Research Project: Increasing Accuracy of Genomic Prediction, Developing Algorithms, Selecting Markers, and Evaluating New Traits to Improve Dairy Cattle

Location: Animal Genomics and Improvement Laboratory

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

Use of intrauterine dextrose as an alternative to systemic antibiotics for treatment of clinical metritis in dairy cattle: a microbiome perspective - (Peer Reviewed Journal)

Investigating alternative strategies to evaluate the feasibility of genomic selection for heat tolerance in US Holstein cattle - (Abstract Only)

Exploring test-day production yields for US Holstein cows in Texas state for heat-tolerance genomic predictions - (Abstract Only)

Association of individual cow milk fatty acid proportion and variance with milk production - (Proceedings)

All-breed single-step GBLUP evaluations for fertility traits in U.S. dairy cattle - (Peer Reviewed Journal)

Short communication: Artificially reared ewes cannot be distinguished from natural reared ewes based on observed maternal behavior or lamb weaning weights - (Peer Reviewed Journal)

A million-cow genome-wide association study of productive life in U.S. Holstein cows - (Peer Reviewed Journal)
Zuoxiang, L., Dzianis, P., Zaabza, H.B., Van Raden, P.M., Van Tassell, C.P., Da, Y. 2024. A million-cow genome-wide association study of productive life in U.S. Holstein cows. Genetic Selection Evolution. 56:67. https://doi.org/10.1186/s12711-024-00935-1.

Validating genomic predictions for economic traits in purebred U.S. dairy heifers - (Peer Reviewed Journal)
Toghiani, S., Van Raden, P.M., Null, D.J., Miles, A.M., Van Tassell, C.P. 2024. Validating genomic predictions for economic traits in purebred U.S. dairy heifers. Journal of Dairy Science. https://doi.org/10.3168/jds.2024-25267.

Effect of germplasm exchange strategies on genetic gain, homozygosity, and genetic diversity in dairy stud populations: A simulation study - (Peer Reviewed Journal)

Analysis of factors affecting daily milk yields: an initial case study in an automatic thrice-milking farm - (Proceedings)
Wu, X., Caputo, M.J., Wiggans, G.R., Norman, H.D., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Sievert, S., Mattison, J., Burchard, J., Durr, J.W. 2024. Analysis of factors affecting daily milk yields: an initial case study in an automatic thrice-milking farm. Interbull Bulletin. 60:34-41.

Breeding programs compared across countries, continents, and breeds - (Proceedings)
Van Raden, P.M., McWhorter, T.M., Carrillo, J.A., Mota, R.R. 2024. Breeding programs compared across countries, continents, and breeds. Interbull Bulletin. 60:29-33.

Technical options for all-breed Single Step GBLUP for US dairy cattle - (Proceedings)
Legarra, A., Bermann, M., Van Raden, P.M., Nicolazzi, E., Mota, R., Tabet, J., Lourenco, D.L., Misztal, I. 2024. Technical options for all-breed Single Step GBLUP for US dairy cattle. Interbull Bulletin. 60:143-147.

Guidelines for approximating genomic reliabilities of the single-step genomic model - (Proceedings)
Liu, Z., Stranden, I., Vandenplas, J., Eding, H., Lidauer, M., Haugaard, K., Van Raden, P.M. 2024. Guidelines for approximating genomic reliabilities of the single-step genomic model. Interbull Bulletin. 60:148-160.

Genomic validation software: USA update including truncated MACE - (Proceedings)
Mota, R., Sullivan, P., Nicolazzi, E., McWhorter, T.M., Legarra, A., Van Raden, P.M. 2024. Genomic validation software: USA update including truncated MACE. Interbull Bulletin. 60:200-206.

Multibreed single-step genomic best linear unbiased predictor evaluations for fertility traits in US dairy cattle - (Abstract Only)
Tabet, J., Lourenco, D., Bermann, M., Misztal, I., Van Raden, P.M., Legarra, A. 2024. Multibreed single-step genomic best linear unbiased predictor evaluations for fertility traits in US dairy cattle [abstract]. Journal of Dairy Science. 107(Suppl. 1):130(abstr. 1516).

Shifting paradigms in daily milk yield correction factors: the DeLorenzo-Wiggans method revisited - (Abstract Only)
Wu, X., Caputo, M.J., Wiggans, G.R., Norman, H.D., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Burchard, J., Durr, J. 2024. Shifting paradigms in daily milk yield correction factors: The DeLorenzo-Wiggans method revisited [abstract]. Journal of Dairy Science. 107(Suppl. 1):18-19(abstr. 1142).

