Validation of whole genome linkage-linkage disequilibrium and association results, and identification of markers to predict genetic merit for twinning.

A previous genome-wide search with a moderate density 10K marker set identified many marker associations with twinning rate, either through single-marker analysis or combined linkage-linkage disequilibrium (LLD; haplotype) analysis. The objective of the current study was to validate putative marker associations using an independent set of phenotypic data. Holstein bulls (n = 921) from 100 paternal half-sib families were genotyped. 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 this data provided the validation of results from analysis of Data I. Single nucleotide polymorphisms (SNPs) were selected to validate previously significant single-marker associations and LLD results. Bulls were genotyped for a total of 306 markers. Nine of 13 LLD regions located on chromosomes 1, 2, 3, 6, 9, 22, 23(2) and 26 were validated, showing significant results for both Data I and II. Association analysis revealed 55 of 174 markers validated, equating to a single-marker validation rate of 31%. Stepwise backward elimination and cross-validation analyses identified 18 SNPs for use in a final reduced marker panel explaining 34% of the genetic variation, and to allow prediction of genetic merit for twinning rate.