598 Prasad et al. addition to their abundance in the genome (Snelling et al. 2005), SNP markers have low genotyping costs (Hinds et al. 2005). Khatkar et al. (2006b) reported a ﬁrst-generation LD map of bovine chromosome 6 in Australian Holstein–Frie- sian cattle using SNP loci and estimated the extent of LD using D¢. The distance over which LD is likely to be useful for association mapping was found to be 13.3 Mb con- ﬁrming that the range of LD is extensive in Holstein–Frie- sian dairy cattle. McKay et al. (2007) generated LD maps for eight breeds of cattle from the Bos taurus and Bos indicus subspecies using 2670 SNP markers and observed that the extent of LD (estimated using r2) available for association analysis does not exceed 500 kb. The differences in the extent of LD between the study by McKay et al. (2007) and previous studies were attributed to the differences in mea- sures used to report LD, which is speciﬁcally D¢ vs. r2. D¢ has been reported to overestimate the extent of LD (Ardlie et al. 2002; Ke et al. 2004) thus resulting in extensive LD at long intermarker distances in previous studies (Farnir et al. 2000; Tenesa et al. 2003; Vallejo et al. 2003; Khatkar et al. 2006a; Odani et al. 2006). Here, we report a study of the extent of LD on chromo- somes 19 and 29 and of the pattern of selection signatures on these chromosomes in Bos taurus beef and dairy breeds (Angus and Holstein) using dense SNP markers. We have chosen BTA19 and BTA29 as candidate chromosomes for mapping because QTL for several economically important traits has been identiﬁed on these chromosomes (Stone et al. 1999; Mosig et al. 2001; MacNeil & Grosz 2002; Casas et al. 2003; Li et al. 2004; Ashwell et al. 2005; Nkrumah et al. 2007). The information generated from this study, with a relatively large number of animals per breed compared to other studies, has important implications for the design and application of association studies in cattle populations as well as for selective breeding programmes. Materials and methods Collection of DNA samples DNA was collected from Angus (n = 126, USA) and Hol- stein (n = 321, Semex Alliance) cattle. To maximize the genetic diversity within each sampled population, families were selected to span the diversity of each breed. Three- generation families were sampled so that chromosomes could be phased using linkage information. The general family structure consisted of a grandparent, parent and three or more progeny. Marker selection and genotyping A total of 1001 and 535 evenly spaced SNP markers for BTA19 and 29 respectively were chosen from bovine sequence BUILD 2.0 (ftp://ftp.hgsc.bcm.tmc.edu/pub/data/ Btaurus/snp). The markers were genotyped within each population of beef and dairy animals using the Illumina BeadStation 500G genotyping system (Oliphant et al. 2002). However, only 555 and 253 SNP markers from BTA19 and 29 respectively were used for the LD analysis. These loci had successfully been mapped on the high-res- olution 12 000 rad radiation hybrid panel and were considered to be correctly ordered on both BTA19 and 29 (Prasad et al. 2007). Some loci did not amplify in the genotyped animals and those loci that were monomorphic or that had a minor allele frequency (MAF) < 0.03 were removed from the study. After these ﬁltering procedures, the LD analysis was performed using 370 and 367 markers on BTA19 and 186 and 179 markers on BTA29 for the Angus and Holstein populations respectively. The sequence and the NCBI IDs of the SNPs used in the LD analysis are described in the work of Prasad et al. (2007). To test whether Holstein differ signiﬁcantly from Angus in the distribution of MAF, the PROC FREQ procedure in SAS (V. 9.1, SAS, Inc.) was run using a two-way contingency table of loci against breeds. Marker positions Genomic sequence coordinates for SNPs were obtained by performing BLAST (Altschul et al. 1990) comparisons between SNP-ﬂanking sequences and the 7.1· bovine genome assembly (Btau 3.1). The marker order and their corresponding genomic coordinates were corrected if they disagreed with the RH map order of Prasad et al. (2007). For each chromosome, a bp/cR conversion ratio was esti- mated by dividing the highest base-pair position by its corresponding cR position. The resultant ratios were 13 816.49 and 15 413.2 for BTA19 and 29 respectively. The relative positions of markers (in bp) were estimated by multiplying the conversion ratio with the RH position. Markers that could not be separated by their RH positions were ordered according to their order in the bovine genome sequence assembly; RH mapping has difﬁculty ordering closely linked markers, although the sequence assembly is accurate at a ﬁne scale. The list of SNPs used in the LD analyses and their inferred chromosomal positions in base pairs are in Table S1. Estimation of phased haplotypes We used GENOPROB V2.0 (Thallman et al. 2001a,b) for data- quality checking and estimated phased haplotypes based on the pedigree and estimated recombination rates, which were set proportional to the physical distances among the loci. Both the pedigree and the marker locations (map) were used to estimate the segregation of alleles throughout the entire pedigree. By tracing closely linked markers through a multigenerational pedigree, the linkage phase of the alleles was inferred. A set of ﬁve loci on BTA29 were chosen to illustrate this point, as shown in Table S2. Four progeny of 2008 The Authors, Journal compilation 2008 International Society for Animal Genetics, Animal Genetics, 39, 597–605