Research Project: Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals

Location: Animal Genomics and Improvement Laboratory

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

Improving national fertility evaluations by accounting for the rapid rise of embryo transfer in US dairy cattle - (Peer Reviewed Journal)
Miles, A.M., Hutchison, J.L., Van Raden, P.M. 2023. Improving national fertility evaluations by accounting for the rapid rise of embryo transfer in US dairy cattle. Journal of Dairy Science. https://doi.org/10.3168/jds.2022-22298.

The association of hyperketonemia with fecal and rumen microbiota at time of diagnosis in a case-control cohort of early lactation cows - (Peer Reviewed Journal)
Miles, A.M., McArt, J.A., Lima, S.F., Neves, R.C., Ganda, E. 2022. The association of hyperketonemia with fecal and rumen microbiota at time of diagnosis in a case-control cohort of early lactation cows. BMC Veterinary Research. 18:411. https://doi.org/10.1186/s12917-022-03500-4.

Temporal and spatial dynamics of bacterial and fungal microbiomes in nursery soils post-steaming - (Peer Reviewed Journal)
Crandall, S.G., Miles, A.M., Chung, T., Cloutier, M.L., Garcia-Rodriguez, R., Schweigkofler, W., Couradeau, E. 2022. Temporal and spatial dynamics of bacterial and fungal microbiomes in nursery soils post-steaming. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-07-22-0071-R.

An exponential regression model to estimate daily milk yields - (Proceedings)
Wu, X.-L., Wiggans, G.R., Norman, H.D., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Burchard, J., Durr, J. 2022. An exponential regression model to estimate daily milk yields. Interbull Bulletin. 57:67-73.

Considerations in using quantitative measurements of milking speed for genetic evaluations for all dairy breeds in the USA - (Proceedings)
Miles, A.M., Fourdraine, R.F., Sievert, S., Parker Gaddis, K.L., Bewley, J., Eaglen, S., Weiker, J., Hutchison, J.L., Durr, J. 2022. Considerations in using quantitative measurements of milking speed for genetic evaluations for all dairy breeds in the USA. Interbull Bulletin. 57:48-53.

Daily milk yield correction factors: what are they? - (Peer Reviewed Journal)
Wu, X., Wiggans, G.R., Norman, H.D., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Burchard, J., Durr, J. 2022. Daily milk yield correction factors: what are they? Journal of Dairy Science Communications. https://doi.org/10.3168/jdsc.2022-0230.

Statistical methods revisited for estimating daily milk yields: how well do they work? - (Peer Reviewed Journal)
Wu, X., Wiggans, G.R., Norman, H.D., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Burchard, J., Durr, J. 2022. Statistical methods revisited for estimating daily milk yields: how well do they work? Frontiers in Genetics. 13:943705. https://doi.org/10.3389/fgene.2022.943705.

Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle - (Peer Reviewed Journal)
Lozada-Soto, E.A., Maltecca, C., Jiang, J., Cole, J.B., Van Raden, P.M., Tiezzi, F. 2022. Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle. Journal of Dairy Science. 105(11):8956-8971. https://doi.org/10.3168/jds.2022-22116.

Sustainable dairy breeding: working within the US National Evaluation System - (Abstract Only)
Miles, A.M. 2022. Sustainable dairy breeding: working within the US National Evaluation System [abstract]. Journal of Animal Science. 100(Suppl. S3):14(abstr. 25). https://doi.org/10.1093/jas/skac247.025.

Getting milk yield right - (Popular Publication)
Miles, A.M. 2022. Getting milk yield right. Progressive Dairyman. https://www.progressivedairy.com/topics/management/getting-milk-yield-right.

Considerations in using quantitative measurements of milking speed for genetic evaluations for all dairy breeds in the USA - (Proceedings)
Miles, A.M., Fourdraine, R., Sievert, S., Parker Gaddis, K.L., Bewley, J., Eaglen, S., Weiker, J., Hutchison, J.L., Durr, J. 2022. Considerations in using quantitative measurements of milking speed for genetic evaluations for all dairy breeds in the USA. Interbull Bulletin. 57:48-53.

Genetic analysis of retained placenta and its association with reproductive disorder, production, and fertility traits of Iranian Holstein dairy cows - (Peer Reviewed Journal)
Mahnani, A., Sadeghi-Sefidmazgi, A., Ansari-Mahyari, S., Ghiasi, H., Toghiani, S. 2022. Genetic analysis of retained placenta and its association with reproductive disorder, production, and fertility traits of Iranian Holstein dairy cows. Theriogenology. 189:59-63. https://doi.org/10.1016/j.theriogenology.2022.04.008.

Effects of antibiotic versus dextrose treatment on microbial populations in metritic cow vaginal discharge - (Abstract Only)

The increasing popularity of embryo transfer has implications for U.S. dairy cattle fertility evaluations - (Abstract Only)
Miles, A.M., Hutchison, J.L., Van Raden, P.M. 2022. The increasing popularity of embryo transfer has implications for U.S. dairy cattle fertility evaluations [abstract]. Journal of Dairy Science. 105(Suppl. 1):200(abstr. 1501V).

Single-step genomic evaluation of crossbreed dairy cattle in the US - (Abstract Only)
Cesarani, A., Lourenco, D., Tsuruta, S., Legarra, A., Nicolazzi, E., Van Raden, P.M., Misztal, I. 2022. Single-step genomic evaluation of crossbreed dairy cattle in the US [abstract]. Journal of Dairy Science. 105(Suppl. 1):45(abstr. 1117).

Mixed-model GWAS on milk production traits of 1.16M genotyped Holstein cattle - (Abstract Only)
Jiang, J., Cheng, J., Maltecca, C., Ma, L., Van Raden, P.M., O'Connell, J.R. 2022. Mixed-model GWAS on milk production traits of 1.16M genotyped Holstein cattle [abstract]. Journal of Dairy Science. 105(Suppl. 1):19(abstr. 1047).

