Project Plan np 101 Food Animal Production April–July 2012 Old ars research Project Number

Dechow, C.D., H.D. Norman, and C.A. Pelensky. 2008a. Short communication: Variance estimates among herds stratified by individual herd heritability. HJ. Dairy Sci. 91:1648–1651H.

Dechow, C.D., H.D. Norman, N.R. Zwald, C.M. Cowan, and O.M. Meland. 2008b. Relationship between individual herd-heritability estimates and sire misidentification rate. HJ. Dairy Sci. 91:1640–1647H.

Dekkers, J.C.M. 2004. Commercial application of marker- and gene-assisted selection in livestock: Strategies and lessons. J. Anim. Sci. 82:E313–E328.

Dekkers, J.C.M. 2007. Prediction of response to marker-assisted and genomic selection using selection index theory. J. Anim. Breed. Genet. 124:331–341.

Dickerson, G.E., and L.N. Hazel. 1944. Effectiveness of selection on progeny performance as a supplement to earlier culling in livestock.H J. Agric. Res. 69:459–476H.

Dikmen, S., J.B. Cole, D.J. Null, and P.J. Hansen. 2012b. Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle. HJ. Dairy Sci. 95:3401–3405.

Druet, T., C. Schrooten and A.P.W. de Roos. 2010. Imputation of genotypes from different single nucleotide polymorphism panels in dairy cattle. HJ. Dairy. Sci. 93:5443–5454H.

Duthie, C., G. Simm, A. Doeschl-Wilson, E. Kalm, P.W. Knap, and R. Roehe. 2010. Epistatic analysis of carcass characteristics in pigs reveals genomic interactions between quantitative trait loci attributable to additive and dominance genetic effects. HJ. Anim. Sci. 88:2219–2234H.

Elsik, C.G., R.L. Tellam, and K.C. Worley. 2009. The genome sequence of taurine cattle: A window to ruminant biology and evolution. Science 324:522–528.

Gay, K.D., N.J. Olynk, T.D. Nennich, A.P. Schinckel, and M.M. Schutz. 2012. Development of a merit-based genetic selection index for dairy grazing systems. J. Dairy Sci. 95(Suppl. 2):234(Abstr. 256).

Georges, M., W. Coppieters, C. Charlier, J.S. Agerholm, and M. Fredholm. 2010. A genetic marker test for brachyspina and fertility in cattle. International HPatent Publ. No. WO2010/012690H.

Gusev, A., J.K. Lowe, M. Stoffel, M.J. Daly, D. Altshuler, J.L. Breslow, J.M. Friedman, and I. Pe’er. 2009. Whole population, genome-wide mapping of hidden relatedness. HGenome Res. 19:318–326H.

Harris, B.L., F.E. Creagh, A.M. Winkelman, and D.L. Johnson. 2011. Experiences with the Illumina high density bovine beadchip. HInterbull Bull. 44:3–7H.

Harris, B.L., and D.L. Johnson. 2010a. Genomic predictions for New Zealand dairy bulls and integration with national genetic evaluation. HJ. Dairy Sci. 93:1243–1252H.

Harris, B.L., and D.L. Johnson. 2010b. The impact of high density SNP chips on genomic evaluation in dairy cattle. HInterbull Bull. 42:40–43H.

Hayes, B.J., P.J. Bowman, A.C. Chamberlain, K. Verbyla, and M.E. Goddard. 2009. Accuracy of genomic breeding values in multi-breed dairy cattle populations. HGenet. Sel. Evol. 41:51H.

Heaton, M.P., W.M. Snelling, T.P.L. Smith, J.W. Keele, G.P. Harhay, R.T. Wiedmann, G.L. Bennett, B.A.Freking, C.P. Van Tassell, T.S. Sonstegard, L.C. Gasbarre, S.S. Moore, B. Murdoch, S.D. McKay, T. Kalbfleisch, and W.W. Laegreid. 2007. A market set for parentage-based DNA traceback in beef and dairy cattle. HProc. Plant & Anim. Genome XV Conf., Abstr. P516H.

Heyen, D.W., J.E. Beever, Y. Da, R.E. Evert, C. Green, S.R.E. Bates, J.S. Ziegle, and H.A. Lewin. 1997. Exclusion probabilities of 22 bovine microsatellite markers in fluorescent multiplexes for semiautomated parentage testing. HAnim. Genet. 28:21–27H.