Large-sample genome-wide association study of resistance to retained placenta in U.S. Holstein cows - (Peer Reviewed Journal)
Prakapenka, D., Liang, Z., Zaabza, H.B., Van Raden, P.M., Van Tassell, C.P., Da, Y. 2024. Large-sample genome-wide association study of resistance to retained placenta in U.S. Holstein cows. International Journal of Molecular Sciences. 25(10):5551. https://doi.org/10.3390/ijms25105551.

Dry matter intake in US Holstein cows: exploring the genomic and phenotypic impact of milk components and body weight composite - (Peer Reviewed Journal)
Toghiani, S., Van Raden, P.M., VandeHaar, M.J., Baldwin, R.L., Weigel, K., White, H., Penagaricano, F., Koltes, J.E., Santos, J.P., Parker Gaddis, K.L., Tempelman, R.J. 2024. Dry matter intake in US Holstein cows: Exploring the genomic and phenotypic impact of milk components and body weight composite. Journal of Dairy Science. 107(9):7009–7021. https://doi.org/10.3168/jds.2023-24296.

Effects of a direct-fed microbial inclusion on the gastrointestinal and environmental microbiomes of turkey toms - (Abstract Only)

Comprehensive reporting of the resistome utilizing real-time sequencing technology - (Abstract Only)

Genetic and genomic evaluations of milking speed and duration from automated milk recording - (Abstract Only)
O'Connell, J.R., Miles, A.M., Hutchison, J.L., Toghiani, S., Fourdraine, R.H., Van Raden, P.M. 2024. Genetic and genomic evaluations of milking speed and duration from automated milk recording [abstract]. Journal of Dairy Science. 107(Suppl. 1):41(abstr. 1197).

Improved tracking of recent mutations within common haplotypes causing cholesterol deficiency, muscle weakness, and BLIRD - (Abstract Only)
Null, D.J., Van Raden, P.M., Al-Khudhair, A.S., Nicolazzi, E.L. 2024. Improved tracking of recent mutations within common haplotypes causing cholesterol deficiency, muscle weakness, and BLIRD [abstract]. Journal of Dairy Science. 107(Suppl. 1):409(abstr. 2655).

Comparison of genomic merit, pedigree completeness, inbreeding, and relationships of genotyped animals across continents - (Abstract Only)
Van Raden, P.M. 2024. Comparison of genomic merit, pedigree completeness, inbreeding, and relationships of genotyped animals across continents [abstract]. Journal of Dairy Science. 107(Suppl. 1):129(abstr. 1512).

Validation of genomic prediction for economic traits in heifers across five U.S. dairy breeds - (Abstract Only)
Toghiani, S., Van Raden, P.M., Null, D.J., Miles, A.M., Van Tassell, C.P. 2024. Validation of genomic prediction for economic traits in heifers across five U.S. dairy breeds [abstract]. Journal of Dairy Science. 107(Suppl. 1):129(abstr. 1513).

Six direct health traits for the United States: Updated variance component estimates and implementation of variance adjusted weights - (Abstract Only)
McWhorter, T.M., Parker Gaddis, K.L., Nicolazzi, E., Van Raden, P.M. 2024. Six direct health traits for the United States: Updated variance component estimates and implementation of variance adjusted weights [abstract]. Journal of Dairy Science. 107(Suppl. 1):97(abstr. 1378).

Association of individual cow milk fatty acids and milk performance - (Abstract Only)
Caputo, M.J., Miles, A.M., Mattison, J., Wu, X., Baldwin, R.L., Burchard, J., Durr, J. 2024. Association of individual cow milk fatty acids and milk performance [abstract]. Journal of Dairy Science. 107(Suppl. 1):428(abstr. 2706).

The value of a national evaluation system in promoting dairy sustainability - (Abstract Only)
Miles, A.M., Parker Gaddis, K.L., Fourdraine, R.H. 2024. The value of a national evaluation system in promoting dairy sustainability [abstract]. Journal of Dairy Science. 107(Suppl. 1):70(abstr. 1312).

Alterations of rumen and fecal microbiome in growing beef and dairy steers fed rumen protected Capsicum oleoresin - (Peer Reviewed Journal)
Bierly, S.A., Van Syoc, E., Westphalen, M.F., Miles, A.M., Gaeta, N.C., Felix, T.L., Hristov, A.N., Ganda, E.K. 2024. Alterations of rumen and fecal microbiome in growing beef and dairy steers fed rumen protected Capsicum oleoresin. Journal of Animal Science. https://doi.org/10.1093/jas/skae014.

