A Primer-Extension Assay for simultaneous use in cattle Genotype Assisted Selection, parentage and traceability analysis

The use of genotype information as an aid to selection can be a cheap and effective way to improve the genetic progress in beef cattle breeds, specially in the case of high cost phenotypic recording which is true for many economic traits in beef cattle. SNPs located at candidate genes underlying economic traits allow prediction of the genetic merit of individuals and, combined with parentage and traceability analysis, guarantee consumer protection. Here we present a cost-effective technology, the Capillary Primer-Extension Assay, to genotype validated mutations which identify differences between individuals in candidate genes associated directly or potentially with meat tenderness, marbling and muscle growth, milk yield, protein and fat content, sex or coat colour. We genotyped 70 SNPs in 8 beef, 3 dairy and one semi-feral (never selected for any production trait) breeds and present a panel of 53 SNPs with the aim of enabling a reasonable tool for parentage analysis, animal identification and production of markers usable in GAS in small local breeds for which other tools are unaffordable.