Open Access Highly Accessed Research article

Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows

John B Cole1, George R Wiggans1, Li Ma2, Tad S Sonstegard3, Thomas J Lawlor4, Brian A Crooker2, Curtis P Van Tassell13, Jing Yang2, Shengwen Wang2, Lakshmi K Matukumalli3 and Yang Da2*

Author Affiliations

1 Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland, USA

2 Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA

3 Bovine Functional Genomics Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland, USA

4 Holstein Association USA, Brattleboro, Vermont, USA

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BMC Genomics 2011, 12:408  doi:10.1186/1471-2164-12-408

Published: 11 August 2011

Additional files

Additional file 1:

Figure S1. Global view of P-values of 45,878 SNP effects per trait for 31 production, health, reproduction and body conformation traits by Mahattan plot. MY, milk yield; FY, fat yield; PY, protein yield; FPC, fat percentage; PPC, protein percentage; SCS, somatic cell score; DPR, daughter pregnancy rate; PL, productive life; SCE, sire calving ease; DCE, daughter calving ease; SSB, sire stillbirth; DSB, daughter stillbirth; NM, net merit; STA, stature; STR, strength; BD, body depth; RW, rump width; DF, dairy form; RA, rump angle; FUA, fore udder attachment; RUH, rear udder height; UD, udder depth; UC, udder cleft; FTP, front teat placement; RTP, rear teat placement; TL, teat length; FA, foot angle; RLS, rear legs (side view); RLR, rear legs (rear view); FL, feet and legs; FS, final score.

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Additional file 2:

Table S1. Output file of all 1,586 SNP markers with 1,300 effects on 31 dairy traits by chromosome (Chr). Chr30 is the X chromosome, and Chr32 indicates markers with unknown chromosome locations. MY, milk yield; FY, fat yield; PY, protein yield; FPC, fat percentage; PPC, protein percentage; SCS, somatic cell score; DPR, daughter pregnancy rate; PL, productive life; SCE, sire calving ease; DCE, daughter calving ease; SSB, sire stillbirth; DSB, daughter stillbirth; NM, net merit; STA, stature; STR, strength; BD, body depth; RW, rump width; DF, dairy form; RA, rump angle; FUA, fore udder attachment; RUH, rear udder height; UD, udder depth; UC, udder cleft; FTP, front teat placement; RTP, rear teat placement; TL, teat length; FA, foot angle; RLS, rear legs (side view); RLR, rear legs (rear view); FL, feet and legs; FS, final score. Columns B and C show UMD 3.0 chromosome and positions, columns D and E show Btau_4.0 chromosome and position, respectively; column G is A1F, A1 allele frequency; column H is MAF, minor allele frequency; columns J to AN are P values (top 100 effects in red); columns AO to CY are t values (those corresponding to top 100 effects for P values in blue); column CZ is N, number of traits for which SNP was among top 100.

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Additional file 3:

Figure S2. Map of SNP position (Mb) by P-value and Bos taurus chromosome for 725 SNPs that comprise the top 100 effects for each of 13 production, health, and reproduction traits of contemporary U.S. Holsteins.

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Additional file 4:

Figure S3. Map of SNP position (Mb) by P-value and Bos taurus chromosome for 1,005 SNPs that comprise the top 100 effects for each of 18 conformation traits of contemporary U.S. Holsteins.

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Additional file 5:

Table S2. Top 20 most significant SNP effects for each of the thirty one traits.

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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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Additional file 7:

Figure S5. Examples of gene regions associated with significant effects of SNPs for daughter stillbirth and milk yield. A) The 211.67 kb MOCS1-LRFN2 region of Bos taurus (BTA) chromosome 23 with nine highly significant effects (red arrows) for predicted transmitting ability (PTA) for daughter stillbirth. B) The most significant SNP effect (red arrow) for daughter stillbirth was 23.9 kb upstream from the second CD82 gene on BTA15. C) The BTA13 region with the most significant SNP effect (19.7 kb downstream from GNAS2 or GNAS) for PTA for milk yield.

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Additional file 8:

Figure S6. Examples of gene regions associated with significant SNP effects for body conformation traits; a boxed gene contained at least one top-100 effect, and numbers above red arrows (significant SNP effects) indicate rank of SNP effect. A) The 1 Mb region of Bos taurus (BTA) chromosome X with the most significant SNP effect (LOC515732 is PHKA2) for predicted transmitting ability (PTA) for stature. B) The 10.2 Mb region of BTA 11 with eight of the top 20 SNP effects for stature. C) The 1 Mb region of BTA16 with the most significant SNP effect (REN) for PTA for strength. D) The 1.75 Mb region of BTA19 with five genes with highly significant SNP effects for rump width and udder cleft. E) A BTA21 gene cluster with three genes associated with teat length.

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Additional file 9:

Table S3. Output file of 725 SNP markers with top 100 effects per trait from least squares analysis and weighted least squares analysis. MY, milk yield; FY, fat yield; PY, protein yield; FPC, fat percentage; PPC, protein percentage; SCS, somatic cell score; DPR, daughter pregnancy rate; PL, productive life; SCE, sire calving ease; DCE, daughter calving ease; SSB, sire stillbirth; DSB, daughter stillbirth; NM, net merit. Subscript 'w' indicates P-values from weighted least squares analysis. Trait name with subscript 'w' indicates tests using weighted least squares, and trait name without subscript indicates tests using least squares.

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