A million-cow validation of a chromosome 14 region interacting with all chromosomes for fat percentage in U.S. Holstein cows - (Peer Reviewed Journal)
Prakapenka, D., Liang, Z., Zaabza, H.B., Jiang, J., Ma, L., Van Raden, P.M., Van Tassell, C.P., Da, Y. 2024. A million-cow validation of a chromosome 14 region interacting with all chromosomes for fat percentage in U.S. Holstein cows. International Journal of Molecular Sciences. 25:674. https://doi.org/10.3390/ijms25010674.

New mutation within a common haplotype is associated with calf muscle weakness in Holsteins - (Peer Reviewed Journal)
Al-Khudhair, A.S., Van Raden, P.M., Null, D.J., Neupane, M., Mcclure, M.C., Dechow, C.D. 2024. New mutation within a common haplotype is associated with calf muscle weakness in Holsteins. Journal of Dairy Science. 107(6):3768-3779. https://doi.org/10.3168/jds.2023-24121.

Updating test-day milk yield factors for use in genetic evaluations and dairy production systems: A comprehensive review - (Peer Reviewed Journal)
Wu, X.-L., Wiggans, G.R., Norman, H.D., Caputo, M., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Sievert, S., Mattison, J., Burchard, J., Durr, J. 2023. Updating test-day milk yield factors for use in genetic evaluations and dairy production systems: A comprehensive review. Frontiers in Genetics. 14:1298114. https://doi.org/10.3389/fgene.2023.1298114.

Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle - (Peer Reviewed Journal)
Lozada Soto, E., Parker Gaddis, K., Tiezzi, F., Jiang, J., Ma, L., Toghiani, S., Van Raden, P.M., Maltecca, C. 2024. Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle. Journal of Dairy Science. 107(5):3032-3046. https://doi.org/10.3168/jds.2023-23909.

Single-step genomic predictions for crossbred Holstein and Jersey cows in the United States - (Peer Reviewed Journal)
Cesarani, A., Lourenco, D., Bermann, M., Nicolazzi, E., Van Raden, P.M., Misztal, I. 2024. Single-step genomic predictions for crossbred Holstein and Jersey cows in the United States. Journal of Dairy Science Communications. 5(2):124-128. https://doi.org/10.3168/jdsc.2023-0399.

System and biological effects on quantitative milking speed phenotypes from inline milk meters - (Proceedings)
Miles, A.M., Fourdraine, R., Hutchison, J.L., Sievert, S., Gaddis, K., Bewley, J., Eaglen, S., Weiker, J., Durr, J. 2023. System and biological effects on quantitative milking speed phenotypes from inline milk meters. In: Proceedings of the International Committee on Animal Recording (ICAR), May 21-26, 2023, Toledo, Spain. p. 155-159.

Effect of modelling unknown parent groups and metafounders on the historical genetic trend of fertility traits - (Proceedings)
Legarra, A., Van Raden, P.M. 2023. Effect of modelling unknown parent groups and metafounders on the historical genetic trend of fertility traits. Interbull Bulletin. 59:11-14.

Quality and value of imputing gene tests for all animals - (Proceedings)
O'Connell, J.R., Van Raden, P.M. 2023. Quality and value of imputing gene tests for all animals. Interbull Bulletin. 59:51-55.

Inheritance of a new mutation affecting muscle weakness within a common haplotype in Holsteins - (Proceedings)
Al-Khudhair, A.S., Nicolazzi, E.L., Van Raden, P.M., Null, D.J., Neupane, M., Dechow, C.D. 2023. Inheritance of a new mutation affecting muscle weakness within a common haplotype in Holsteins. Interbull Bulletin. 59:202-206.

Modeling identical twins and clones in genetic evaluations - (Proceedings)
Van Raden, P.M., Fok, G.C., Toghiani, S., Nicolazzi, E.L. 2023. Modeling identical twins and clones in genetic evaluations. Interbull Bulletin. 59:63-68.

International evaluations for clinical mastitis in Brown Swiss - (Proceedings)
Mota, R.R., Parker Gaddis, K.L., Van Raden, P.M., Mcwhorter, T.M., Nicolazzi, E. 2023. International evaluations for clinical mastitis in Brown Swiss. Interbull Bulletin. 59:182-186.

