Awad et al. Genetics Selection Evolution 2011, 43:8 http://www.gsejournal.org/content/43/1/8 support intervals are 4.7 cM for FY1, 10.4 cM for PY1 and 11.5 cM for MY1. Since the confidence interval achieved by LDL ana- lyses using pedigree MSPED1038 was still too large for a positional candidate gene approach, we analysed pedi- gree SNPPED723 using the LDL approach. The results were similar to those obtained with microsatellite mar- kers and pedigree MSPED2089, namely, multiple peaks suggesting multiple QTL or no QTL (Figure 4). To resolve this dilemma, we divided pedigree SNPP ED723 into pedigree SNPPED421 consisting of all pro- geny-tested animals descending from ancestor A0, and pedigree SNPPED308 consisting of the remaining pro- geny-tested animals. The LDL analyses of SNPPED308 pedigree showed a moderately flat, non-significant test statistic along the investigated chromosomal segment (Figure 5). Only LRT values for FY1 reached an indica- tive level of 3.99 (P = 0.046). Conversely, it was possible to map a QTL with pedigree SNPPED421 whose minor allele is most probably originating from ancestor A0 (Figure 6). There were two distinct peaks; one with LRT values over 17 (P < 0.000037) for both MY1 and PY1 in a region of 0.5 Mb (from 118.107 to 118.606 Mb), and one with a very high LRT value for only PY1 (LRT = 20.72, P = 0.0000053) at position 122.115 Mb. Consider- ing 1-LOD drop-off support intervals, the 97% confi- dence intervals were located between 117.962 Mb and 119.018 Mb (i.e. 1.056 Mb) for the QTL affecting MY1 24 22 20 18 16 14 TR12 L10 8 6 4 2 0 MY1 PY1 FY1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 3 4 5 6 7 8 1 1 1 1 1 1 1 1 2 2 2 2 2 2 9 0 1 2 3 4 5 Position (Mb) Figure 4 LDL analysis by variance component approach using SNP in a complex pedigree of 723 animals. Joint linkage disequilibrium and linkage (LDL) analysis for three milk yield traits; Milk Yield (MY1), Milk Protein Yield (PY1) and Milk Fat Yield (FY1) during first lactation using 240 SNPs covered the most likely region containing the QTL in the distal part of bovine chromosome 5 (BTA5), a complex pedigree of 723 animals, EBV as phenotype and AIREML as implemented in LDLRAMS and LDL program. Chromosome length in Megabase (Mb) on the X-axis, log-likelihood ratio test (LRT) values on the Y-axis. Page 8 of 11 1 1 1 1 1 1 2 3 4 1 1 1 1 1 1 1 1 5 6 7 8 1 1 1 1 1 2 2 2 9 0 1 2 1 1 1 2 2 2 3 4 5 Position (Mb) Figure 5 LDL analysis by variance component approach using SNP in a complex pedigree of 308 animals. Joint linkage disequilibrium and linkage (LDL) analysis for three milk yield traits; Milk Yield (MY1), Milk Protein Yield (PY1) and Milk Fat Yield (FY1) during first lactation using 240 SNPs covered the most likely region containing the QTL in the distal part of bovine chromosome 5 (BTA5), a complex pedigree of 308 animals, EBV as phenotype and AIREML as implemented in LDLRAMS and LDL program. Chromosome length in Megabase (Mb) on the X-axis, log-likelihood ratio test (LRT) values on the Y-axis. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 3 4 5 6 7 8 1 1 1 1 1 1 1 1 2 2 2 2 2 2 9 0 1 2 3 4 5 Position (Mb) Figure 6 LDL analysis by variance component approach using SNP in a complex pedigree of 421 animals. Joint linkage disequilibrium and linkage (LDL) analysis for three milk yield traits; Milk Yield (MY1), Milk Protein Yield (PY1) and Milk Fat Yield (FY1) during first lactation using 240 SNPs covering the most likely region containing the QTL in the distal part of bovine chromosome 5 (BTA5), a complex pedigree of 421 animals, EBV as phenotype and AIREML as implemented in LDLRAMS and LDL program. Chromosome length in Megabase (Mb) on the X-axis, log-likelihood ratio test (LRT) values on the Y-axis. The long homozygous region (~5 Mb) in ancestor A0 was shown (A0 Homo). 24 22 20 18 16 14 TR12 L10 8 6 4 2 0 24 22 20 18 16 14 TR12 L10 8 6 4 2 0 MY1 PY1 FY1 MY1 PY1 FY1 A0 Homo