Hickey, J.M., B.P. Kinghorn, B. Tier, J.F. Wilson, N. Dunstan, and J.H.J. van der Werf. 2011. A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes. HGenet. Sel. Evol. 43:12H.

Hou, Y., G.E. Liu, D.M. Bickhart, M.F. Cardone, K. Wang, E.-S. Kim, L.K. Matukumalli, M. Ventura, J. Song, P.M. Vanraden, T.S. Sonstegard, and C.P. Van Tassell. 2011. Genomic characteristics of cattle copy number variations. HBMC Genomics 12:127H.

Huquet, B., H. Leclerc, and V. Ducrocq. 2012. Characterization of French dairy farm environments from herd-test-day profiles. J. Dairy Sci. 95:4085–4098.

Illumina. 2010. HBovineHD Genotyping BeadChipH. Illumina, San Diego, CA.

Illumina. 2011a. HBovineLD Genotyping BeadChipH. Illumina, San Diego, CA.

Illumina. 2011b. HBovineSNP50 Genotyping BeadChipH. Illumina, San Diego, CA.

Illumina. 2011c. HGoldenGate Bovine3K Genotyping BeadChipH. Illumina, San Diego, CA.

Imumorin, I.G., E.-H. Kim, Y.-M. Lee, D.-J. De Koning, J.A. van Arendonk, M. De Donato, J.F. Taylor, and J.-J. Kim. 2011. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits. Front. Genet. 2:44.

Johnston, J., G. Kistemaker, and P.G. Sullivan. 2011. Comparison of different imputation methods. Interbull Bull. 44:25–33.

Kirkpatrick, B., S.C. Li, R.M. Karp, and E. Halperin. 2011. Pedigree reconstruction using identity by descent. Lecture Notes in Computer Sci. 6577:136–152.

Kizilkaya, K., R.L. Fernando, and D.J. Garrick. 2010. Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes.H J. Anim. Sci. 88:544–551.

Kolmodin, R., E. Strandberg, P. Madsen, J. Jensen, and H. Jorjani. 2002. Genotype by environment interaction in Nordic dairy cattle studied using reaction norms. Acta Agric. Scand. A 52:11–24.

Konig, S., H. Simianer, and A. Willam. 2009. Economic evaluation of genomic breeding programs. J. Dairy Sci. 92:382–391.

Legarra, A., I. Misztal, and I. Aguilar. 2011. The single step: Genomic evaluation for all. HBook of Abstracts of the 62nd Annual Meeting of the European Federation of Animal Science No. 17:1H. Wageningen Academic Publishers, The Netherlands.

Liu, Z., J. Jaitner, F. Reinhardt, E. Pasman, S. Rensing, and R. Reents. 2008. Genetic evaluation of fertility traits of dairy cattle using a multiple-trait animal model. HJ. Dairy Sci. 91:4333–4343H.

Long, C.R., and K.E. Gregory. 1978. Inheritance of the horned, scurred, and polled condition in cattle. J. Hered. 69:395–400.

Ma, L., T.S. Sonstegard, J.B. Cole, G.R. Wiggans, B.A. Crooker, C.P. Van Tassell, J. Yang, L. K. Matukumalli, and Y. Da. 2010. X chromosome SNPs were heavily involved in epistasis effects of net merit component traits in contemporary U.S. Holstein cows. HProc. Plant & Anim. Genome XVIII Conf., Abstr. P542H.

Macciotta, N.P.P., and J.B. Cole. 2011. Multivariate factor analysis of genomic correlation matrices in three US dairy cattle breeds. HJ. Dairy Sci. 94(E-Suppl. 1):i–-ii(Abstr. LB3)H.

Macciotta, N.P.P., G. Gaspa, R. Steri, E.L. Nicolazzi, C. Dimauro, C. Pieramati, and A. Cappio-Borlino. 2010. Using eigen values as variance priors in the prediction of genomic breeding values by principal component analysis. HJ. Dairy Sci. 93:2765–2774H.

Magee, D.A., D.P. Berry, E.W. Berkowicz, K.M. Sikora, D.J. Howard, M.P. Mullen, R.D. Evans, C. Spillane, and D.E. MacHugh. 2010. Single nucleotide polymorphisms within the bovine DLK1-DIO3 imprinted domain are associated with economically important production traits in cattle. HJ. Hered. 102:94–101H.

Makgahlela, M.L., E.A. Mäntysaari, I. Strandén, M. Koivula, M.J. Sillanpää, U.S. Nielsen, and J. Juga. 2011. Across breed multi-trait random regression genomic predictions in the Nordic Red dairy cattle. HInterbull Bull. 44:42–46H.