Evaluating fertility in the wake of embryo transfer - (Trade Journal)
Miles, A.M. 2023. Evaluating fertility in the wake of embryo transfer. Progressive Dairyman. https://www.agproud.com/articles/58397-evaluating-fertility-in-the-wake-of-embryo-transfer.

Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle - (Peer Reviewed Journal)
Schmidt, P., Mota, L., Fonseca, L., Dos Santos Silva, D., Frezzarim, G., Arikawa, L., De Abreu Santos, D., Magalhaes, A., Cole, J., Carvalheiro, R., De Oliveira, H., Null, D.J., Van Raden, P.M., Ma, L., De Albuquerque, L. 2023. Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle. Scientific Reports. 13:10399. https://doi.org/10.1038/s41598-023-37586-z.

A million-cow genome-wide association study of three fertility traits in U.S. Holstein cows - (Peer Reviewed Journal)
Liang, Z., Prakapenka, D., Van Raden, P.M., Jiang, J., Ma, L., Da, Y. 2023. A million-cow genome-wide association study of three fertility traits in U.S. Holstein cows. International Journal of Molecular Sciences. 24(13):10496. https://doi.org/10.3390/ijms241310496.

Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle - (Peer Reviewed Journal)
Deru, V., Tiezzi, F., Van Raden, P.M., Lozada-Soto, E.L., Toghiani, S., Maltecca, C. 2024. Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle. Journal of Dairy Science. 107(1):398-411. https://doi.org/10.3168/jds.2023-23250.

Estimating test day milk yields by modeling proportional daily yields: Going beyond linearity - (Peer Reviewed Journal)
Wu, X., Wiggans, G.R., Norman, H.D., Enzenauer, H.A., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Burchard, J., Durr, J. 2023. Estimating test day milk yields by modeling proportional daily yields: Going beyond linearity. Journal of Dairy Science. 106(12):8979-9005. https://doi.org/10.3168/jds.2023-23479.

Characterization of additive, dominance, and runs of homozygosity effects inbreeds of dairy cattle - (Abstract Only)
Ben Zaabza, H., Neupane, M., Jaafar, M., Srikanth, K., Mckay, S., Miles, A.M., Stranden, I., Huson, H.J., Blackburn, H.D., Van Tassell, C.P. 2023. Characterization of additive, dominance, and runs of homozygosity effects inbreeds of dairy cattle [abstract]. European Association of Animal Production Proceedings. p. 806.

Effect of germplasm exchange strategies on genetic gain, accumulation of homozygosity, and genetic diversity in dairy cattle stud populations: A simulation study - (Abstract Only)

Effects of different treatment approaches on microbial populations in the vaginal discharge of cows diagnosed with clinical metritis - (Abstract Only)
Lection, J.M., Van Syoc, E., Miles, A.M., Hamilton, J., Barragan, A., Ganda, E. 2023. Effects of different treatment approaches on microbial populations in the vaginal discharge of cows diagnosed with clinical metritis [abstract]. Penn State 7th Annual Life Sciences Symposium. p. 32.

Genotype by environment interaction in dairy cattle raised in California and New England - (Abstract Only)
Santana, B., Miles, A.M., Tiezzi, F., Fragomeni, B. 2023. Genotype by environment interaction in dairy cattle raised in California and New England [abstract]. Journal of Animal Science. ASAS-CSAS-WSASAS Meeting, July 16-20, Albuquerque, NM, United States.

rhAMR: A comprehensive and cost-effective resistome profiling method - (Abstract Only)

Genomic validation software: USA results - (Proceedings)
Mota, R.R., Nicolazzi, E., Mcwhorter, T.M., Van Raden, P.M. 2023. Genomic validation software: USA results. Interbull Bulletin. 58:27-32.

Editorial: Lactation genomics and phenomics in farm animals: Where are we at? - (Other)
Wu, X.-L., Ding, X., Zaho, Y., Miles, A.M., Brito, L.F., Heringstad, B., Zhao, S., Jiang, Z. 2023. Editorial: Lactation genomics and phenomics in farm animals: Where are we at? Frontiers in Genetics. 14:1173595. https://doi.org/10.3389/fgene.2023.1173595.

Colostrum microbiome as a predictor of future milk solids production - (Abstract Only)
Jewell, S.E., Krishnamoorthy, S., Miles, A.M., Huson, H.J. 2023. Colostrum microbiome as a predictor of future milk solids production [abstract]. Journal of Dairy Science. 106(Suppl. 1):406-407(abstr. 1646W).

