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United States Department of Agriculture

Agricultural Research Service

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Genetic base changes for December 2014 - (Government Publication)
Van Raden, P.M., Tooker, M.E., Wright, J.R., Cole, J.B., Null, D.J., Lawlor, T.J. 2014. Genetic base changes for December 2014. AIP Research Report BASE3(10-14).
Net merit as a measure of lifetime profit: 2014 revision - (Government Publication)
Van Raden, P.M., Cole, J.B. 2014. Net merit as a measure of lifetime profit: 2014 revision. AIP Research Report NM$5 (10-14).
Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects - (Peer Reviewed Journal)
Sun, C., Van Raden, P.M., Cole, J.B., O'Connell, J.R. 2014. Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects. PLoS One. 9(8):e103934.
The development of genomics applied to dairy breeding - (Peer Reviewed Journal)
(16-May-14)
Including cow information in genomic prediction of Holstein dairy cattle in the US - (Proceedings)
Cooper, T.A., Wiggans, G.R., Van Raden, P.M. 2014. Including cow information in genomic prediction of Holstein dairy cattle in the US. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Improving genomic prediction for Danish Jersey using a joint Danish-US reference population - (Proceedings)
Guosheng, S., Nielsen, U.S., Wiggans, G.R., Aamand, G.P., Guldbrandtsen, B., Lund, M.S. 2014. Improving genomic prediction for Danish Jersey using a joint Danish-US reference population. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Fast imputation using medium- or low-coverage sequence data - (Proceedings)
Van Raden, P.M., Sun, C. 2014. Fast imputation using medium- or low-coverage sequence data. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Increasing predictive ability using dominance in genomic selection - (Proceedings)
Sun, C., Van Raden, P.M., Cole, J.B., O'Connell, J.R. 2014. Increasing predictive ability using dominance in genomic selection. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Increasing the number of single nucleotide polymorphisms used in genomic evaluations of dairy cattle - (Proceedings)
Wiggans, G.R., Cooper, T.A., Null, D.J., Van Raden, P.M. 2014. Increasing the number of single nucleotide polymorphisms used in genomic evaluations of dairy cattle. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Approximation of reliability of direct genomic breeding values - (Proceedings)
Sargolzaei, M., Schaeffer, L.R., Chesnais, J., Kistemaker, G., Wiggans, G.R., Schenkel, F.S. 2014. Approximation of reliability of direct genomic breeding values. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Using haplotypes to unravel the inheritance of Holstein coat color for a larger audience - (Proceedings)
Lawlor, T.J., Van Raden, P.M., Null, D.J., Levisee, J., Dorhorst, B. 2014. Using haplotypes to unravel the inheritance of Holstein coat color for a larger audience. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Impact of adding foreign genomic information on Mexican Holstein imputation - (Proceedings)
García-Ruiz, A., Ruiz-Lopez, F.J., Wiggans, G.R., Van Tassell, C.P., Montaldo, H. 2014. Impact of adding foreign genomic information on Mexican Holstein imputation. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Single nucleotide polymorphisms in candidate genes related to daughter pregnancy rate in Holstein cows - (Proceedings)
Ortega, M.S., Denicol, A.C., Null, D.J., Cole, J.B., Hansen, P.J. 2014. Single nucleotide polymorphisms in candidate genes related to daughter pregnancy rate in Holstein cows. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 2 pp.
The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle - (Proceedings)
Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Using the whole read: structural variant detection using NGS data - (Proceedings)
Bickhart, D.M., Cole, J.B., Hutchison, J.L., Xu, L., Liu, G. 2014. Using the whole read: structural variant detection using NGS data. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 5 pp.
Genotypes are useful for more than genomic evaluation - (Proceedings)
Van Raden, P.M., Sun, C., Cooper, T.A., Null, D.J., Cole, J.B. 2014. Genotypes are useful for more than genomic evaluation. International Committee on Animal Recording(ICAR). Proc. 39th Int. Comm. Anim. Recording Sess., Berlin, Germany, May 19–23, 4 pp.
An updated version of lifetime net merit incorporating additional fertility traits and new economic values - (Abstract Only)
Cole, J.B., Van Raden, P.M. 2014. An updated version of lifetime net merit incorporating additional fertility traits and new economic values. Journal of Dairy Science. 97(E-Suppl. 1):78 (abstr. 0153).
