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Items: 1 to 50 of 116


A Large-Scale Genome-Wide Association Study in U.S. Holstein Cattle.

Jiang J, Ma L, Prakapenka D, VanRaden PM, Cole JB, Da Y.

Front Genet. 2019 May 14;10:412. doi: 10.3389/fgene.2019.00412. eCollection 2019.


Variance of gametic diversity and its application in selection programs.

Santos DJA, Cole JB, Lawlor TJ Jr, VanRaden PM, Tonhati H, Ma L.

J Dairy Sci. 2019 Jun;102(6):5279-5294. doi: 10.3168/jds.2018-15971. Epub 2019 Apr 10.


Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle.

Fang L, Jiang J, Li B, Zhou Y, Freebern E, Vanraden PM, Cole JB, Liu GE, Ma L.

Commun Biol. 2019 Mar 14;2:100. doi: 10.1038/s42003-019-0341-6. eCollection 2019.


Calling known variants and identifying new variants while rapidly aligning sequence data.

VanRaden PM, Bickhart DM, O'Connell JR.

J Dairy Sci. 2019 Apr;102(4):3216-3229. doi: 10.3168/jds.2018-15172. Epub 2019 Feb 14.


Modeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasets.

Bradford HL, Masuda Y, Cole JB, Misztal I, VanRaden PM.

J Dairy Sci. 2019 Mar;102(3):2308-2318. doi: 10.3168/jds.2018-15419. Epub 2019 Jan 11.


Modeling missing pedigree in single-step genomic BLUP.

Bradford HL, Masuda Y, VanRaden PM, Legarra A, Misztal I.

J Dairy Sci. 2019 Mar;102(3):2336-2346. doi: 10.3168/jds.2018-15434. Epub 2019 Jan 11.


Symposium review: Genetics, genome-wide association study, and genetic improvement of dairy fertility traits.

Ma L, Cole JB, Da Y, VanRaden PM.

J Dairy Sci. 2019 Apr;102(4):3735-3743. doi: 10.3168/jds.2018-15269. Epub 2018 Sep 27. Review.


Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins.

Weller JI, Bickhart DM, Wiggans GR, Tooker ME, O'Connell JR, Jiang J, Ron M, VanRaden PM.

J Dairy Sci. 2018 Oct;101(10):9089-9107. doi: 10.3168/jds.2018-14816. Epub 2018 Jul 19.


Differing genetic trend estimates from traditional and genomic evaluations of genotyped animals as evidence of preselection bias in US Holsteins.

Masuda Y, VanRaden PM, Misztal I, Lawlor TJ.

J Dairy Sci. 2018 Jun;101(6):5194-5206. doi: 10.3168/jds.2017-13310. Epub 2018 Mar 21.


A 100-Year Review: Methods and impact of genetic selection in dairy cattle-From daughter-dam comparisons to deep learning algorithms.

Weigel KA, VanRaden PM, Norman HD, Grosu H.

J Dairy Sci. 2017 Dec;100(12):10234-10250. doi: 10.3168/jds.2017-12954. Review.


Symposium review: Possibilities in an age of genomics: The future of selection indices.

Cole JB, VanRaden PM.

J Dairy Sci. 2018 Apr;101(4):3686-3701. doi: 10.3168/jds.2017-13335. Epub 2017 Nov 2.


Genomic evaluation of age at first calving.

Hutchison JL, VanRaden PM, Null DJ, Cole JB, Bickhart DM.

J Dairy Sci. 2017 Aug;100(8):6853-6861. doi: 10.3168/jds.2016-12060. Epub 2017 Jun 16.


Dissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattle.

Jiang J, Shen B, O'Connell JR, VanRaden PM, Cole JB, Ma L.

BMC Genomics. 2017 May 30;18(1):425. doi: 10.1186/s12864-017-3821-4.


Selecting sequence variants to improve genomic predictions for dairy cattle.

VanRaden PM, Tooker ME, O'Connell JR, Cole JB, Bickhart DM.

Genet Sel Evol. 2017 Mar 7;49(1):32. doi: 10.1186/s12711-017-0307-4.


Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility.

Cole JB, Null DJ, VanRaden PM.

J Dairy Sci. 2016 Sep;99(9):7274-7288. doi: 10.3168/jds.2015-10777. Epub 2016 Jul 7.


Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection.

García-Ruiz A, Cole JB, VanRaden PM, Wiggans GR, Ruiz-López FJ, Van Tassell CP.

Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):E3995-4004. doi: 10.1073/pnas.1519061113. Epub 2016 Jun 27. Erratum in: Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):E4928.


Identification of a nonsense mutation in APAF1 that is likely causal for a decrease in reproductive efficiency in Holstein dairy cattle.