Maki-Tanila, A. 2010. Candidate genes turning sour. J. Anim. Breed. Genet. 127:253–254.

Mäntysaari, E.A., and I. Strandén I. 2010. Use of bivariate EBV-DGV model to combine genomic and conventional breeding value evaluations. HProc. 9th World Congr. Genet. Appl. Livest. Prod., Comm. 0353H.

Meuwissen, T., and M. Goddard. 2010. Accurate prediction of genetic values for complex traits by whole-genome resequencing. HGenetics 185:623–631H.

Miglior, F., B.L. Muir, and B.J. Van Doormaal. 2005. Selection indices in Holstein cattle of various countries. HJ. Dairy Sci. 88:1255–1263H.

Miller, R.H., H.D. Norman, M.T. Kuhn, J.S. Clay, and J.L. Hutchison. 2007. Voluntary waiting period and adoption of synchronized breeding in Dairy Herd Improvement herds. HJ. Dairy Sci. 90:1594–1606H.

Norman, H.D., J.L. Hutchison, and R.H. Miller. 2010. Use of sexed semen and its effect on conception rate, calf sex, dystocia, and stillbirth of Holsteins in the United States. HJ. Dairy Sci. 93:3880–3890H.

Norman, H.D., J.L. Hutchison, and P.M. VanRaden. 2011. Evaluations for service-sire conception rate for heifer and cows inseminations with conventional and sexed semen. HJ. Dairy Sci. 94:6135–6142H.

Norman, H.D., J.R. Wright, M.T. Kuhn, S.M. Hubbard, J.B. Cole, and P.M. VanRaden. 2009. Genetic and environmental factors that affect gestation length in dairy cattle. J. Dairy Sci. 92:2259–2269.

Norman, H.D., J.R. Wright, and R.L. Powell. 2006. Is there a need for different genetics in dairy grazing systems? HProc. 6th Mid-Atlantic Dairy Grazing Conf., Goldsboro, NC, Oct. 31–Nov. 1, 5 ppH.

Olson, K.M., J.L. Hutchison, P.M. VanRaden, and H.D. Norman. 2011a. Changes in the use of young bulls. HJ. Dairy Sci. 94(E-Suppl. 1):27(Abstr. M67)H.

Olson, K.M., P.M. VanRaden, and D.J. Null. 2011b. Impacts of inclusion of foreign data in genomic evaluation of dairy cattle. HJ. Dairy Sci. 94(E-Suppl. 1):164–165(Abstr. 35)H.

Olson, K.M., P.M. VanRaden, and M.E. Tooker. 2012. Multibreed genomic evaluations using purebred Holsteins, Jerseys, and Brown Swiss. J. Dairy Sci. 95:(in press).

Parker Gaddis, K.L, J. B. Cole, J.S. Clay, and C. Maltecca. 2012. Incidence validation and causal relationship analysis of producer-recorded health event data from on-farm computer systems in the U.S. J. Dairy Sci. (accepted).

Patry, C., and V. Ducrocq. 2011. Accounting for genomic pre-selection in national BLUP evaluations in dairy cattle. Genet. Sel. Evol. 43:30.

Reyher, K.K., S. Dufour, H.W. Barkema, L. Des Côteaux, T.J. DeVries, I.R. Dohoo, G.P. Keefe, J.-P. Roy, and D.T. Scholl. 2011. The National Cohort of Dairy Farms—A data collection platform for mastitis research in Canada. HJ. Dairy Sci. 94:1616–1626H.

Rincon, G., K.L. Weber, A.L. Van Eenennaam, B.L. Golden, and J.F. Medrano. 2011. Hot topic: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys. HJ. Dairy Sci. 94:6116–6121H.

Sargolzaei, M., J.P. Chesnais, and F.S. Schenkel. 2011. FImpute – An efficient imputation algorithm for dairy cattle populations. HJ. Dairy Sci. 94(E-Suppl. 1):421(Abstr. 333)H.

Schaeffer, L.R., J. Jamrozik, G.J. Kistemaker, and B.J. Van Doormaal. 2000. Experience with a test-day model. J. Dairy Sci. 83: 1135–1144.

Schaeffer, L.R. 2006. Strategy for applying genome-wide selection in dairy cattle. HJ. Anim. Breed. Genet. 123:218–223H.