Multi-trait, multi-breed conception rate evaluations - (Abstract Only)
Van Raden, P.M., Wright, J.R., Sun, C., Hutchison, J.L., Tooker, M.E. 2014. Multi-trait, multi-breed conception rate evaluations. Journal of Dairy Science. 97(E-Suppl. 1):472 (abstr. 0946/T044).
Determination of single nucleotide polymorphisms associated with subclinical ketosis in Jersey cattle - (Abstract Only)
Fugate, R.T., Dauten, L.H., Wiggans, G.R., White, H.M. 2014. Determination of single nucleotide polymorphisms associated with subclinical ketosis in Jersey cattle. Journal of Dairy Science. 97(E-Suppl. 1):472 (abstr. 0945/T043).
Calculation and delivery of US genomic evaluations for dairy cattle - (Abstract Only)
Wiggans, G.R., Cooper, T.A., Van Raden, P.M., Null, D.J., Hutchison, J.L., Meland, O.M., Tooker, M.E., Norman, H.D. 2014. Calculation and delivery of US genomic evaluations for dairy cattle. Journal of Dairy Science. 97(E-Suppl. 1):77–78 (abstr. 0152).
Development of a lifetime merit-based selection index for US dairy grazing systems - (Peer Reviewed Journal)
Gay, K.D., Widmar, N.J., Nennich, T.D., Schinckel, A.P., Cole, J.B., Schutz, M.M. 2014. Development of a lifetime merit-based selection index for US dairy grazing systems. Journal of Dairy Science. 97(7):4568-4578.
Accuracy of genomic predictions in Bos indicus (Nellore) cattle     Reprint Icon - (Peer Reviewed Journal)
Neves, H.H., Carvalheiro, R., Perez O'Brien, A.M., Utsunomiya, Y.T., Do Carmo, A.S., Schenkel, F.S., Solkner, J., Ncewab, J.C., Van Tassell, C.P., Sonstegard, T.S., Cole, J.B., Da Silva, M.V., Queiroz, S.A., Garcia, J.F. 2014. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Genetic Selection Evolution. Genet Sel Evol. 2014 Feb 27;46:17.
Genomic selection for producer-recorded health event data in US dairy cattle     Reprint Icon - (Peer Reviewed Journal)
Gaddis Parker, K., Cole, J.B., Clay, J., Maltecca, C. 2014. Genomic selection for producer-recorded health event data in US dairy cattle. Journal of Dairy Science. 97(5):3190-3199.
Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle     Reprint Icon - (Peer Reviewed Journal)
Cooper, T.A., Wiggans, G.R., Null, D.J., Hutchison, J.L., Cole, J.B. 2014. Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle. Journal of Dairy Science. 97(6):3878-3882.
The challenges and importance of structural variation detection in livestock - (Review Article)
Bickhart, D.M., Liu, G. 2014. The challenges and importance of structural variation detection in livestock. Frontiers in Genetics. 5:37.
Genotypes are useful for more than genomic evaluation - (Proceedings)
Van Raden, P.M., Sun, C., Cooper, T.A., Cole, J.B. 2014. Genotypes are useful for more than genomic evaluation. International Committee on Animal Recording(ICAR). Proc. 39th Int. Comm. Anim. Recording Sess., Berlin, Germany, May 19–23, 4 pp.
A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits     Reprint Icon - (Peer Reviewed Journal)
Cole, J.B., Waurich, B., Wensch-Dorendorf, M., Bickhart, D.M., Swalve, H.H. 2014. A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits. Journal of Dairy Science. 97(5):3156-3172.
Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls - (Abstract Only)
Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls. Plant and Animal Genome Conference Proceedings. Plant Animal Genome XXII, San Diego, CA, Jan. 11–15, P1097.
The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds - (Abstract Only)
Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J.F., Taylor, J.F., Schnabel, R.D., Lewin, H., Liu, G. 2014. The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds. Plant and Animal Genome Conference Proceedings. Plant Animal Genome XXII, San Diego, CA, Jan. 11–15, P078.
