genobu

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	THE PROJECT
	The project aims to improve quality and quantity of bufaline production by using information obtained from complete genome sequencing of domestic buffalo (water buffalo). The genomic sequence is the starting point for subsequent analyses aimed at identifying gene markers confering traits of productive interest or disease resistance, and genotyping of livestock for breeding purposes.



	THE RESULTS
	The activities conducted within OR 1 resulted in the generation of a chromosome-level genome assembly. The newly assembled genome is available with preliminary annotation and has been used as a reference for identifying inter-individual variants through whole-genome resequencing of unrelated individuals. The reference genome assembled served as the foundation for the development of a novel SNP panel, designed to complement and extend existing commercial genotyping platforms. This new tool is intended for applications in breeding selection, parentage verification, and livestock traceability.



	REFERENCE GENOME SEQUENCING
	The genome of a male individual (designated as BUF_03) is available at chromosome-level assembly, obtained with a coverage of 120x. Oxford Nanopore Technologies (ONT) long-reads approach was firstly used, after integrated with Illumina-based sequencing of short reads to resolve small gaps or inconsistencies.



	GENOMIC VARIATIONS
	Inter-individuals nucleotide differencies were investigated by sequencing samples from 25 different adult males belonging to farms in the area of Battipaglia and the province of Caserta, two of the principal area of production in Campania.



	BROWSE THE REFERENCE GENOME
	The new annotated genome is accessible via a genome browser, which enables sequence exploration at multiple levels of resolution, chromosome by chromosome, ranging from broad genomic regions down to individual genes.



	GENOTYPING FOR BREEDER SELECTION
	The project generated a collection of 122,017 genotyping SNPs for use in breeder selection, parentage testing, and traceability studies. The new chip expands the currently available commercial panel by adding over 50,000 newly identified markers, including those located on the Y chromosome.



	X AND Y CHROMOSOMES
	The X chromosome was obtained using an assembly strategy based on the pre-filtering of reads mapping to the autosomes and on the combination of sequences derived from both male and female individuals. The Y chromosome was assembled using as reference the Y chromosome of the domestic yak, the closest related species with the Y chromosome assembly available.



	TOOLS
	The project has benefited from the development of dedicated computational tools aimed at supporting data management, storage, and results analysis. These tools were specifically designed to meet the needs of the project and have been made available to the broader scientific community as web-based applications and/or analysis pipelines, openly accessible via GitHub.