Publications

2021

Contribution to journal

Milkevych, V., Madsen, P., Gao, H. & Jensen, J. (2021). The relative effect of genomic information on efficiency of Bayesian analysis of the mixed linear model with unknown variance. Journal of Animal Breeding and Genetics (Online), 138(1), 14-22. https://doi.org/10.1111/jbg.12497, https://doi.org/10.1111/jbg.12497

Cao, L., Mulder, H. A., Liu, H., Nielsen, H. M. & S⊘rensen, A. C. (2021). Competitive gene flow does not necessarily maximize the genetic gain of genomic breeding programs in the presence of genotype-by-environment interaction. Journal of Dairy Science, 104(7), 8122-8134. https://doi.org/10.3168/jds.2020-19823

Wang, L., Janss, L. L., Madsen, P., Henshall, J., Huang, C.-H., Marois, D., Alemu, S., Sørensen, A. C. & Jensen, J. (2020). Effect of genomic selection and genotyping strategy on estimation of variance components in animal models using different relationship matrices. Genetics, selection, evolution : GSE, 52(1), Article 31. https://doi.org/10.1186/s12711-020-00550-w

Tsai, H.-Y., Janss, L. L., Andersen, J. R., Orabi, J., Jensen, J. D., Jahoor, A. & Jensen, J. (2020). Genomic prediction and GWAS of yield, quality and disease-related traits in spring barley and winter wheat. Scientific Reports, 10(1), Article 3347. https://doi.org/10.1038/s41598-020-60203-2

Tessema, B. B., Liu, H., Sørensen, A. C., Andersen, J. R. & Jensen, J. (2020). Strategies Using Genomic Selection to Increase Genetic Gain in Breeding Programs for Wheat. Frontiers in Genetics, 11, Article 578123. https://doi.org/10.3389/fgene.2020.578123

Madsen, M. D., Villumsen, T. M., Hansen, B. K., Møller, S. H., Jensen, J. & Shirali, M. (2020). Combined analysis of group recorded feed intake and individually recorded body weight and litter size in mink. Animal : an international journal of animal bioscience, 14(9), 1793-1801. https://doi.org/10.1017/S1751731120000762

Liu, A., Lund, M. S., Boichard, D. A., Karaman, E., Fritz, S., Aamand, G. P., Nielsen, U. S., Wang, Y. & Su, G. (2020). Improvement of genomic prediction by integrating additional single nucleotide polymorphisms selected from imputed whole genome sequencing data. Heredity, 124(1), 37-49. https://doi.org/10.1038/s41437-019-0246-7

Ørsted, M., Hoffmann, A. A., Rohde, P. D., Sørensen, P. & Kristensen, T. N. (2019). Strong impact of thermal environment on the quantitative genetic basis of a key stress tolerance trait. Heredity, 122(3), 315-325. https://doi.org/10.1038/s41437-018-0117-7

Mesbah-Uddin, M., Hoze, C., Michot, P., Barbat, A., Lefebvre, R., Boussaha, M., Sahana, G., Fritz, S., Boichard, D. & Capitan, A. (2019). A missense mutation (p.Tyr452Cys) in the CAD gene compromises reproductive success in French Normande cattle. Journal of Dairy Science, 102(7), 6340-6356. https://doi.org/10.3168/jds.2018-16100

Mesbah-Uddin, M., Guldbrandtsen, B., Lund, M. S., Boichard, D. & Sahana, G. (2019). Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle. Journal of Dairy Science, 102(12), 11193-11206. https://doi.org/10.3168/jds.2019-16946

Kristensen, P. S., Jensen, J., Andersen, J. R., Guzmán, C., Jihad, O. & Jahoor, A. (2019). Genomic Prediction and Genome-Wide Association Studies of Flour Yield and Alveograph Quality Traits Using Advanced Winter Wheat Breeding Material. Genes, 10(9), Article 669. https://doi.org/10.3390/genes10090669

Gebreyesus, G., Buitenhuis, A. J., Poulsen, N. A., Visker, M. H. P. W., Zhang, Q., van Valenberg, H. J. F., Sun, D. & Bovenhuis, H. (2019). Combining multi-population datasets for joint genome-wide association and meta-analyses: The case of bovine milk fat composition traits. Journal of Dairy Science, 102(12), 11124-11141. https://doi.org/10.3168/jds.2019-16676

Gebreyesus, G., Buitenhuis, A. J., Poulsen, N. A., Visker, M. H. P. W., Zhang, Q., van Valenberg, H. J. F., Sun, D. & Bovenhuis, H. (2019). Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition. BMC Genomics, 20, Article 178. https://doi.org/10.1186/s12864-019-5573-9