Short communication: Use of young bulls in the United States     Reprint Icon - (Peer Reviewed Journal)
Hutchison, J.L., Cole, J.B., Bickhart, D.M. 2014. Short communication: Use of young bulls in the United States. Journal of Dairy Science. 97(5):3213-3220.
Increasing long-term response by selecting for favorable minor alleles - (Peer Reviewed Journal)
Sun, C., Van Raden, P.M. 2014. Increasing long-term response by selecting for favorable minor alleles. PLoS One. 9(2):e88510.
Application of the a posteriori granddaughter design to the Holstein genome     Reprint Icon - (Peer Reviewed Journal)
Weller, J.I., Cole, J.B., Van Raden, P.M., Wiggans, G.R. 2014. Application of the a posteriori granddaughter design to the Holstein genome. Animal. 8(4):511-519.
Genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle     Reprint Icon - (Peer Reviewed Journal)
Yao, C., Weigel, K.A., Cole, J.B. 2014. Genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle. Journal of Dairy Science. 97(4):2474-2480.
Increasing long term response by selecting for favorable minor alleles - (Proceedings)
Sun, C., Van Raden, P.M. 2013. Increasing long term response by selecting for favorable minor alleles. Interbull Annual Meeting Proceedings. Interbull Bulletin 47:151-155.
Mating programs including genomic relationships and dominance effects - (Peer Reviewed Journal)
Sun, C., Van Raden, P.M., O'Connell, J.R., Weigel, K.A., Gianola, D. 2013. Mating programs including genomic relationships and dominance effects. Journal of Dairy Science. 96(10):8014-8023.
Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects - (Peer Reviewed Journal)
Weller, J.I., Van Raden, P.M., Wiggans, G.R. 2013. Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects. Journal of Dairy Science. 96(8)5376-5387.
Single nucleotide polymorphisms in candidate genes associated with fertilizing ability of sperm and subsequent embryonic development in cattle     Reprint Icon - (Peer Reviewed Journal)
Cochran, S.D., Cole, J.B., Null, D.J., Hansen, P.J. 2013. Single nucleotide polymorphisms in candidate genes associated with fertilizing ability of sperm and subsequent embryonic development in cattle. Biology of Reproduction. 89(3):69.
Random forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle - (Peer Reviewed Journal)
Yao, C., Spurlock, D., Armentano, L., Page, D., Vandehaar, M., Bickhart, D.M., Weigel, K. 2013. Random forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle. Journal of Dairy Science. 96(10):6716-6729.
Genome-wide association mapping for identification of quantitative trait loci for rectal temperature during heat stress in Holstein cattle     Reprint Icon - (Peer Reviewed Journal)
Dikmen, S., Cole, J.B., Null, D.J., Hansen, P.J. 2013. Genome-wide association mapping for identification of quantitative trait loci for rectal temperature during heat stress in Holstein cattle. PLoS One. 8(7):e69202.
We are making inroads on health and fitness traits - (Popular Publication)
Parker Gaddis, K.L., Maltecca, C., Cole, J.B. 2013. We are making inroads on health and fitness traits. Hoard's Dairyman. 158(12):455.
Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle     Reprint Icon - (Peer Reviewed Journal)
Cochran, S.D., Cole, J.B., Null, D.J., Hansen, P.J. 2013. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BioMed Central (BMC) Genetics. 14:49.
Open source tools to exploit DNA sequence data from livestock species - (Proceedings)
Bickhart, D.M., Hutchison, J.L., Xu, L., Song, J., Liu, G. 2013. Open source tools to exploit DNA sequence data from livestock species. BARC Poster Day. p. 9, abstract 4.
Mating programs including genomic relationships and dominance effects - (Proceedings)
Sun, C., Van Raden, P.M., O'Connell, J.R. 2013. Mating programs including genomic relationships and dominance effects. BARC Poster Day. p. 46, abstract 41.
Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects - (Abstract Only)
Weller, J.I., Van Raden, P.M., Wiggans, G.R. 2013. Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects. Journal of Dairy Science. 96(E-Suppl. 1):617 (abstr. 538).
Genomic evaluation and identification of haplotype affecting fertility for Ayrshire dairy cattle - (Abstract Only)
Cooper, T.A., Wiggans, G.R., Null, D.J., Hutchison, J.L. 2013. Genomic evaluation and identification of haplotype affecting fertility for Ayrshire dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):74 (abstr. T206).