Schierenbeck, S., E.C.G. Pimentel, M. Tietze, J. Körte, R. Reents, F. Reinhardt, H. Simianer, S. König. 2011. Controlling inbreeding and maximizing genetic gain using semi-definite programming with pedigree-based and genomic relationships. J. Dairy Sci. 94: 6143–6152.

Schrooten, C., H. Bovenhuis, J.A.M. van Arendonk, and P. Bijma. 2005. Genetic progress in multistage dairy cattle breeding schemes using genetic markers. J. Dairy Sci. 88:1569–1581.

Shook, G.E. 2006. Major advances in determining appropriate selection goals. J. Dairy Sci. 89:1349–1361.

Solberg, T.R., B. Heringstad, M. Svendsen, H. Grove, and T.H.E. Meuwissen. 2011. Genomic predictions for production- and functional traits in Norwegian Red from BLUP analyses of imputed 54K and 777K SNP data. HInterbull Bull. 44:240–243H.

Stoop, W.M., H. Eding, M.L. van Pelt, and G. de Jong. 2011. Combining genomic and conventional data in the Dutch national evaluation. HInterbull Bull. 44:169–172H.

Su, G., R.F. Brøndum, P. Ma, B. Guldbrandtsen, G.P. Aamand, and M.S. Lund. 2011. Genomic prediction using high-density SNP markers in Nordic Holstein and Red.H Interbull Bull. 44:157–161H.

Toosi, A., R.L. Fernando, and J.C.M. Dekkers. 2010. Genomic selection in admixed and crossbred populations. HJ. Anim. Sci. 88:32–46H.

Tsuruta, S., I. Misztal, I. Aguilar, and T.J. Lawlor. 2011. Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins. HJ. Dairy Sci. 94:4198–4204H.

Van Tassell, C.P., and L.D. Van Vleck. 1991. Estimates of genetic selection differentials and generation intervals for four paths of selection. HJ. Dairy Sci. 74:1078–1086H.

VanRaden, P.M. 2004. Invited review: Selection on net merit to improve lifetime profit.H J. Dairy Sci. 87:3125–3131H.

VanRaden, P.M. 2005. Inbreeding adjustments and effect on genetic trend estimates. HInterbull Bull. 33:81–84H.

VanRaden, P.M. 2006a. Fertility trait economics and correlations with other traits. HInterbull Bull. 34:53–56H.

VanRaden, P.M. 2006b. Predicting genetic interactions within and across breeds. HProc. 8th World Congr. Genet. Appl. Livest. Prod., Comm. 01-39H.

VanRaden, P.M., and R.H. Miller. 2008. The USDA Animal Improvement Programs Laboratory: A century old and just getting started. HAIPL Res. Rep. HIST1 (10-08)H.

VanRaden, P.M., D.J. Null, G.R. Wiggans, T.S. Sonstegard, and E.E. Connor. 2011a. Genomic imputation and evaluation using 342 high-density Holstein genotypes. HJ. Dairy Sci. 94(E-Suppl. 1):533(Abstr. W53)H.

VanRaden, P.M., J.R. O’Connell, G.R. Wiggans, and K.A. Weigel. 2011b. Genomic evaluations with many more genotypes. HGenet. Sel. Evol. 43:10H.

VanRaden, P.M., K.M. Olson, D.J. Null, and J.L. Hutchison. 2011c. Harmful recessive effects on fertility detected by absence of homozygous haplotypes. HJ. Dairy Sci. 94:6153–6161H.

VanRaden, P.M., M.E. Tooker, J.B. Cole, G.R. Wiggans, and J.H. Megonigal Jr. 2007. Genetic evaluations for mixed-breed populations. HJ. Dairy Sci. 90:2434–2441H.

Varona, L., and M.A. Toro. 2011. The use of two types of mating to profit from dominance in genomic selection. HBook of Abstracts of the 62nd Annual Meeting of the European Federation of Animal Science No. 17:5H. Wageningen Academic Publishers, The Netherlands.

Veerkamp, R.F., D.P. Berry, E. Wall, Y. de Haas, S. McParland, M. Coffey, and M.P.L. Calus. 2011. Use of phenotypes from research herds to develop genomic selection for scarcely recorded traits like feed efficiency. HInterbull Bull. 44:249–254H.

Vitezica, Z.G., I. Aguilar, and A. Legarra. 2010. One-step vs. multi-step methods for genomic prediction in presence of selection. HProc. 9th World Congr. Genet. Appl. Livest. Prod., Comm. 0131H.

