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.)

Dry matter intake in US Holstein cows: exploring the genomic and phenotypic impact of milk components and body weight composite - (Peer Reviewed Journal)

Genetic and genomic evaluations of milking speed and duration from automated milk recording - (Abstract Only)

Improved tracking of recent mutations within common haplotypes causing cholesterol deficiency, muscle weakness, and BLIRD - (Abstract Only)

Comparison of genomic merit, pedigree completeness, inbreeding, and relationships of genotyped animals across continents - (Abstract Only)

Six direct health traits for US: updated variance component estimates and implementation of variance adjusted weights - (Abstract Only)

The value of a national evaluation system in promoting dairy sustainability - (Abstract Only)

Alterations of rumen and fecal microbiome in growing beef and dairy steers fed rumen protected Capsicum oleoresin - (Peer Reviewed Journal)

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)

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)

Single-step genomic predictions for crossbred Holstein and Jersey cows in the US - (Peer Reviewed Journal)

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.

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)

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.

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