Using 90,113 single nucleotide polymorphisms in genomic evaluation of dairy cattle - (Abstract Only)
Wiggans, G.R., Cooper, T.A., Van Raden, P.M. 2013. Using 90,113 single nucleotide polymorphisms in genomic evaluation of dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):617 (abstr. 539).
Tools to exploit sequence data to find new markers and disease loci in dairy cattle - (Abstract Only)
Bickhart, D.M., Harris, L., Liu, G. 2013. Tools to exploit sequence data to find new markers and disease loci in dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):624 (abstr. 557).
Optimal age at first calving for U.S. dairy cattle - (Abstract Only)
Cole, J.B., Hutchison, J.L., Bickhart, D.M., Null, D.J. 2013. Optimal age at first calving for U.S. dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):289–290 (abstr. W188).
Dissection of genomic correlation matrices using multivariate factor analysis in dairy and dual-purpose cattle breeds - (Abstract Only)
Macciotta, N.P., Dimauro, C., Vicario, D., Cole, J.B., Null, D.J. 2013. Dissection of genomic correlation matrices using multivariate factor analysis in dairy and dual-purpose cattle breeds. Journal of Dairy Science. 96(E-Suppl. 1):618 (abstr. 541).
Mating programs including genomic relationships - (Abstract Only)
Sun, C., Van Raden, P.M. 2013. Mating programs including genomic relationships. Journal of Dairy Science. 96(E-Suppl. 1):653 (abstr. 635).
Heritability estimates of performance and health traits of Holstein calves - (Abstract Only)
Mousa, M.S., Seykora, A.J., Chester-Jones, H., Ziegler, D.M., Cole, J.B. 2013. Heritability estimates of performance and health traits of Holstein calves. Journal of Dairy Science. 96(E-Suppl. 1):291 (abstr. W194).
Trends in noncompliance with milk quality standards for Dairy Herd Improvement herds in the United States - (Abstract Only)
Norman, H.D., Wright, J.R. 2013. Trends in noncompliance with milk quality standards for dairy herd improvement herds in the United States. Journal of Dairy Science. 96(E-Suppl. 1):603 (abstr. TH375).
Regression metamodels of an optimal genomic testing strategy in dairy cattle when selection intensity is low - (Abstract Only)
De Vries, A., Cole, J.B., Galligan, D.T. 2013. Regression metamodels of an optimal genomic testing strategy in dairy cattle when selection intensity is low. Journal of Dairy Science. 96(E-Suppl. 1):74 (abstr. T207).
Breeding for polled dairy cows versus dehorning: Preliminary cost assessments & discussion - (Abstract Only)
Widmar, N.O., Schutz, M.M., Cole, J.B. 2013. Breeding for polled dairy cows versus dehorning: Preliminary cost assessments & discussion. Journal of Dairy Science. 96(E-Suppl. 1):602 (abstr. TH373).
Analysis of health trait data from on-farm computer systems in the U.S. II: Comparison of genomic analyses including two-stage and single-step methods - (Abstract Only)
Parker Gaddis, K.L., Cole, J.B., Clay, J.S., Maltecca, C. 2013. Analysis of health trait data from on-farm computer systems in the U.S. II: Comparison of genomic analyses including two-stage and single-step methods. Journal of Dairy Science. 96(E-Suppl. 1):444 (abstr. 447).
Analysis of health trait data from on-farm computer systems in the U.S. I: Pedigree and genomic variance components estimation - (Abstract Only)
Parker Gaddis, K.L., Cole, J.B., Clay, J.H., Maltecca, C. 2013. Analysis of health trait data from on-farm computer systems in the U.S. I: Pedigree and genomic variance components estimation. Journal of Dairy Science. 96(E-Suppl. 1):443–444 (abstr. 446).
Systems Biology in Animal Breeding: Identifying relationships among markers, genes, and phenotypes - (Peer Reviewed Journal)
Cole, J.B., Lewis, R.M., Maltecca, C., Newman, S., Olson, K.M., Tait, R. 2013. Systems Biology in Animal Breeding: Identifying relationships among markers, genes, and phenotypes. Journal of Animal Science. 91(2):521-522.
Last Modified: 10/25/2014
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