Fine-mapping quantitative trait loci for twinning rate on Bos taurus chromosome 14 in North American Holsteins

A previous genome-wide search with a moderate-density 10,000-SNP set identified many marker associations with twinning rate on BTA14 through either single-marker analysis or combined linkage-linkage disequilibrium (LLD; haplotype) analysis. The objective of the current study was to fine-map putative QTL using a more densely populated marker map and both a larger and an independent set of phenotypic data. Holstein bulls (n = 921) from 100 paternal half-sib families were genotyped for 129 SNP markers that included both original and additionally selected markers for increasing marker density in the targeted 34 megabase region. Twinning rate predicted transmitting abilities were calculated using calving records from 1994 to 1998 (data I) and 1999 to 2006 (data II), and the underlying liability scores from threshold model analysis were used as the trait in marker association analyses. The previous analysis used 201 bulls with daughter records in data I. In the current analysis, this was increased to 434, providing a revised estimate of effect and significance. Bulls with daughter records in data II totaled 851, and analysis of these data provided an opportunity for an independent analysis separate from data I. Single-marker association and LLD analyses were performed. Fifteen significant single-marker associations were found (minimally exceeding P < 8.74 x 10(-3)) to concur between data sets. Three and 12 regions in data I and data II, respectively, showed positive results for the presence of QTL from LLD analysis (P < 0.001) within the respective data sets. After combining results from single-marker association, LLD analysis, and model-building strategies, 3 QTL were identified on BTA14. Based on single-marker results from data II, BTA14 harbors QTL responsible for approximately 24% of the variation in twinning rate predicted transmitting ability.