Accuracy of genomic predictions including or excluding foreign data in reference populations - (Abstract Only)
Mota, R.R., Van Raden, P.M. 2022. Accuracy of genomic predictions including or excluding foreign data in reference populations [abstract]. Journal of Dairy Science. 105(Suppl. 1):130(abstr. 1330).

Improved, expanded, and automated ancestor discovery - (Abstract Only)
Null, D.J., Wiggans, G.R., Ogwo, E.O., Van Raden, P.M. 2022. Improved, expanded, and automated ancestor discovery [abstract]. Journal of Dairy Science. 105(Suppl. 1):389(abstr. 2422V).

Flexible testing and use of milk-only records - (Abstract Only)
Van Raden, P.M., Fok, G.C., Bacheller, L.R., Jansen, G.B., Carrillo, J.A. 2022. Flexible testing and use of milk-only records [abstract]. Journal of Dairy Science. 105(Suppl. 1):199(abstr. 1498V).

Phenotypic and genotypic impact of milk components and bodyweight composite on dry matter intake - (Abstract Only)
Toghiani, S., Van Raden, P.M., Parker Gaddis, K.L., Vandehaar, M.J., Tempelman, R.J. 2022. Phenotypic and genotypic impact of milk components and bodyweight composite on dry matter intake [abstract]. Journal of Dairy Science. 105(Suppl. 1):200(abstr. 1499V).

Evidence of selection against recessive defects - (Abstract Only)
Norman, H.D., Null, D.J., Van Raden, P.M. 2022. Evidence of selection against recessive defects [abstract]. Journal of Dairy Science. 105(Suppl. 1):47(abstr. 1124).

SLEMM: Million-scale genomic best linear unbiased predictions with window-based SNP weighting - (Abstract Only)
Cheng, J., Maltecca, C., Van Raden, P.M., O'Connell, J.R., Ma, L., Jiang, J. 2022. SLEMM: Million-scale genomic best linear unbiased predictions with window-based SNP weighting [abstract]. Journal of Dairy Science. 105(Suppl. 1):19(abstr. 1048).

Current state of inbreeding, genetic diversity, and selection history in all major breeds of U.S. dairy cattle - (Abstract Only)
Lozada-Soto, E.A., Maltecca, C., Cole, J.B., Van Raden, P.M., Tiezzi, F. 2022. Current state of inbreeding, genetic diversity, and selection history in all major breeds of U.S. dairy cattle [abstract]. Journal of Dairy Science. 105(Suppl. 1):188(abstr. 1475V).

Effects of direct-fed microbial inclusion on turkey intestinal resistome - (Abstract Only)
Kenney, S., Miles, A.M., Erb, L., Boney, J., Ganda, E. 2022. Effects of direct-fed microbial inclusion on turkey intestinal resistome [abstract]. American Society for Microbiology. June 9-13, Washington, D.C., United States.

The rising popularity of embryo transfer in U.S. dairy cattle and implications for national fertility evaluations - (Proceedings)
Miles, A.M., Hutchison, J.L., Van Raden, P.M. 2022. The rising popularity of embryo transfer in U.S. dairy cattle and implications for national fertility evaluations. World Congress of Genetics Applied in Livestock Production. https://www.wageningenacademic.com/pb-assets/wagen/WCGALP2022/52_013.pdf.

Patterns of inbreeding and selection using runs of homozygosity in North American dairy cattle - (Proceedings)
Lozada-Soto, E.A., Tiezza, F., Cole, J.B., Van Raden, P.M., Maltecca, C. 2022. Patterns of inbreeding and selection using runs of homozygosity in North American dairy cattle. World Congress of Genetics Applied in Livestock Production. Front Matter, Commun. 188, pp. 806-809. https://doi.org/10.3920/978-90-8686-940-4_188.

Comparison of single-step and multi-step evaluations for U.S. milk, fat, and protein - (Proceedings)
Mota, R.R., Cesarani, A., Van Raden, P.M. 2022. Comparison of single-step and multi-step evaluations for U.S. milk, fat, and protein. World Congress of Genetics Applied in Livestock Production. Front Matter, Commun. 323, pp. 1356-1359. https://doi.org/10.3920/978-90-8686-940-4_323.

Recent advances and future needs in genotype imputation - (Proceedings)
Van Raden, P.M., Null, D.J., Al-Khudhair, A.S. 2022. Recent advances and future needs in genotype imputation. World Congress of Genetics Applied in Livestock Production. Front Matter, Commun. 349, pp. 1463-1466. https://doi.org/10.3920/978-90-8686-940-4_349.

Options for evaluating multiple breeds in a single-step GBLUP for the US dairy population - (Proceedings)
Cesarani, A., Lourenco, D., Van Raden, P.M., Nicolazzi, E.L., Legarra, A., Misztal, I. 2022. Options for evaluating multiple breeds in a single-step GBLUP for the US dairy population. World Congress of Genetics Applied in Livestock Production. Front Matter, Commun. 669, pp. 2761-2764. https://doi.org/10.3920/978-90-8686-940-4_669.

Multibreed genomic evaluation for dairy cattle in the US using single-step GBLUP - (Peer Reviewed Journal)

Mastering mastitis: how genetics can help & where we go from here - (Proceedings)
Miles, A.M., Parker Gaddis, K.L. 2022. Mastering mastitis: how genetics can help & where we go from here. National Mastitis Council Meeting Proceedings. p. 33-46.

Current state of inbreeding, genetic diversity, and selection history in all major breeds of U.S. dairy cattle - (Abstract Only)

Inheritance of a mutation causing neuropathy with splayed forelimbs in Jersey cattle - (Peer Reviewed Journal)
Al-Khudhair, A.S., Null, D.J., Cole, J.B., Wolfe, C.W., Steffen, D.J., Van Raden, P.M. 2022. Inheritance of a mutation causing neuropathy with splayed forelimbs in Jersey cattle. Journal of Dairy Science. 105(2):1338–1345. https://doi.org/10.3168/jds.2021-20600.

