QTL analysis associated to single nucleotide polymorphisms (SNP) involved in the dairy phenotype of Holstein cattle

Abstract

The aim was to identify QTLs associated with single nucleotide polymorphisms (SNPs) whose action contributes to the productive, reproductive and health phenotypic development of Holstein dairy cattle. 341 QTLs located in 120 genes of the Bos taurus UMD_3.1.1 genome and associated with 189 SNPs with effects on productive (FY, NM, MY, MTCAS, MBLF and PL), reproductive (CONCRATE, DPR, EMBSUR, DAYOPEN and CONCEPT) and health traits (SCC, BTBS and RESRATE) were identified. SNPs were verified in the dbSNP-NCBI database, according to which 42 % were located in introns. The Jvenn platform revealed that the SNPs rs135744058, rs110828053 and rs109503725 were common in all three traits. The network of correlations between traits and genes generated by MetScape (Cytoscape 3.4), showed a positive correlation between PL, DPR, DAYOPEN, CONCRATE and CONCEPT, and a negative correlation of FY with PL, NM, DPR and CONCRATE. The functionality of each gene was validated in the Gene-NCBI and UniProt databases, and ClueGo (Cytoscape 3.4) was used to select functional pathways with a significance value less than 0.05, which rendered an intertwining between the development of the mammary gland, the activation of the immune system and the response to steroid hormones evident, the GH gene being the one that directs this functionality. Although the genetic panorama shows that there is an antagonism between productive and reproductive traits, the functional genetic activity due to the 189 SNPs analyzed exhibits an interwoven action in ontological pathways that influence the production processes, as well as in reproductive and health pathways.