Gebreyesus, G., Bovenhuis, H., Lund, M. S., Poulsen, N. A., Sun, D. & Buitenhuis, B. (2019). Reliability of genomic prediction for milk fatty acid composition by using a multi-population reference and incorporating GWAS results. Genetics Selection Evolution, 51(1), Article 16. https://doi.org/10.1186/s12711-019-0460-z

Cai, Z., Guldbrandtsen, B., Lund, M. S. & Sahana, G. (2019). Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle. BMC Genetics, 20, Article 15. https://doi.org/10.1186/s12863-019-0717-0

2018

Contribution to conference

Gebreyesus, G., Buitenhuis, A. J., Poulsen, N. A., Visker, M. H. P. W., Zhang, Q., van Valenberg, H. J. F., Sun, D. & Bovenhuis, H. (2018). Genome-wide association study of the de novo synthesized milk fatty acids based on Dutch, Danish and Chinese Holstein Friesians. 141. Abstract from The 11th World Congress on Genetics Applied to Livestock Production , Auckland, New Zealand.

Rohde, P. D., Sørensen, I. F. & Sørensen, P. (2018). Genomic Feature Prediction Models - Improved Prediction Accuracy by Joint Marker Estimation. Poster session presented at ESHG 2018: European Society of Human Genetics, Milano, Italy.

Mesbah-Uddin, M., Guldbrandtsen, B., Lund, M. S. & Sahana, G. (2018). Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle. Poster session presented at The 11th World Congress on Genetics Applied to Livestock Production , Auckland, New Zealand.

2018

Contribution to book anthology

Villumsen, T. M., Su, G., Cai, Z., Guldbrandtsen, B., Asp, T., Sahana, G. & Lund, M. S. (2018). Genomic selection in mink yield higher accuracies with a Bayesian approach allowing for heterogeneous variance than a GBLUP model. In Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018: Volume Methods and Tools - Prediction 2 Article 11.618 http://www.wcgalp.org/proceedings/2018/genomic-selection-mink-yield-higher-accuracies-bayesian-approach-allowing

Marete, A. G., Janss, L., Guldbrandtsen, B., Hoze, C., Sahana, G., Boichard, D. A. & Lund, M. S. (2018). Exploring non-additive variance using genome-wide dense SNP in four French and Nordic dairy cattle breeds. In Proceedings of the World Congress on Genetics Applied to Livestock Production Article 70

Liu, A., Lund, M. S., Boichard, D., Fritz, S., Karaman, E., Wang, Y. & Su, G. (2018). Using additional single nucleotide polymorphisms selected from whole genome sequence data for genomic prediction in Danish Jersey. In Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018 Article 586 http://www.wcgalp.org/system/files/proceedings/2018/using-additional-single-nucleotide-polymorphisms-selected-whole-genome-sequence-data-genomic.pdf

Guldbrandtsen, B., Cai, Z., Sahana, G., Villumsen, T. M., Asp, T., Thomsen, B. & Lund, M. S. (2018). Genomics using the Assembly of the Mink Genome. In Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018: Volume Electronic Poster Session - Molecular Genetics 1 Article 539 http://www.wcgalp.org/proceedings/2018/genomics-using-assembly-mink-genome

Boichard, D. A., Boussaha, M., Capitan, A., Rocha, D., Hoze, C., Sanchez, M.-P., Tribout, T., Letaief, R., Croiseau, P., Grohs, C., Li, W., Harland, C., Charlier, C., Lund, M. S., Sahana, G., Georges, M., Barbier, S., Coppieters, W., Fritz, S. & Guldbrandtsen, B. (2018). Experience from large scale use of the EuroGenomics custom SNP chip in cattle. In Proceedings of the World Congress on Genetics Applied to Livestock Production: Volume Molecular Genetics 4 (Vol. 11). Article 11.675 http://www.wcgalp.org/proceedings/2018/experience-large-scale-use-eurogenomics-custom-snp-chip-cattle

2018

Contribution to journal

Xiang, T., Christensen, O. F., Vitezica, Z. G. & Legarra, A. (2018). Genomic model with correlation between additive and dominance effects. Genetics, 209(3), 711-723. https://doi.org/10.1534/genetics.118.301015

Sverrisdóttir, E., Sundmark, E. H. R., Johnsen, H. Ø., Kirk, H. G., Asp, T., Janss, L., Bryan, G. & Nielsen, K. L. (2018). The value of expanding the training population to improve genomic selection models in tetraploid potato. Frontiers in Plant Science, 9, Article 1118. https://doi.org/10.3389/fpls.2018.01118

Rohde, P. D., Østergaard, S., Kristensen, T. N., Sørensen, P., Loeschcke, V., F C Mackay, T. & Sarup, P. M. (2018). Functional validation of candidate genes detected by genomic feature models. G3: Genes, Genomes, Genetics (Bethesda), 8(5), 1659-1668. https://doi.org/10.1534/g3.118.200082