Adding genomically discovered maternal grandsires and maternal great grandsires to the US evaluation system - (Abstract Only)
Mota, R., Wiggans, G.R., Nani, J.P., Bacheller, L.R., Fok, G.C., Carillo, J., Van Raden, P.M. 2022. Adding genomically discovered maternal grandsires and maternal great grandsires to the US evaluation system [abstract]. In: Proceedings of the Animal Genetics and Genomics Conference, Visions III: Star gazing into the galaxy of animal genetics and genomics, Iowa State University, November 3-4, 2021, Ames, Iowa. p. 50.

Invited review: Unknown-parent groups and metafounders in single-step genomic BLUP - (Peer Reviewed Journal)
Masuda, Y., Van Raden, P.M., Tsuruta, S., Lourenco, D.A.L., Misztal, I. 2022. Invited review: Unknown-parent groups and metafounders in single-step genomic BLUP. Journal of Dairy Science. 105(2):923–939. https://doi.org/10.3168/jds.2021-20293.

Genomic evaluation of crossbred dairy cattle in the United States – an update - (Proceedings)
Wiggans, G.R., Van Raden, P.M., Null, D.J., Nicolazzi, E., Jansen, G.B., Megonigal, Jr., J.H. 2021. Genomic evaluation of crossbred dairy cattle in the United States – an update. Interbull Bulletin. 56:17–21.

National index correlations and actual vs. expected use of foreign sires - (Proceedings)
Toghiani, S., Van Raden, P.M. 2021. National index correlations and actual vs. expected use of foreign sires. Interbull Bulletin. 56:52–59.

Implementation of feed saved evaluations in the U.S. - (Proceedings)
Parker Gaddis, K.L., Van Raden, P.M., Tempelman, R.J., Weigel, K.A., White, H.M., Penagaricano, F., Koltes, J.E., Santos, J.E., Baldwin, R.L., Burchard, J., Durr, J., Vandehaar, M.J. 2021. Implementation of feed saved evaluations in the U.S. Interbull Bulletin. 56:147–152.

Improved genomic validation including extra regressions - (Proceedings)
Van Raden, P.M. 2021. Improved genomic validation including extra regressions.Interbull Bulletin. 56:65–69.

Use of international clinical mastitis data as independent trait in the US evaluation system - (Proceedings)
Mota, R.R., Nicolazzi, E., Megonigal, Jr, J.H., Parker Gaddis, K.L., Durr, J., Van Raden, P.M. 2021. Use of international clinical mastitis data as independent trait in the US evaluation system. Interbull Bull. 56:11–16.

An alternative interpretation of residual feed intake by phenotypic recursive relationships in dairy cattle - (Peer Reviewed Journal)
Wu, X., Parker Gaddis, K.L., Burchard, J., Norman, H.D., Nicolazzi, E., Cole, J.B., Connor, E.E., Durr, J. 2021. An alternative interpretation of residual feed intake by phenotypic recursive relationships in dairy cattle. Journal of Dairy Science Communications. 2(6):371-375. https://doi.org/10.3168/jdsc.2021-0080.

Trends in genetic diversity and the effect of inbreeding in American Angus Cattle under genomic selection - (Peer Reviewed Journal)
Lozada-Soto, E.A., Maltecca, C., Lu, D., Miller, S., Cole, J.B., Tiezzi, F. 2021. Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection. Genetics Selection Evolution. 53:50. https://doi.org/10.1186/s12711-021-00644-z.

Net merit as a measure of lifetime profit: 2021 revision - (Government Publication)
Van Raden, P.M., Cole, J.B., Neupane, M., Toghiani, S., Parker Gaddis, K.L., Tempelman, R.J. 2021. Net merit as a measure of lifetime profit: 2021 revision. AIPL Research Reports. NM$8(05-21).

Direct phenotyping and principal component analysis of type traits implicate novel QTL in bovine mastitis through genome-wide association - (Peer Reviewed Journal)
Miles, A.M., Posbergh, C.J., Huson, H.J. 2021. Direct phenotyping and principal component analysis of type traits implicate novel QTL in bovine mastitis through genome-wide association. Animals. 11(4):1147. https://doi.org/10.3390/ani11041147.

Effects of incorporating dry matter intake and residual feed intake into a selection index for dairy cattle using deterministic modeling - (Peer Reviewed Journal)
Houlahan, K., Schenkel, F.S., Hailemariam, D., Lassen, J., Kargo, M., Cole, J.B., Connor, E.E., Wegmann, S., Oliveira Jr, G.A., Miglior, F., Fleming, A., Chud, T.C., Baes, C.F. 2021. Effects of incorporating dry matter intake and residual feed intake into a selection index for dairy cattle using deterministic modeling. Animals. 11(4):1157. https://doi.org/10.3390/ani11041157.

Accounting for X chromosome and allele frequencies in genomic inbreeding estimation - (Abstract Only)
Nani, J.P., Van Raden, P.M. 2021. Accounting for X chromosome and allele frequencies in genomic inbreeding estimation [abstract]. Journal of Dairy Science. 104(Suppl. 1):79–80(abstr. 205).

Genomic evaluations for Feed Saved in Holsteins - (Abstract Only)
Parker Gaddis, K.L., Van Raden, P.M., Tempelman, R.J., Weigel, K.A., White, H.M., Penagaricano, F., Koltes, J.E., Santos, J.E., Baldwin, R.L., Durr, J.W., Burchard, J.F., Vandehaar, M.J. 2021. Genomic evaluations for Feed Saved in Holsteins [abstract]. Journal of Dairy Science. 104(Suppl. 1):120(abstr. 302).

Genomic heritability and prediction accuracy of additive and nonadditive effects for daughter pregnancy rate in crossbred dairy cows - (Abstract Only)
Liang, Z., Prakapenka, D., Van Raden, P.M., Da, Y. 2021. Genomic heritability and prediction accuracy of additive and nonadditive effects for daughter pregnancy rate in crossbred dairy cows [abstract]. Journal of Dairy Science. 104(Suppl. 1):224(abstr. P168).