Adams HA, Sonstegard TS, VanRaden PM, Null DJ, Van Tassell CP, Larkin DM, Lewin HA.

J Dairy Sci. 2016 Aug;99(8):6693-6701. doi: 10.3168/jds.2015-10517. Epub 2016 Jun 8.


Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes.

Bickhart DM, Hutchison JL, Null DJ, VanRaden PM, Cole JB.

J Dairy Sci. 2016 Jul;99(7):5526-5534. doi: 10.3168/jds.2015-10347. Epub 2016 Apr 13.


Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle.

Wiggans GR, Cooper TA, VanRaden PM, Van Tassell CP, Bickhart DM, Sonstegard TS.

J Dairy Sci. 2016 Jun;99(6):4504-4511. doi: 10.3168/jds.2015-10456. Epub 2016 Mar 31.


Practical implications for genetic modeling in the genomics era.

VanRaden PM.

J Dairy Sci. 2016 Mar;99(3):2405-2412. doi: 10.3168/jds.2015-10038. Epub 2016 Jan 6.


Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.

Ma L, O'Connell JR, VanRaden PM, Shen B, Padhi A, Sun C, Bickhart DM, Cole JB, Null DJ, Liu GE, Da Y, Wiggans GR.

PLoS Genet. 2015 Nov 5;11(11):e1005387. doi: 10.1371/journal.pgen.1005387. eCollection 2015 Nov.


Fast imputation using medium or low-coverage sequence data.

VanRaden PM, Sun C, O'Connell JR.

BMC Genet. 2015 Jul 14;16:82. doi: 10.1186/s12863-015-0243-7.


Short communication: Improving accuracy of Jersey genomic evaluations in the United States and Denmark by sharing reference population bulls.

Wiggans GR, Su G, Cooper TA, Nielsen US, Aamand GP, Guldbrandtsen B, Lund MS, VanRaden PM.

J Dairy Sci. 2015 May;98(5):3508-13. doi: 10.3168/jds.2014-8874. Epub 2015 Mar 12.


Short communication: Analysis of genomic predictor population for Holstein dairy cattle in the United States--Effects of sex and age.

Cooper TA, Wiggans GR, VanRaden PM.

J Dairy Sci. 2015 Apr;98(4):2785-8. doi: 10.3168/jds.2014-8894. Epub 2015 Jan 31.


Technical note: Rapid calculation of genomic evaluations for new animals.

Wiggans GR, VanRaden PM, Cooper TA.

J Dairy Sci. 2015 Mar;98(3):2039-42. doi: 10.3168/jds.2014-8868. Epub 2014 Dec 31.


Comparison of single-trait to multi-trait national evaluations for yield, health, and fertility.

VanRaden PM, Tooker ME, Wright JR, Sun C, Hutchison JL.

J Dairy Sci. 2014 Dec;97(12):7952-62. doi: 10.3168/jds.2014-8489. Epub 2014 Oct 3.


Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins.

Xu L, Cole JB, Bickhart DM, Hou Y, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP, Liu GE.

BMC Genomics. 2014 Aug 15;15:683. doi: 10.1186/1471-2164-15-683.


Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects.

Sun C, VanRaden PM, Cole JB, O'Connell JR.

PLoS One. 2014 Aug 1;9(8):e103934. doi: 10.1371/journal.pone.0103934. eCollection 2014.


Application of the a posteriori granddaughter design to the Holstein genome.

Weller JI, Cole JB, Vanraden PM, Wiggans GR.

Animal. 2014 Apr;8(4):511-9. doi: 10.1017/S1751731114000111.


Increasing long-term response by selecting for favorable minor alleles.

Sun C, VanRaden PM.

PLoS One. 2014 Feb 5;9(2):e88510. doi: 10.1371/journal.pone.0088510. eCollection 2014.


Mating programs including genomic relationships and dominance effects.

Sun C, VanRaden PM, O'Connell JR, Weigel KA, Gianola D.

J Dairy Sci. 2013;96(12):8014-23. doi: 10.3168/jds.2013-6969. Epub 2013 Oct 11.


Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects.

Weller JI, VanRaden PM, Wiggans GR.

J Dairy Sci. 2013 Aug;96(8):5376-87. doi: 10.3168/jds.2013-6650. Epub 2013 Jun 5.


Short communication: relationship of call rate and accuracy of single nucleotide polymorphism genotypes in dairy cattle.

Cooper TA, Wiggans GR, VanRaden PM.

J Dairy Sci. 2013 May;96(5):3336-9. doi: 10.3168/jds.2012-6208. Epub 2013 Mar 15.


Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle.

Sonstegard TS, Cole JB, VanRaden PM, Van Tassell CP, Null DJ, Schroeder SG, Bickhart D, McClure MC.

PLoS One. 2013;8(1):e54872. doi: 10.1371/journal.pone.0054872. Epub 2013 Jan 22.


