A new version of buffalo SNP array to support Mediterranean breed genomic improvement

Domestic water buffalo is an important worldwide species, despite the smaller population in comparison with bovine. Two types of buffalo are recognized: swamp and river. The former are populations supporting people in many developing countries for draft purposes. The latter are breeds mainly selected for milk production. In Italy, Mediterranean (MED) river breed is bred, from which the famous “Mozzarella di Bufala Campana” is obtained. Recently, the breeding association ANASB published the first genomic breeding index for MED. However, the use of the current buffalo array (ABA1) has limitations (eg, number of usable markers and their density), because its aim was for biodiversity characterization and not genomic selection in MED. In the framework of the GENOBU project, thus, a specific MED version of the Axiom Buffalo array was developed. The markers included in the ABA1 were validated using previously genotyped MED animals; compatibility with the ABA1 and IMAGE array was considered, and SNPs associated with milk characteristics were prioritized. Finally, 72,223 SNPs were retained. New markers were identified using short and long reads (ONT) sequences from MED animals (unpublished data kindly provided by F. Salvatore and G. Paolella, CEINGE, Napoli, Italy, within the GENOBU project), to optimize the array density and fill the almost 123k spots available. The data were aligned to the most recent MED reference sequence to identify new variants, using state-of-the-art bioinformatic pipelines. Markers from Y chromosome, together with SNPs from candidate genes affecting functional traits (eg, casein cluster), were also included. The final number of markers included in the new version is 122,646, reaching 21.8±7.7 kbp average marker distance.