Multi-breed genomic evaluation for dairy cattle in the US using single-step GBLUP - (Abstract Only)
Cesarani, A., Lourenco, D., Masuda, Y., Legarra, A., Tsuruta, S., Nicolazzi, E., Van Raden, P.M., Misztal, I. 2021. Multi-breed genomic evaluation for dairy cattle in the US using single-step GBLUP [abstract]. Journal of Dairy Science. 104(Suppl. 1):78(abstr. 200).

Partitioning SNP heritability using related individuals - (Abstract Only)
Jiang, J., Van Raden, P.M., Ma, L., O'Connell, J.R. 2021. Partitioning SNP heritability using related individuals [abstract]. Journal of Dairy Science. 104(Suppl. 1):79(abstr. 203).

Scalable mixed model approach for finding the omnigenic core genes - (Abstract Only)
Jiang, J., Van Raden, P.M., Ma, L., O'Conell, J.R. 2021. Scalable mixed model approach for finding the omnigenic core genes [abstract]. Journal of Dairy Science. 104(Suppl. 1):79(abstr. 204).

Multiple trait random regression modelling of feed efficiency in dairy cattle - (Abstract Only)
Khanal, P., Parker Gaddis, K.L., Van Raden, P.M., Weigel, K.A., White, H.M., Penagaricano, F., Koltes, J.E., Santos, J.E., Baldwin, R.L., Burchard, J.F., Durr, J.W., Vandehaar, M.J., Tempelman, R. 2021. Multiple trait random regression modelling of feed efficiency in dairy cattle [abstract]. Journal of Dairy Science. 104(Suppl. 1):120(abstr. 303).

Genomic evaluation of dairy heifer livability - (Peer Reviewed Journal)
Neupane, M., Hutchison, J.L., Van Tassell, C.P., Van Raden, P.M. 2021. Genomic evaluation of dairy heifer livability. Journal of Dairy Science. 104(8):8959–8965. https://doi.org/10.3168/jds.2020-19687.

Genetic mechanisms of reproductive heterosis in crossbred dairy cows involve genome-wide additive and nonadditive effects - (Abstract Only)
Prakapenka, D., Liang, Z., Van Raden, P.M., Santos, D., Jiang, J., Ma, L., Garbe, J.R., Melticca, C., Hansen, P.J., Da, Y. 2021. Genetic mechanisms of reproductive heterosis in crossbred dairy cows involve genome-wide additive and nonadditive effects [abstract]. Journal of Dairy Science. 104(Suppl. 1):224(abstr. P169).

Genetic and genomic evaluation of late term abortion recorded through Dairy Herd Improvement test plans - (Abstract Only)
Neupane, M., Hutchison, J.L., Cole, J.B., Van Tassell, C.P., Van Raden, P.M. 2021. Genetic and genomic evaluation of late term abortion recorded through Dairy Herd Improvement test plans [abstract]. Journal of Dairy Science. 104(Suppl 1):77(abstr. 196).

Inheritance of a mutation causing neuropathy with splayed forelimbs in Jersey cattle - (Abstract Only)
Al-Khudhair, A.S., Null, D.J., Cole, J.B., Wolfe, C.W., Van Raden, P.M. 2021. Inheritance of a mutation causing neuropathy with splayed forelimbs in Jersey cattle [abstract]. Journal of Dairy Science. 104(Suppl. 1):77–78(abstr. 199).

Genomic evaluation of crossbred dairy cattle in the United States - (Abstract Only)

Improved genomic validation including extra regressions - (Abstract Only)

Index correlations and actual vs. expected use of foreign sires - (Abstract Only)

Use of international clinical mastitis data as independent trait in the US evaluation system - (Abstract Only)

Implementation of Feed Saved evaluations in the U.S. - (Abstract Only)

Improving dairy feed efficiency, sustainability, and profitability by impacting farmer's breeding and culling decisions - (Abstract Only)
Vandehaar, M.J., Tempelman, R., Koltes, J.E., Appuhamy, R., White, H.M., Weigel, K.A., Baldwin, R.L., Van Raden, P.M., Penagaricano, F., Santos, J.E., Durr, J.W., Nicolazzi, E., Burchard, J.F., Parker Gaddis, K.L. 2021. Improving dairy feed efficiency, sustainability, and profitability by impacting farmer's breeding and culling decisions [abstract]. International Committee on Animal Recording(ICAR), April 26-30, Leeuwarden, The Netherlands. Abstract 8.6.

Improving the model for genetic evaluation of calving traits in the US Holstein and Brown Swiss - (Abstract Only)

Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the tropically adapted Australian beef cattle population - (Peer Reviewed Journal)
Mueller, M.L., Cole, J.B., Connors, N.K., Johnston, D.J., Randhawa, I.A.S., Van Eenennaam, A.L. 2021. Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the tropically adapted Australian beef cattle population. Frontiers in Genetics. 12:593154. https://doi.org/10.3389/fgene.2021.593154.

Invited review: The future of selection decisions and breeding programs: What are we breeding for, and who decides? - (Review Article)
Cole, J.B., Durr, J.W., Nicolazzi, E.L. 2021. Invited review: The future of selection decisions and breeding programs: What are we breeding for, and who decides? Journal of Dairy Science. 104(5):5111–5124. https://doi.org/10.3168/jds.2020-19777.

Genomic predictions for yield traits in US Holsteins with unknown parent groups - (Peer Reviewed Journal)
Cesarani, A., Masuda, Y., Tsuruta, S., Nicolazzi, E.L., Van Raden, P.M., Lourenco, D., Misztal, I. 2021. Genomic predictions for yield traits in US Holsteins with unknown parent groups. Journal of Dairy Science. 104(5):5843–5853. https://doi.org/10.3168/jds.2020-19789.

Haplotype tests for economically important traits of dairy cattle - (Government Publication)
Cole, J.B., Van Raden, P.M., Null, D.J., Hutchison, J.L., Hubbard, S.M. 2020. Haplotype tests for economically important traits of dairy cattle. AIP Research Report. GENOMICS5 (12-20).