Confirmation and discovery of maternal grandsires and great-grandsires in dairy cattle.

VanRaden PM, Cooper TA, Wiggans GR, O'Connell JR, Bacheller LR.

J Dairy Sci. 2013 Mar;96(3):1874-9. doi: 10.3168/jds.2012-6176. Epub 2013 Jan 16.


Technical note: Changes to herd cutoff date in conception rate evaluations.

Hutchison JL, VanRaden PM, Norman HD, Cole JB.

J Dairy Sci. 2013 Feb;96(2):1264-8. doi: 10.3168/jds.2012-6203. Epub 2012 Dec 6.


Methods to approximate reliabilities in single-step genomic evaluation.

Misztal I, Tsuruta S, Aguilar I, Legarra A, VanRaden PM, Lawlor TJ.

J Dairy Sci. 2013 Jan;96(1):647-54. doi: 10.3168/jds.2012-5656. Epub 2012 Nov 3.


Genomic imputation and evaluation using high-density Holstein genotypes.

VanRaden PM, Null DJ, Sargolzaei M, Wiggans GR, Tooker ME, Cole JB, Sonstegard TS, Connor EE, Winters M, van Kaam JB, Valentini A, Van Doormaal BJ, Faust MA, Doak GA.

J Dairy Sci. 2013 Jan;96(1):668-78. doi: 10.3168/jds.2012-5702. Epub 2012 Oct 11.


Multibreed genomic evaluations using purebred Holsteins, Jerseys, and Brown Swiss.

Olson KM, VanRaden PM, Tooker ME.

J Dairy Sci. 2012 Sep;95(9):5378-5383. doi: 10.3168/jds.2011-5006.


Technical note: adjustment of all cow evaluations for yield traits to be comparable with bull evaluations.

Wiggans GR, Vanraden PM, Cooper TA.

J Dairy Sci. 2012 Jun;95(6):3444-7. doi: 10.3168/jds.2011-5000.


Design of a bovine low-density SNP array optimized for imputation.

Boichard D, Chung H, Dassonneville R, David X, Eggen A, Fritz S, Gietzen KJ, Hayes BJ, Lawley CT, Sonstegard TS, Van Tassell CP, VanRaden PM, Viaud-Martinez KA, Wiggans GR; Bovine LD Consortium.

PLoS One. 2012;7(3):e34130. doi: 10.1371/journal.pone.0034130. Epub 2012 Mar 28.


Use of the Illumina Bovine3K BeadChip in dairy genomic evaluation.

Wiggans GR, Cooper TA, Vanraden PM, Olson KM, Tooker ME.

J Dairy Sci. 2012 Mar;95(3):1552-8. doi: 10.3168/jds.2011-4985.


Technical note: adjustment of traditional cow evaluations to improve accuracy of genomic predictions.

Wiggans GR, Cooper TA, Vanraden PM, Cole JB.

J Dairy Sci. 2011 Dec;94(12):6188-93. doi: 10.3168/jds.2011-4481.


Harmful recessive effects on fertility detected by absence of homozygous haplotypes.

VanRaden PM, Olson KM, Null DJ, Hutchison JL.

J Dairy Sci. 2011 Dec;94(12):6153-61. doi: 10.3168/jds.2011-4624.


Evaluations for service-sire conception rate for heifer and cow inseminations with conventional and sexed semen.

Norman HD, Hutchison JL, VanRaden PM.

J Dairy Sci. 2011 Dec;94(12):6135-42. doi: 10.3168/jds.2010-3875.


Use of haplotypes to estimate Mendelian sampling effects and selection limits.

Cole JB, VanRaden PM.

J Anim Breed Genet. 2011 Dec;128(6):446-55. doi: 10.1111/j.1439-0388.2011.00922.x. Epub 2011 Apr 13.


Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss.

VanRaden PM, Olson KM, Wiggans GR, Cole JB, Tooker ME.

J Dairy Sci. 2011 Nov;94(11):5673-82. doi: 10.3168/jds.2011-4500.


The genomic evaluation system in the United States: past, present, future.

Wiggans GR, Vanraden PM, Cooper TA.

J Dairy Sci. 2011 Jun;94(6):3202-11. doi: 10.3168/jds.2010-3866.


Differences among methods to validate genomic evaluations for dairy cattle.

Olson KM, Vanraden PM, Tooker ME, Cooper TA.

J Dairy Sci. 2011 May;94(5):2613-20. doi: 10.3168/jds.2010-3877.


Genomic evaluations with many more genotypes.

VanRaden PM, O'Connell JR, Wiggans GR, Weigel KA.

Genet Sel Evol. 2011 Mar 2;43:10. doi: 10.1186/1297-9686-43-10.

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