Water buffalo are economically important animals in many regions of the world, especially in developing countries. The International Water Buffalo Consortium will sequence an Italian inbred female (33-fold coverage) to build the genome assembly and additional individuals to screen for SNPs. Based on these data, we launched an effort to produce copy number variation (CNV) and segmental duplication (SD) maps in water buffalo. After PCR and array CGH validation, we expect to deliver a high-quality collection of water buffalo CNVs and SDs. We plan to compare this collection to the CNV results from Bos Taurus, Bos indicus and other ruminants. Whole-genome sequencing and comparative analyses of domestic water buffalo and other related species would allow an evolutionary analysis of genome structure to define those features that are associated with domestication, selection for production traits and with speciation events.