Marker selection and genomic prediction of economically important traits multiple traits using imputed high-density genotypes for 5 breeds of dairy cattle - (Peer Reviewed Journal)

Major quantitative trait loci influencing milk production and conformation traits in Guernsey dairy cattle detected on Bos taurus autosome 19 - (Peer Reviewed Journal)
Li, B., Van Raden, P.M., Null, D.J., O'Connell, J.R., Cole, J.B. 2021. Major quantitative trait loci influencing milk production and conformation traits in Guernsey dairy cattle detected on Bos taurus autosome 19. Journal of Dairy Science. 104(1):550–560. https://doi.org/10.3168/jds.2020-18766.

Investigating conception rate for beef service sires bred to dairy cows and heifers - (Peer Reviewed Journal)
McWhorter, T.M., Hutchison, J.L., Norman, H.D., Cole, J.B., Fok, G.C., Lourenco, D.A.L., Van Raden, P.M. 2020. Investigating conception rate for beef service sires bred to dairy cows and heifers. Journal of Dairy Science. 103(11):10374–10382. https://doi.org/10.3168/jds.2020-18399.

What’s changing about the calving traits? - (Trade Journal)

What’s changing about the calving traits? - (Trade Journal)

What is going on with calving ease? - (Other)
Eaglen, S.A., Cole, J.B. 2020. What is going on with calving ease?. CDCB Connection newsletter. May 2020. Available: https://mailchi.mp/uscdcb.com/cdcb-connection-february-1376910?e=46d6707343.

Scaling up community-based breeding programmes via multi-stakeholder collaboration - (Peer Reviewed Journal)
Kaumbata, W., Nakimbugwe, H.N., Haile, A., Banda, L.J., Meszaros, G., Gondwe, T.N., Woodward Greene, M.J., Rosen, B.D., Van Tassell, C.P., Solkner, J., Wurzinger, M. 2020. Scaling up community-based breeding programmes via multi-stakeholder collaboration. Journal of Agriculture and Rural Development in the Tropics and Subtropics. 12(1):99-112. https://doi.org/10.17170/kobra-202005281298.

Haplotype- and sequence-based identification of a deletion associated with early embryonic loss in Holstein cattle and functional validation using CRISPR-Cas9 knockouts - (Abstract Only)

Symposium review: Development, implementation, and future perspectives of health evaluations in the United States - (Peer Reviewed Journal)
Parker Gaddis, K.L., Van Raden, P.M., Cole, J.B., Norman, H.D., Nicolazzi, E., Durr, J.W. 2020. Symposium review: Development, implementation, and future perspectives of health evaluations in the United States. Journal of Dairy Science. 103(6):5354-5365. https://doi.org/10.3168/jds.2019-17687.

Symposium review: Exploiting homozygosity in the era of genomics-- Selection, inbreeding, and genomic mating programs - (Peer Reviewed Journal)
Maltecca, C., Tiezzi, F., Cole, J.B., Baes, C. 2020. Symposium review: Exploiting homozygosity in the era of genomics-- Selection, inbreeding, and genomic mating programs. Journal of Dairy Science. 103(6):5302-5313. https://doi.org/10.3168/jds.2019-17846.

Gamevar.f90: A software package for calculating individual gametic diversity - (Peer Reviewed Journal)
Santos, D.J., Cole, J.B., Liu, G., Van Raden, P.M., Ma, L. 2020. Gamevar.f90: A software package for calculating individual gametic diversity. BMC Bioinformatics. 21:100. https://doi.org/10.1186/s12859-020-3417-x.

The future of phenomics in dairy cattle breeding - (Review Article)
Cole, J.B., Eaglen, S.A.E., Maltecca, C., Mulder, H.A., Pryce, J.E. 2020. The future of phenomics in dairy cattle breeding. Animal Frontiers. 10(2):37-44. https://doi.org/10.1093/af/vfaa007.

The new USDA blueprint for animal genome research 2018–2027: A quantitative geneticist's perspective - (Other)

Identification, validation, and management of Mendelian traits in livestock breeding programs - (Abstract Only)
Cole, J.B. 2020. Identification, validation, and management of Mendelian traits in livestock breeding programs [abstract]. Plant and Animal Genome Conference. San Diego, California, January 11-15, 2020, W216.

Symposium review: How to implement genomic selection - (Peer Reviewed Journal)
Van Raden, P.M. 2020. Symposium review: How to implement genomic selection. Journal of Dairy Science. 103(6):5291-5301. https://doi.org/10.3168/jds.2019-17684.

Genomic prediction of residual feed intake in US Holstein dairy cattle - (Peer Reviewed Journal)
Li, B., Van Raden, P.M., Guduk, E., O'Connell, J.R., Null, D.J., Connor, E.E., VandeHaar, M.J., Tempelman, R.J., Weigel, K.A., Cole, J.B. 2020. Genomic prediction of residual feed intake in US Holstein dairy cattle. Journal of Dairy Science. 103(3):2477-2486. https://doi.org/10.3168/jds.2019-17332.

Using the ARS-UCD1.2 reference genome in U.S. evaluations - (Proceedings)
Null, D.J., Van Raden, P.M., Rosen, B.D., O'Connell, J.R., Bickhart, D.M. 2019. Using the ARS-UCD1.2 reference genome in U.S. evaluations. Interbull Bulletin. 55:30-34.

Enhancements to U.S. genetic and genomic evaluations in 2018 and 2019 - (Proceedings)
Nicolazzi, E., Bacheller, L.R., Fok, G.C., Parker Gaddis, K.L., Jensen, L., Megonigal, Jr, J.H., Norman, H.D., Null, D.J., Walton, L.M., Wiggans, G.R., Cole, J.B., Durr, J.W., Van Raden, P.M. 2019. Enhancements to U.S. genetic and genomic evaluations in 2018 and 2019. Interbull Bulletin. 55:26-29.

Extending genomic evaluation to crossbred dairy cattle – US implementation - (Proceedings)
Wiggans, G.R., Van Raden, P.M., Nicolazzi, E., Tooker, M.E., Megonigal, Jr, J.H., Walton, L.M. 2019. Extending genomic evaluation to crossbred dairy cattle – US implementation. Interbull Bulletin. 55:46-49.

