated multiple biological processes related to lactogenesis, including cell cycle, apoptosis, endoplasmic reticulum, amino acid transport and biosynthesis, etc. These finding indicated that YAP1 is essential for mammary epithelial cells growth and secretion and played an essential role in the lactating endocrine network by mediating key hormone functions.

Deng, T. -xian, X. -ya Ma, A. Duan, X. -rong Lu, and H. Abdel-Shafy, "Genome-wide copy number variant analysis reveals candidate genes associated with milk production traits in water buffalo (Bubalus bubalis).", Journal of dairy science, vol. 107, issue 9, pp. 7022-7037, 2024. Abstract

Buffaloes are vital contributors to the global dairy industry. Understanding the genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 buffalo genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp buffaloes, and 126 crossbred buffaloes. We identified 36,548 copy number variants (CNV) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 CNV regions (CNVR), with 1,993 shared CNVR being found within the studied buffalo types. Analyzing CNVR highlighted distinct genetic differentiation between river and swamp buffalo subspecies, verified by evolutionary tree and principal component analyses. Admixture analysis grouped buffaloes into river and swamp categories, with crossbred buffaloes displaying mixed ancestry. To identify candidate genes associated with milk production traits, we employed 3 approaches. First, we used Vst-based population differentiation, revealing 11 genes within CNVR that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci analysis revealed differentially expressed CNVR-derived genes (DECG) associated with milk production traits. Notably, known milk production-related genes were among these DECG, validating their relevance. Last, a GWAS identified 3 CNVR significantly linked to peak milk yield. Our study provides comprehensive genomic insights into buffalo populations and identifies candidate genes associated with milk production traits. These findings facilitate genetic breeding programs aimed at increasing milk yield and improving quality in this economically important livestock species.

Wei, K., Y. Lu, X. Ma, A. Duan, X. Lu, H. Abdel-Shafy, and T. Deng, "Transcriptome-Wide Association Study Reveals Potentially Candidate Genes Responsible for Milk Production Traits in Buffalo.", International journal of molecular sciences, vol. 25, issue 5, 2024. Abstract

Identifying key causal genes is critical for unraveling the genetic basis of complex economic traits, yet it remains a formidable challenge. The advent of large-scale sequencing data and computational algorithms, such as transcriptome-wide association studies (TWASs), offers a promising avenue for identifying potential causal genes. In this study, we harnessed the power of TWAS to identify genes potentially responsible for milk production traits, including daily milk yield (MY), fat percentage (FP), and protein percentage (PP), within a cohort of 100 buffaloes. Our approach began by generating the genotype and expression profiles for these 100 buffaloes through whole-genome resequencing and RNA sequencing, respectively. Through comprehensive genome-wide association studies (GWAS), we pinpointed a total of seven and four single nucleotide polymorphisms (SNPs) significantly associated with MY and FP traits, respectively. By using TWAS, we identified 55, 71, and 101 genes as significant signals for MY, FP, and PP traits, respectively. To delve deeper, we conducted protein-protein interaction (PPI) analysis, revealing the categorization of these genes into distinct PPI networks. Interestingly, several TWAS-identified genes within the PPI network played a vital role in milk performance. These findings open new avenues for identifying potentially causal genes underlying important traits, thereby offering invaluable insights for genomics and breeding in buffalo populations.

El Nagar, A. G., M. M. I. Salem, A. M. S. Amin, M. H. Khalil, A. F. Ashour, M. M. Hegazy, and H. Abdel-Shafy, "A Single-Step Genome-Wide Association Study for Semen Traits of Egyptian Buffalo Bulls.", Animals : an open access journal from MDPI, vol. 13, issue 24, 2023. Abstract

The present study aimed to contribute to the limited research on buffalo () semen traits by incorporating genomic data. A total of 8465 ejaculates were collected. The genotyping procedure was conducted using the Axiom Buffalo Genotyping 90 K array designed by the Affymetrix Expert Design Program. After conducting a quality assessment, we utilized 67,282 SNPs genotyped in 192 animals. We identified several genomic loci explaining high genetic variance by employing single-step genomic evaluation. The aforementioned regions were located on buffalo chromosomes no. 3, 4, 6, 7, 14, 16, 20, 22, and the X-chromosome. The X-chromosome exhibited substantial influence, accounting for 4.18, 4.59, 5.16, 5.19, and 4.31% of the genomic variance for ejaculate volume, mass motility, livability, abnormality, and concentration, respectively. In the examined genomic regions, we identified five novel candidate genes linked to male fertility and spermatogenesis, four in the X-chromosome and one in chromosome no. 16. Additional extensive research with larger sample sizes and datasets is imperative to validate these findings and evaluate their applicability for genomic selection.

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.

Tourism