Hamdy Abdel-Shafy

Reproductive efficiency is a crucial factor in the sustainability and profitability of buffalo production systems. However, genetic improvement of reproductive traits is challenging due to low heritability, environmental sensitivity, limited recording, and shrinking reference populations caused by crossbreeding. This study aimed to estimate genetic parameters and detect the genomic architecture of key reproductive traits in Egyptian buffalo using pedigree‐based analyses and genome‐wide association studies (GWAS). Over a 44‐year period (1980–2024), reproductive records from five Egyptian experimental herds were analysed. The dataset comprised 2843 buffalo cows, sired by 140 bulls and out of 1328 dams. In total, 2359 records were available for age at first calving (AFC), 10,478 for gestation length (GL), 7966 for calving interval (CI), 6705 for days open (DO), and 12,909 for calving ease (CE) and stillbirth (SB). For genome‐wide association analysis, 275 Egyptian buffaloes were genotyped using the Affymetrix Buffalo 90 K array, and 66,295 high‐quality SNPs were retained after quality control. De‐regressed proofs derived from pedigree‐based genetic evaluations were used as response variables in a mixed linear model implemented in the rMVP package. Genome‐wide association analysis identified putative genomic regions associated with GL, CI, CE, and SB, whereas no genome‐wide significant associations were detected for AFC and DO. Functional annotation and QTL enrichment analyses were subsequently used to provide exploratory biological context for the identified genomic regions. Heritability estimates were generally low: 0.16 for AFC, 0.06 for GL, 0.02 for CI, 0.02 for DO, 0.18 for CE, and 0.06 for SB. Manhattan plots revealed that 15 genomic regions containing significant SNPs were identified on chromosomes 2, 4, 10, 12, 13, 15, 19, 20, and 25 for the reproductive traits of GL, CI, CE, and SB. These findings provide preliminary evidence of genomic regions potentially contributing to variation in reproductive traits in Egyptian buffalo, although the relatively small number of genotyped animals limits the power to detect and validate small effect loci. Seven significant genomic regions on chromosomes 10, 13, 15, 20, and 25 were associated with the GL trait. Additionally, three suggestive SNPs mapped to chromosomes 2 and 19 were associated with the CE trait, and three suggestive SNPs mapped on chromosome 12 were significantly associated with the SB trait. The results of KEGG enrichment analyses and QTL classification analyses for reproductive traits in Egyptian buffalo suggest that candidate genes within known QTL may be involved in complex biological networks involving immune competence, cellular homeostasis, and systemic physiological resilience. Among the enriched pathways, Fc gamma R‐mediated phagocytosis, protein export, viral myocarditis, and arrhythmogenic right ventricular cardiomyopathy (ARVC) were highlighted. Most annotated genomic regions (QTL) were related to reproductive traits (63.4%), followed by 17.3% for milk production traits, 9.95% for general production traits, 3.47% for meat and carcass traits, 3.71% for body conformation and robustness exterior traits, and 2.08% for health traits.

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.

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 variant (CNVs) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 copy number variant regions (CNVRs), with 1,993 shared CNVRs being found within the studied buffalo types. Analyzing CNVRs 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 CNVRs that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci (eQTL) analysis revealed differential expression of CNVR-driven genes (DECGs) associated with milk production traits. Notably, known milk production-related genes were among these DECGs, validating their relevance. Last, a genome-wide association study (GWAS) identified 3 CNVRs 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.

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.

The present study aimed to contribute to the limited research on buffalo (Bubalus bubalis) 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.

Background: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) is a candidate gene for milk fat in livestock. The present study was carried out to investigate polymorphism in PPARGC1A and study its potential association. Methods: Two hundred forty animals from Murrah and Bhadawari Indian buffalo breeds and Egyptian buffaloes were selected. The statistical analysis used was Tukey’s honest significance test to investigate the association of different genotypes. The PCR-SSCP (polymerase chain reaction-single strand conformation polymorphism) assays and sequencing technologies were used to confirm the SNPs. Results: Three Novel single nucleotide polymorphisms (SNP1- g.993A greater than T, SNP2- g.1237T greater than A and SNP3-g.1238G greater than C) and one insertion (g.1240_ greater than G bp) were identified in this gene. Due to nucleotide mutations, four non-synonymous mutations were observed in amino acid sequences of buffalo breeds. Significant differences in protein and SNF output were discovered in Egyptian buffalo breeds. In both Murrah and Bhadawari buffaloes, fat, protein and SNF yield were substantially correlated with detected genotypes while there was non-significant association of protein and SNF percent in buffalo breeds. The information provided will be valuable in studying the involvement of PPARGC1A in regulating fat synthesis and enhancing milk quality in buffaloes.

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.

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.

Editorial: Buffalo Genetics and Genomics