Awad et al. Genetics Selection Evolution 2011, 43:8 http://www.gsejournal.org/content/43/1/8 Table 1 Microsatellite markers used for QTL mapping Nb Marker ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 LMU0502 DIK2336 BM315 DIK4843 DIK1135 DIK5238 ETH2 DIK2122 BM2830 BM49 BM733 DIK2035 DIK5277 DIK5106 LMU0505 ETH152 URB060 DIK5212 DIK5247 MNB71 NOR44 cM 95.00 99.79 103.17 107.02 108.22 110.97 112.43 114.68 116.91 118.06 119.95 120.85 121.53 121.47 123.64 124.95 127.55 129.17 129.80 133.09 133.98 bp 98418609-98419268 101071987-101072659 104045839-104046013 107077504-107078179 10181410-10182069 111864734-111865363 112903902-112909263 113216193-113216706 115262054-115262075 116205343-116205972 117125799-117126005 119370626-119371127 120099447-120100247 118461214-118461602 121423920-121424520 Unknown 122472602-122473177 123262266-123262905 123619504-123619855 Unknown 125340968-125341598 Forward primer Reverse primer TGGAAGAATATGCAGGTAACTCT GTCGCTCTTTGTGGCTTCAC ATGTGGAATGTAGGGCAAGG TCCCTCACCTTTCGAACAAA TGGTTTAGCAGAGAGCACATG GCTCCTAGCCCTGCACAC CATGCAAGCTTTCAAGAATGA TGCAGAGATAAGCCGAGGAC GTCTGCCATCTAGCCAAAAA GTTTTTCAGTGGGCATTTGG TGGAACCAGTGAAGTTTAGGG GAAATGCCCACTGAAGCTCT ATTTGCCCTGCTAGCTTTGA AAGACTCTGGGCTTCAAAAGG CAACAAACTGTGCGTTGTGA ACTCAGCAGTTGCCCTCAGT AATGGGCGTATAAACACAGATG TGAGTCCTGTCACCATCAGC CACCATATTTGCCAGGATCA GCGGGATCTCACTAAACCAG CTGGAGTCTCCTCCGTTGAG AGAGAGGGCCCTTGTGAGAT CAGTCAATGCAGGAAAAGCA GCTGCTAGAGGGAGACAGGA ACCCAAACTTAGCGTGGATG GTCTCCAAGGCTGCTCACTC GCATGTGTGCAGAAGAAGGA TGTTCAGTGGTTCCCTGTGA TGCAAGGAGAAGCGGTAGAT TGCACACTTACCCCATGTTC GTTCTCAGGCTTCAGCTTCG TGATCAGAGGGCACCTGTCT TTGTCATTTCTGGACTCCACTG TGATCAGAGGGCACCTGTCT GGCTGGAACAGTGACTCTGG GGACCCAGATTTCAATGGAG GGGTCTGTAGGGAGAAGCTG GCTTTCGAGAAGCATCCACT CATCTAAGGCAGAGCCAACC TTCTTGGTGCCTCTCTCTCC ACCCACCCGTACACATTCAA GGGGAGGAGATGGACTGTTC Page 4 of 11 Remark Set1 Set1 Set0 Set4 Set1 Set3 Set1 Set3 Set0 Set3 Set4 Set3 Set3 Set3 Set3 Set1 Set1 Set3 Set3 Set1 Set3 Marker name, relative position (cM), physical position (bp), forward and reverse primer sequences and marker set (set: Set0 & Set1 as in previous study; Set3 and Set4 comprise multiplex 1&2 in this study). the 12 markers, relevant information was obtained from the MARC-ARS-USDA public database at http://www. ars.usda.gov/Main/docs.htm?docid=12539 [27]. The new marker LMU0505 was obtained by a targeted search for dinucleotide repeats in genomic regions with a low mar- ker density. The unique sequences flanking the newly identified dinucleotide repeats were tested for informa- tivity by genotyping a small set of animals first. Primers for the 12 new microsatellite markers were optimized using Primer3 (v.0.4.0) according to the bovine genome sequence data currently available (i.e. Baylor release Btau_4.0, http://genome.ucsc.edu/cgi-bin/hgGateway) and the appropriate fragment size in the currently designed marker set. New markers were divided into two PCR multiplex sets (Table 1) that were combined again after PCR for electrophoresis and fragment analy- sis. The fragment analysis of the PCR products was per- formed on ABI377 and ABI Prism 310 sequencers.