A vision for development and utilization of high-throughput phenotyping and big data analytics in livestock - (Peer Reviewed Journal)
Koltes, J.E., Cole, J.B., Clemmens, R., Dilger, R.N., Kramer, L.M., Lunney, J.K., Mccue, M.E., Mckay, S., Mateescu, R., Murdoch, B.M., Reuter, R., Rexroad III, C.E., Rosa, G.J.M., Serao, N.V.L., White, S.N., Woodward Greene, M.J., Worku, M., Zhang, H., Reecy, J.M., editors. 2019. A vision for development and utilization of high-throughput phenotyping and big data analytics in livestock. Frontiers in Genetics. 10:1197. https://doi.org/10.3389/fgene.2019.01197.

Discovering ancestors and connecting relatives in large genomic databases - (Peer Reviewed Journal)
Nani, J.P., Bacheller, L.R., Cole, J.B., Van Raden, P.M. 2020. Discovering ancestors and connecting relatives in large genomic databases. Journal of Dairy Science. 103(2):1729-1734. https://doi.org/10.3168/jds.2019-17580.

Genomic predictions for crossbred dairy cattle - (Peer Reviewed Journal)
Van Raden, P.M., Tooker, M.E., Chud, T.C.S., Norman, H.D., Megonigal, Jr, J.H., Haagen, I.W., Wiggans, G.R. 2020. Genomic predictions for crossbred dairy cattle. Journal of Dairy Science. 103(2):1620–1631. https://doi.org/10.3168/jds.2019-16634.

High-density genome-wide association study for residual feed intake in Holstein dairy cattle - (Peer Reviewed Journal)
Li, B., Fang, L., Null, D.J., Hutchison, J.L., Connor, E.E., Van Raden, P.M., Cole, J.B. 2019. High-density genome-wide association study for residual feed intake in Holstein dairy cattle. Journal of Dairy Science. 102(12):11067-11080. https://doi.org/10.3168/jds.2019-16645.

Alternative SNP weighting for single-step genomic best linear unbiased predictor evaluation of stature in US Holsteins in the presence of selected sequence variants - (Peer Reviewed Journal)
Fragomeni, B.O., Lourenco, D.A.L., Legarra, A., Van Raden, P.M., Misztal, I. 2019. Alternative SNP weighting for single-step genomic best linear unbiased predictor evaluation of stature in US Holsteins in the presence of selected sequence variants. Journal of Dairy Science. 102(11):10012–10019. https://doi.org/10.3168/jds.2019-16262.

Ranking sires using genetic selection indices based on financial investment methods versus lifetime net merit - (Peer Reviewed Journal)
Schmitt, M.R., Van Raden, P.M., De Vries, A. 2019. Ranking sires using genetic selection indices based on financial investment methods versus lifetime net merit. Journal of Dairy Science. 102(10):9060-9075. https://doi.org/10.3168/jds.2018-16081.

Short communication: Phenotypic and genetic effects of the polled haplotype on yield, longevity, and fertility in US Brown Swiss, Holstein, and Jersey cattle - (Peer Reviewed Journal)
Cole, J.B., Null, D.J. 2019. Short communication: Phenotypic and genetic effects of the polled haplotype on yield, longevity, and fertility in US Brown Swiss, Holstein, and Jersey cattle. Journal of Dairy Science. 102(9):8247–8250. https://doi.org/10.3168/jds.2019-16530.

Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls - (Peer Reviewed Journal)
Jiang, J., Cole, J.B., Freebern, E., Da, Y., Van Raden, P.M., Ma, L. 2019. Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls. Communications Biology. 2:212. https://doi.org/10.1038/s42003-019-0454-y.

A large-scale genome-wide association study in U.S. Holstein cattle - (Peer Reviewed Journal)
Jiang, J., Ma, L., Prakapenka, D., Van Raden, P.M., Cole, J.B., Da, Y. 2019. A large-scale genome-wide association study in U.S. Holstein cattle. Frontiers in Genetics. 10:412. https://doi.org/10.3389/fgene.2019.00412.

Genomic prediction and marker selection using high-density genotypes from 5 dairy breeds - (Abstract Only)
Van Raden, P.M., Null, D.J., O'Connell, J.R., Cole, J.B., Li, B. 2019. Genomic prediction and marker selection using high-density genotypes from 5 dairy breeds . Journal of Dairy Science. 102(Suppl. 1):400(abstr. 471).

Alternative input parameters for Wood’s curve within Best Prediction used by USDA-AGIL for genetic evaluation of production traits in the United States - (Abstract Only)
Houdek, E.S., Heins, B.J., Hazel, A.R., Hansen, L.B., Cole, J.B. 2019. Alternative input parameters for Wood’s curve within Best Prediction used by USDA-AGIL for genetic evaluation of production traits in the United States. Journal of Dairy Science. 102(Suppl. 1):399(abstr. 468).

Approximate generalized least squares method for large-scale genome-wide association study - (Abstract Only)
Ma, L., Jiang, J., Prakapenka, D., Cole, J.B., Da, Y. 2019. Approximate generalized least squares method for large-scale genome-wide association study. Journal of Dairy Science. 102(Suppl. 1):30(abstr. M64).

How to implement genomic selection - (Abstract Only)
Van Raden, P.M. 2019. How to implement genomic selection. Journal of Dairy Science. 102(Suppl. 1):98(abstr. 66).

Genomic predictions using more markers and gene tests - (Abstract Only)
Wiggans, G.R., Van Raden, P.M., Null, D.J., Cole, J.B. 2019. Genomic predictions using more markers and gene tests. Journal of Dairy Science. 102(Suppl. 1):397(abstr. 462).

Development, implementation, and future perspectives of health evaluations in the United States - (Abstract Only)
Parker Gaddis, K.L., Cole, J.B., Van Raden, P.M., Niccolazi, E., Durr, J.W. 2019. Development, implementation, and future perspectives of health evaluations in the United States [abstract]. Journal of Dairy Science. 102(Suppl. 1):141.

