Additional file 6.

Figure S4. Gene clusters that overlapped localized concentrations of SNP effects or contained significant SNP effects on Bos taurus (BTA) chromosomes. A) BTA7 15.4 Mb gene cluster (Btau_4.0:4807980-20004663) of ~1,166 genes (not counting pseudo and RNA genes) with a mean of 75 genes/Mb. Left end was LSM4-JUND region; right end was LSM7-SPPL2B-OAZ1 region. This cluster included ARS-BFGL-NGS-4774 [1.5 kb downstream from INSR (Q95M43; highlighted in green)], which was significant for somatic cell score (1st) and daughter pregnancy rate (1st), productive life (3rd), and net merit (78th)] as well as all 10 significant SNP effects on this chromosome for productive life, 15 of the 16 significant SNP effects for daughter pregnancy rate, and 6 of the 12 significant SNP effects for somatic cell score. B) BTA14 2.81 Mb gene cluster (Btau_4.0:50872-2,859,132) of ~125 genes with a mean of 44 genes/Mb; NIBP (highlighted in green) was the largest gene (387.23 kb) in the cluster. This cluster included 19 significant SNP effects for fat percentage [SNP in DGAT1 was 1st and SNP in NIBP was 2nd], one SNP in VPS28 with effect for milk yield, and one SNP in NIBP with effects for fat yield and protein percentage. C) BTA18 15.82 Mb gene cluster (Btau_4.0:48755332-64574451) of ~1,322 genes with a mean of 83 genes/Mb. The PGLYRP1(PGRP)-IGFL1 (highlighted in green) region had the most significant SNP effects in the cluster [fat and protein yields, service-sire and daughter calving ease, and net merit (1st); service-sire stillbirth (8th); milk yield (9th); productive life (16th); and fat and protein percentages (25th)]. D) BTA3 gene cluster with significant SNPs for fat yield [BFGL-NGS-113990 (49th) and INRA-304 (53rd)]. E) BTA5 gene cluster with ARS-BFGLNGS-36745 (associated with SREBF2) and ARS-BFGL-NGS-71946 in LOC535121, which were among top 100 SNP effects for fat and protein percentages and service-sire calving ease and stillbirth, as well as other significant SNPS for service-sire stillbirth [ARS-BFGL-NGS-2337 in TCF20 (39th) and ARS-BFGL-NGS-7380 in SEPT3 (76th). F) BTA7 gene cluster with ARS-BFGL-NGS-76638 in RGS14, which was significant for somatic cell score (77th). G) BTA10 gene cluster with Hapmap41316-BTA-62253, which was significant for milk yield (60th). H) BTA13 gene cluster with significant SNPs for milk yield [ARS-BFGL-BAC-16372 (65th) and Hapmap41228-BTA-32897 (87th)]. I) BTA17 gene cluster with significant SNPs for milk yield [(ARS-BFGL-NGS-17192 (39th) and BTB-01992588 (63rd)] and fat percentage [ARS-BFGL-NGS-34106 (19th) and Hapmap40427-BTA-41914 (78th)]. J) BTA21 gene cluster with significant SNP effects for service-sire calving ease [BFGL-NGS-113671 (87th) and service-sire stillbirth [BFGL-NGS-116152 (46th), Hapmap39755-BTA-52639 (73rd), and BFGL-NGS-113671 (83rd). K) BTA23 gene cluster with ARS-BFGL-NGS-72191 in ZNF192 and BTA-68781-no-rs, which were among top 100 SNP effects for fat yield, protein yield and percentage, service-sire calving ease, and net merit. L) BTA26 gene cluster with BFGL-NGS-111739, the 14th most significant SNP for service-sire stillbirth. M) BTA29 gene cluster with ARS-BFGL-NGS-24998 in LOC787296, 49th most significant SNP for daughter stillbirth. N) BTAX gene cluster with ARS-BFGL-NGS-42972 in TIMP1, 45th most significant SNP for service-sire stillbirth.

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Cole et al. BMC Genomics 2011 12:408   doi:10.1186/1471-2164-12-408