Association between polymorphisms of APOB, SLC27A6, AGPAT6 and PRLR genes and milk production and quality traits in goats

•Polymorphisms in the APOB and SLC27A6 genes were identified.•Polymorphisms in the goat APOB, SLC27A6 and AGPAT6 genes are associated with milk production and composition traits.•New data about genetic diversity in goats. With this study, we aimed to evaluate the association of new and known polymorphisms in the APOB, SLC27A6, AGPAT6, and PRLR genes with goat’s estimated breeding values (EBVs) for milk production and composition traits: lactation length, somatic cell score, total milk yield (kg), and for production (kg) and content of fat, protein, lactose, and solids non-fat. For that, we estimated animal`s EBVs from milk yield and composition data of multiparous Saanen and Alpine goats using a single-trait model. The number of animals used for EBVs estimations varied from 1070 to 1700, depending on the studied trait. For the association analysis, among the animals with EBVs, we genotyped 106 for the APOB/HaeIII polymorphism, 104 for the APOB/SmaI polymorphism, 118 for the Slc27A6/TspRI polymorphism, 245 for the AGPAT6/NcoI polymorphism, 253 for the PLPR/SmaI, and 252 for the PLPR/SfcI polymorphism. We observed that the APOB/HaeIII polymorphism is associated with lactose content, lactation length, and somatic cell score. The APOB/SmaI polymorphism is associated with lactation length, lactose percentage, and total yield of solids non-fat, lactose, protein, fat, and milk. The SLC27A6/TspRI polymorphism is associated with milk lactose content, and the AGPAT6/NcoI polymorphism is associated with lactose yield and milk content of fat, protein, and lactose. In this study, we present new data about the genetic diversity of Brazilian Saanen and Alpine goats and new potential molecular markers for goat milk production and quality traits.