Refined positioning of a quantitative trait locus affecting somatic cell score on chromosome 18 in the German Holstein using linkage disequilibrium

Abstract

Combined linkage and linkage disequilibrium analy-sis (LALD) was conducted to more accurately map a previously reported quantitative trait locus (QTL) af-fecting somatic cell score on bovine chromosome 18. A granddaughter design consisting of 6 German Holstein grandsire families with 1,054 progeny-tested genotyped sons was used in this study. Twenty microsatellite mark-ers, 5 single nucleotide polymorphisms, and an erythro-cyte antigen marker with an average marker spacing of 1.95 cM were analyzed along a chromosomal segment of 50.80 cM. Variance components were estimated and restricted maximum likelihood test statistics were cal-culated at the midpoint of each marker interval. The test statistics calculated in single-QTL linkage analysis exceeded the genome-wide significance threshold at several putative QTL positions. Using LALD, we were successful in assigning a genome-wide significant QTL to a confidence interval of 10.8 cM between the mark-ers ILSTS002 and BMS833. The QTL in this marker interval was estimated to be responsible for between 5.89 and 13.86% of the genetic variation in somatic cell score. In contrast to the single-QTL linkage analysis model, LALD analyses with a 2-QTL model confirmed the position of one QTL, but gave no conclusive evi-dence for the existence or position of a second QTL. Ultimately, the QTL position was narrowed down con-siderably compared with previous results with a refined confidence interval of less than 11 cM. © american Dairy Science association, 2009.