Variance of gametic diversity and its use in selection programs - (Peer Reviewed Journal)
Santos, D.J., Cole, J.B., Lawlor, T.J., Van Raden, P.M., Tonhati, H., Ma, L. 2019. Variance of gametic diversity and its use in selection programs. Journal of Dairy Science. 102(6):5279-5294. https://doi.org/10.3168/jds.2018-15971.

Advances in dairy cattle breeding to improve resistance to mastitis - (Book / Chapter)
Cole, J.B. 2019. Advances in dairy cattle breeding to improve resistance to mastitis. In: van der Werf, J., Pryce, J. , editors. Advances in Breeding of Dairy Cattle. Sawston, Cambridge, UK: Burleigh Dodds Science Publishing Ltd. p. 229–253. https://doi.org/10.19103/AS.2019.0058.13.

Estimating the impact of the deleterious recessive haplotypes AH1 and AH2 on reproduction performance of Ayrshire cattle - (Peer Reviewed Journal)
Guarini, A., Sargolzaei, M., Brito, L., Kroezen, V., Lourenco, D., Baes, C., Miglior, F., Cole, J.B., Schenkel, F. 2019. Estimating the impact of the deleterious recessive haplotypes AH1 and AH2 on reproduction performance of Ayrshire cattle. Journal of Dairy Science. 102(6):5315-5322. https://doi.org/10.3168/jds.2018-15366.

Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle - (Peer Reviewed Journal)
Fang, L., Jiang, J., Li, B., Zhou, Y., Freebern, E., Van Raden, P.M., Cole, J.B., Liu, G., Ma, L. 2019. Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle. Communications Biology. 2:100. https://doi.org/10.1038/s42003-019-0341-6.

Promotion of alleles by genome engineering - (Review Article)
Cole, J.B. 2019. Promotion of alleles by genome engineering. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. 14(015):1-15.

Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the US dairy cattle population - (Peer Reviewed Journal)
Mueller, M.L., Cole, J.B., Sonstegard, T.S., Van Eenennaam, A.L. 2019. Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the US dairy cattle population. Journal of Dairy Science. 102(5):4215-4226. https://doi.org/10.3168/jds.2018-15892.

Genome changes due to artificial selection in U.S. Holstein cattle - (Peer Reviewed Journal)
Ma, L., Sonstegard, T.S., Cole, J.B., Van Tassell, C.P., Wiggans, G.R., Crooker, B.A., Tan, C., Prakapenka, D., Liu, G., Da, Y. 2019. Genome changes due to artificial selection in U.S. Holstein cattle. BMC Genomics. 20:128. https://doi.org/10.1186/s12864-019-5459-x.

Utilizing variance of gametic diversity in dairy cattle improvement - (Abstract Only)
Santos, D.J., Cole, J.B., Van Raden, P.M., Lawlor, T.J., Ma, L. 2019. Utilizing variance of gametic diversity in dairy cattle improvement [abstract]. Plant and Animal Genome. PE0340.

Haplotype tests for economically important traits of dairy cattle - (Government Publication)
Van Raden, P.M., Cole, J.B., Null, D.J., Hutchison, J.L., Hubbard, S.M. 2018. Haplotype tests for economically important traits of dairy cattle. AIPL Research Reports. GENOMIC4 (12-18).

Modeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasets - (Peer Reviewed Journal)
Bradford, H.L., Masuda, Y., Cole, J.B., Misztal, I., Van Raden, P.M. 2019. Modeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasets. Journal of Dairy Science. 102(3):2308–2318. https://doi.org/10.3168/jds.2018-15419.

Modeling missing pedigree in single-step genomic BLUP - (Peer Reviewed Journal)
Bradford, H.L., Masuda, Y., Van Raden, P.M., Legarra, A., Misztal, I. 2019. Modeling missing pedigree in single-step genomic BLUP. Journal of Dairy Science. 102(3):2336-2346. https://doi.org/10.3168/jds.2018-15434.

Pedigree verification and parentage assignment using genomic information in the Mexican Holstein population - (Peer Reviewed Journal)
Garcia-Ruiz, A., Wiggans, G.R., Ruiz-Lopez, F.J. 2019. Pedigree verification and parentage assignment using genomic information in the Mexican Holstein population. Journal of Dairy Science. 102(2):1806–1810. https://doi.org/10.3168/jds.2018-15076.

Genome-wide association study for milk production traits in a Brazilian Holstein population - (Peer Reviewed Journal)
De Souza Iung, L.H., Petrini, J., Ramirez-Diaz, J., Salvian, M., Rovadoscki, G.A., Pilonetto, F., Dauria, B.D., Machado, P.F., Coutinho, L.L., Wiggans, G.R., Mourao, G.V. 2019. Genome-wide association study for milk production traits in a Brazilian Holstein population. Journal of Dairy Science. 102(6):5305-5314. https://doi.org/10.3168/jds.2018-14811.

Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the tropically adapted Australian beef cattle population - (Proceedings)

Symposium review: Genetics, genome-wide association study, and genetic improvement of dairy fertility traits - (Review Article)
Ma, L., Cole, J.B., Da, Y., Van Raden, P.M. 2019. Symposium review: Genetics, genome-wide association study, and genetic improvement of dairy fertility traits. Journal of Dairy Science. 102(4):3735-3743. https://doi.org/10.3168/jds.2018-15269.

Genetic and nongenetic profiling of milk pregnancy-associated glycoproteins in Holstein cattle - (Peer Reviewed Journal)
Santos, D.A., Cole, J.B., Null, D.J., Byrem, T.M., Ma, L. 2018. Genetic and nongenetic profiling of milk pregnancy-associated glycoproteins in Holstein cattle. Journal of Dairy Science. 101(11):9987-10000. https://doi.org/10.3168/jds.2018-14682.

10 years of revolution: Paul VanRaden looks at the evolution of genomics - (Popular Publication)
Savage, D. 2018. 10 years of revolution: Paul VanRaden looks at the evolution of genomics. Holstein International. 25(8):16–17.