Get test-day milk yields right: what have we learned? - (Abstract Only)
Wu, X., Wiggans, G.R., Norman, H.D., Enzenaur, H.A., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Sievert, S.J., Mattison, J., Burchard, J., Durr, J. 2023. Get test-day milk yields right: What have we learned? [abstract]. Journal of Dairy Science. 106(Suppl. 1):154(abstr. 2624).

Does modeling causal relationships improve the accuracy of estimating lactation milk yields? - (Peer Reviewed Journal)
Wu, X., Miles, A.M., Van Tassell, C.P., Wiggans, G.R., Norman, H.D., Baldwin, R.L., Burchard, J., Durr, J. 2023. Does modeling causal relationships improve the accuracy of estimating lactation milk yields? Journal of Dairy Science Communications. https://doi.org/10.3168/jdsc.2022-0343.

Implementation of feed efficiency in Iranian Holstein breeding program - (Peer Reviewed Journal)
Nadri, S., Sadeghi-Sefidmazgi, A., Zamani, P., Ghorbani, G., Toghiani, S. 2023. Implementation of feed efficiency in Iranian Holstein breeding program. Animals. 13(7):1216. https://doi.org/10.3390/ani13071216.

Standardizing lactation yields from national data with age-parity-season-region corrections for fair comparisons across individual cows and environments - (Abstract Only)
Miles, A.M., Van Raden, P.M., Hutchison, J.L., Fok, G.C., Schutz, M.M. 2023. Standardizing lactation yields from national data with age-parity-season-region corrections for fair comparisons across individual cows and environments. Journal of Dairy Science. 106(Suppl. 1):189-190(abstr. 2716).

Combined effects of milking intervals and frequencies - (Abstract Only)
Van Raden, P.M., Miles, A.M., Wu, X.L., Noordhoff, D.R. 2023. Combined effects of milking intervals and frequencies [abstract]. Journal of Dairy Science. 106(Suppl. 1):190(abstr. 2717).

Haplotype inheritance and livability of recumbent Holstein calves - (Abstract Only)
Al-Khudhair, A.S., Van Raden, P.M., Null, D.J., Neupane, M., Dechow, C.D. 2023. Haplotype inheritance and livability of recumbent Holstein calves [abstract]. Journal of Dairy Science. 106(Suppl. 1):321(abstr. 1348T).

Quality and value of imputing gene tests for all animals - (Abstract Only)
O'Connell, J., Van Raden, P.M., Ogwo, E.O. 2023. Quality and value of imputing gene tests for all animals [abstract]. Journal of Dairy Science. 106(Suppl. 1):189(abstr. 2715).

Candidate mutation for calf recumbency in Holsteins - (Abstract Only)
Dechow, C., VanRaden, P.M., Null, D.J., Al-Khudhair, A.S., McClure, M. 2023. Candidate mutation for calf recumbency in Holsteins [abstract]. Journal of Dairy Science. 106(Suppl. 1):52-53(abstr. 2245).

SLEMM: million-scale genomic predictions with window-based SNP weighting - (Peer Reviewed Journal)
Cheng, J., Maltecca, C., Van Raden, P.M., O'Connell, J., Ma, L., Jiang, J. 2023. SLEMM: million-scale genomic predictions with window-based SNP weighting. Bioinformatics. 39(3):btad127. https://doi.org/10.1093/bioinformatics/btad127.

Is there a genetic piece to milking speed? - (Trade Journal)
Miles, A.M. 2022. Is there a genetic piece to milking speed? Hoard's Dairyman. Available: https://hoards.com/article-32922-is-there-a-genetic-piece-to-milking-speed.html?utm_medium=email&utm_campaign=221201-132Thursday&utm_content=221201-132Thursday+CID_d7f57b576dfcaa74c3fa648c8b073eda&utm_source=Intel&utm_term=Is%20there%20a%20genetic%20piece%20to%20milking%20speed.

Big data genomic analysis in dairy cattle - (Abstract Only)
Lourenco, D., Cesarani, A., Tsuruta, S., Nicolazzi, E.L., Van Raden, P.M., Misztal, I. 2023. Big data genomic analysis in dairy cattle [abstract]. Plant and Animal Genome Conference. Available: https://plan.core-apps.com/pag_2023/abstract/e21f9b00-a05e-48b4-92b5-2ad3192a0208.

Genomic evaluation of dairy cow feed efficiency and metabolic traits - (Proceedings)