Water buffalo (Bubalus bubalis) is an important source of meat and milk in countries with relatively warm weather. Compared to the cattle genome, a little has been done to reveal its genome structure and genomic traits. This is due to the complications stemming from the large genome size, the complexity of the genome, and the high repetitive content. In this paper, we introduce a high-quality draft assembly of the Egyptian water buffalo genome. The Egyptian breed is used as a dual purpose animal (milk/meat). It is distinguished by its adaptability to the local environment, quality of feed changes, as well as its high resistance to diseases. The genome assembly of the Egyptian water buffalo has been achieved using a reference-based assembly workflow. Our workflow significantly reduced the computational complexity of the assembly process, and improved the assembly quality by integrating different public resources. We also compared our assembly to the currently available draft assemblies of water buffalo breeds. A total of 21,128 genes were identified in the produced assembly. A list of milk virgin-related genes; milk pregnancy-related genes; milk lactationrelated genes; milk involution-related genes; and milk mastitis-related genes were identified in the assembly. Our results will significantly contribute to a better understanding of the genetics of the Egyptian water buffalo which will eventually support the ongoing breeding efforts and facilitate the future discovery of genes responsible for complex processes of dairy, meat production and disease resistance among other significant traits.

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The future bio-economy of dairy industry relies on the identification of an affordable approach for increasing milk production and its constituents. Egyptian buffalo (Bubalus bubalis) contributes by about 50% of total milk production in Egypt, therefore it is considered as an essential dairy animal. This study aimed to differentiate between high and low milk producer buffaloes (Bubalus bubalis) using microsatellite and SCoT markers. The results of the six microsatellite primers showed bands of 350, 377, 496, 247, 262 and 280 bp, where three of which were digested by restriction enzyme. SCoT results of bulked samples showed unique bands that were sequenced and aligned to Bubalus bubalis (taxid: 89462) sequences. Alignment results showed similarity to the following encoding genes, Class V myosin, Ubiquitin-conjugating enzyme E2 D4 and acyl-phosphatase 2 (ACYP2), which play a crucial role in organelle trafficking and many pathways, that may affect milk production traits. These results showed that SCoT marker was better than microsatellite in clarifying the difference between high and low milk producing traits in Egyptian buffalo (Bubalus bubalis).

Four buffalo calves were available for this study, aged six months and weighed (BW) 118.0 -119.0 kg at