Possibilities in an age of genomics: The future of the breeding index - (Other)

Net merit as a measure of lifetime profit: 2018 revision - (Government Publication)
Van Raden, P.M., Cole, J.B., Parker Gaddis, K.L. 2018. Net merit as a measure of lifetime profit: 2018 revision. AIPL Research Reports. NM$7 (5-18).

Identification of genomic regions associated with resistance to clinical mastitis in US Holstein cattle - (Abstract Only)

Simulation of introgression of the polled allele into the Jersey breed via conventional breeding versus gene editing - (Proceedings)
Mueller, M.L., Cole, J.B., Sonstegard, T.S., Van Eenennaam, A.L. 2018. Simulation of introgression of the polled allele into the Jersey breed via conventional breeding versus gene editing. Translational Animal Science. 2(Suppl. 1):S57–S60. 10.1093/tas/txy054.

Identification of genomic regions associated with resistance to clinical mastitis in US Holstein cattle - (Abstract Only)
Cole, J.B., Parker Gaddis, K.L., Willard, C., Null, D.J., Maltecca, C., Clay, J.S. 2018. Identification of genomic regions associated with resistance to clinical mastitis in US Holstein cattle. Journal of Dairy Science. 101(Suppl. 2):138(abstr. 58).

Genetic cues from fertilization to pregnancy establishment - (Abstract Only)
Ortega, M.S., Cole, J.B., Spencer, T.E., Hansen, P.J. 2018. Genetic cues from fertilization to pregnancy establishment. Journal of Dairy Science. 101 (Suppl. 2):328(abstr. 278).

Methods to compute reliabilities for genomic predictions of feed intake - (Abstract Only)
Van Raden, P.M., Hutchison, J.L. 2018. Methods to compute reliabilities for genomic predictions of feed intake [abstract]. Journal of Dairy Science. 101(Suppl. 2):370-371(abstr. 392).

Lifetime Net Merit vs. annualized net present value as measures of profitability of selection - (Abstract Only)
Schmitt, M.R., Van Raden, P.M., De Vries, A. 2018. Lifetime Net Merit vs. annualized net present value as measures of profitability of selection. Journal of Dairy Science. 101 (Suppl. 2):182(abstr. 173).

Genomic predictability of single-step GBLUP for production traits in US Holstein - (Abstract Only)
Masuda, Y., Misztal, I.M., Van Raden, P.M., Lawlor, T.J. 2018. Genomic predictability of single-step GBLUP for production traits in US Holstein. Journal of Dairy Science. 101 (Suppl. 2):182(abstr. 171).

Modelling uncertain paternity to address differential pedigree accuracy - (Abstract Only)
Bradford, H.L., Masuda, Y., Cole, J.B., Misztal, I., Van Raden, P.M. 2018. Modelling uncertain paternity to address differential pedigree accuracy [abstract]. Journal of Dairy Science. 101(Suppl. 2):181-182(abstr. 170).

Big data genomic investigation of dairy fertility and related traits with imputed sequences of 24K Holstein bulls - (Abstract Only)
Jiang, J., Van Raden, P.M., Cole, J.B., Da, Y., Ma, L. 2018. Big data genomic investigation of dairy fertility and related traits with imputed sequences of 24K Holstein bulls [abstract]. Journal of Dairy Science. 101(Suppl. 2):328(abstr. 277).

AGIL research report, January 2018 - (Other)

Multitrait modeling of first vs. later parities for US yield, somatic cell score, and fertility traits - (Abstract Only)
Van Raden, P.M., Tooker, M.E. 2018. Multitrait modeling of first vs. later parities for US yield, somatic cell score, and fertility traits. Journal of Dairy Science. 101 (Suppl. 2):139(abstr. 62).

Potential benefits from using a new reference map in genomic prediction - (Abstract Only)
Null, D.J., Van Raden, P.M., Bickhart, D.M., Cole, J.B., O'Connell, J.R., Rosen, B.D. 2018. Potential benefits from using a new reference map in genomic prediction. Journal of Dairy Science. 101 (Suppl. 2):181-182(abstr. 168).

Validating genomic reliabilities and gains from phenotypic updates - (Proceedings)
Van Raden, P.M., O'Connell, J.R. 2018. Validating genomic reliabilities and gains from phenotypic updates. Interbull Bulletin. 53:22-26.

Methods for discovering and validating relationships among genotyped animals - (Proceedings)
Wiggans, G.R., Van Raden, P.M., Bacheller, L.R. 2018. Methods for discovering and validating relationships among genotyped animals. Interbull Bulletin. 53:27-30.

The research mission of the Animal Improvement Program in the Animal Genomics and Improvement Laboratory - (Other)

Genetic improvement programs for U.S. dairy cattle - (Other)

GWAS and fine-mapping of 35 production, reproduction and conformation traits with imputed sequences of 27K Holstein bulls - (Abstract Only)
Jiang, J., Van Raden, P.M., Cole, J.B., Da, Y., Ma, L. 2017. GWAS and fine-mapping of 35 production, reproduction and conformation traits with imputed sequences of 27K Holstein bulls. Plant and Animal Genome Conference. San Diego, CA, Jan. 13-17. abstr. P0484.

Approximating genomic reliabilities for national genomic evaluation - (Proceedings)
Liu, Z., Van Raden, P.M., Lidauer, M., Calus, M., Benhajali, H., Jorjani, H., Ducrocq, V. 2017. Approximating genomic reliabilities for national genomic evaluation. Interbull Bulletin. 51:75-85.

Large-scale GWAS reveals reason for the DGAT1 significance and identifies new SNP effects in Holstein cattle - (Abstract Only)
Ma, L., Jiang, J., Prakapenka, D., Tooker, M.E., Van Raden, P.M., Cole, J.B., Da, Y. 2017. Large-scale GWAS reveals reason for the DGAT1 significance and identifies new SNP effects in Holstein cattle. Livestock High-Throughput Phenotyping and Big Data Analytics, Beltsville, MD. Nov. 13-14.

How selection for better health impacts dairy profitability - (Other)

How selection for better health impacts dairy profitability - (Other)