Weigel, K.A., C.P. Van Tassell, J.R. O’Connell, P.M. VanRaden, and G.R. Wiggans. 2010. Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms. HJ. Dairy Sci. 93:2229–2238H.

Wiggans, G.R, T.A. Cooper, P.M. VanRaden, K.M. Olson, and M.E. Tooker. 2012. Use of the Illumina Bovine3K BeadChip in dairy genomic evaluation. HJ. Dairy Sci. 95:1552–1558.

Wiggans, G.R., and S.P. Miller. 2011. SNP panels/imputation. HInterbull Bull. 43:4 ppH.

Wiggans, G.R., I. Misztal, and L.D. Van Vleck. 1988. Implementation of an animal model for genetic evaluation of dairy cattle in the United States. HJ. Dairy Sci. 71(Suppl. 2):54–69H.

Wiggans, G.R., and P.M. VanRaden. 1991. Method and effect of adjustment for heterogeneous variance. HJ. Dairy Sci. 74:4350–4357H.

Wiggans, G.R., P.M. VanRaden, and T.A. Cooper. 2011. The genomic evaluation system in the United States: Past, present future.H J. Dairy Sci. 94:3202–3211H.

Past Accomplishments of Investigators

1981 University of Illinois, B.S., dairy science

1984 Iowa State University, M.S., animal breeding

1986 Iowa State University, Ph.D., animal breeding

1982–86 Graduate Research Assistant, Iowa State University, Ames, IA

1986 Postdoctoral Research Associate, Iowa State University, Ames, IA

1987–88 Postdoctoral Research Associate, University of Wisconsin, Madison, WI

1988–present Research Geneticist (Animal), USDA, ARS, Beltsville, MD
Accomplishments (past 10 years):

Dr. VanRaden has improved several important areas of animal breeding such as avoidance of inbreeding, selection for more traits, computation of genomic evaluations, and discovery of lethal recessive genes. His methods were made directly available to U.S. dairy producers, and computer programs for routine use have made those advances available to other scientists and producers worldwide. Using methods and programs introduced by Dr. VanRaden in 2005, U.S. genetic evaluations are the only evaluations in the world that adjust for expected inbreeding. He compared crossbred and purebred dairy cattle for economic merit and developed the multibreed evaluation system implemented in 2007. He introduced national rankings for daughter pregnancy rate in 2003, cooperated with Dr. John Cole to introduce stillbirth rate in 2006, and cooperated with Dr. Melvin Kuhn to introduce heifer conception and cow conception rates in 2009. Dr. VanRaden led a team of scientists to revise the lifetime net merit index, which combines genetic merit for available U.S. traits according to economic values into an overall merit for each animal, in 2003 and 2006 and assisted Dr. Cole in a 2009 revision. Official genomic evaluations were implemented for U.S. dairy cattle in January 2009, the first such system in the world, using Dr. VanRaden’s methods and programs. Several other countries quickly adopted those same methods or programs, and the Interbull Centre (Uppsala, Sweden) uses them for the global genomic evaluation of the Brown Swiss breed. Genotypes from a 3,000-marker panel were imputed to 50,000-marker density using methods developed by Dr. VanRaden, and routine genetic predictions from those imputed genotypes were introduced in 2010. His imputation methods also proved to be very efficient for predicting higher density genotypes in large populations. Dr. VanRaden’s methods to split genotypes into haplotypes led to the discovery of five new lethal recessive defects that were reported to breeders in August 2011. Since 2002, Dr. VanRaden has (co)authored 42 scientific journal research papers (senior or sole author of 12) and 57 research abstracts. He has made 11 scientific presentations (including 1 invited paper) at annual meetings of the American Dairy Science Association (ADSA) and formal research presentations in 14 countries. He has (co)authored 1 book chapter and 31 articles in international proceedings. He has (co)authored 25 articles in USDA and popular trade publications and has made over 70 presentations at international, national, State, district, and university meetings. Dr. VanRaden’s accomplishments have resulted in several national awards, including the National Association of Animal Breeders’ Research Award in 2002 and ADSA’s Most Cited Award in 2011 and 2012.

Powell, R.L., and P.M. VanRaden. 2002. International dairy bull evaluations expressed on national, subglobal, and global scales. HJ. Dairy Sci. 85:1863–1868H.

Olson, K.M., P.M. VanRaden, M.E. Tooker, and T.A. Cooper. 2011. Differences among methods to validate genomic evaluations for dairy cattle. HJ. Dairy Sci. 94:2613–2620H.