Ørsted, M., Rohde, P. D., Hoffmann, A. A., Sørensen, P. & Kristensen, T. N. (2018). Environmental variation partitioned into separate heritable components. Evolution, 72(1), 136-152. https://doi.org/10.1111/evo.13391

Mesbah-Uddin, M., Guldbrandtsen, B., Iso-Touru, T., Vilkki, J., De Koning, D.-J., Boichard, D., Lund, M. S. & Sahana, G. (2018). Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. D N A Research, 25(1), 49-59. https://doi.org/10.1093/dnares/dsx037

Marete, A. G., Guldbrandtsen, B., Lund, M. S., Fritz, S., Sahana, G. & Boichard, D. (2018). A Meta-Analysis Including Pre-selected Sequence Variants Associated With Seven Traits in Three French Dairy Cattle Populations. Frontiers in Genetics, 9, Article 522. https://doi.org/10.3389/fgene.2018.00522

Marete, A. G., Lund, M. S., Boichard, D. A. & Ramayo-Caldas, Y. (2018). A system-based analysis of the genetic determinism of udder conformation and health phenotypes across three French dairy cattle breeds. PLoS One, 13(7), Article e0199931. https://doi.org/10.1371/journal.pone.0199931

Marete, A. G., Sahana, G., Fritz, S., Lefebvre, R., Barbat, A., Lund, M. S., Guldbrandtsen, B. & Boichard, D. (2018). Genome-wide association study for milking speed in French Holstein cows. Journal of Dairy Science, 101(7), 6205-6219. https://doi.org/10.3168/jds.2017-14067

Madsen, M. D., Madsen, P., Nielsen, B., Kristensen, T. N., Jensen, J. & Shirali, M. (2018). Macro-environmental sensitivity for growth rate in Danish Duroc pigs is under genetic control. Journal of Animal Science, 96(12), 4967-4977. https://doi.org/10.1093/jas/sky376

Jardim, J. G., Guldbrandtsen, B., Lund, M. S. & Sahana, G. (2018). Association analysis for udder index and milking speed with imputed whole-genome sequence variants in Nordic Holstein cattle. Journal of Dairy Science, 101(3), 2199-2212. https://doi.org/10.3168/jds.2017-12982

Guo, X., Cericola, F., Fè, D., Pedersen, M. G., Lenk, I., Jensen, C. S., Jensen, J. & Janss, L. L. (2018). Genomic prediction in tetraploid ryegrass using allele frequencies based on genotyping by sequencing. Frontiers in Plant Science, 9, Article 1165. https://doi.org/10.3389/fpls.2018.01165

Fang, L., Sørensen, P., Sahana, G., Panitz, F., Su, G., Zhang, S., Yu, Y., Li, B., Ma, L., Liu, G., Lund, M. S. & Thomsen, B. (2018). MicroRNA-guided prioritization of genome-wide association signals reveals the importance of microRNA-target gene networks for complex traits in cattle. Scientific Reports, 8(1), Article 9345. https://doi.org/10.1038/s41598-018-27729-y

Esfandyari, H., Berg, P. & Sørensen, A. C. (2018). Balanced selection on purebred and crossbred performance increases gain in crossbreds. Genetics Selection Evolution, 50(1), Article 8. https://doi.org/10.1186/s12711-018-0379-9

Bouwman, A. C., Daetwyler, H. D., Chamberlain, A. J., Ponce, C. H., Sargolzaei, M., Schenkel, F. S., Sahana, G., Govignon-Gion, A., Boitard, S., Dolezal, M., Pausch, H., Brøndum, R. F., Bowman, P. J., Thomsen, B., Guldbrandtsen, B., Lund, M. S., Servin, B., Garrick, D. J., Reecy, J. ... Hayes, B. J. (2018). Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nature Genetics, 50(3), 362-372. https://doi.org/10.1038/s41588-018-0056-5

2017

Contribution to conference

Thomasen, J. R., Liu, H. & Sørensen, A. C. (2017). Pedigree inbreeding underestimate true inbreeding in genomic dairy cattle breeding schemes. Abstract from 68th Annual Meeting of the European Federation of Animal Science , Tallinn, Estonia.

Gebregiwergis, G. T., Meuwissen, T. H. E., Sørensen, A. C. & Henryon, M. (2017). Alternative genomic relationship matrices in genomic optimum optimun contribution selection. Abstract from 68th Annual Meeting of the European Federation of Animal Science , Tallinn, Estonia. http://www.dairycareaction.org/uploads/2/4/2/6/24266896/eaap2017_book_of_abstracts_-_preliminary_pages.pdf

Esfandyari, H. & Sørensen, A. C. (2017). xbreed: an R package for genomic simulation of purebreds and crossbreds. Abstract from 68th Annual Meeting of the European Federation of Animal Science , Tallinn, Estonia.

Uddin, M. M., Guldbrandtsen, B., Iso-Touru, T., Vilkki, J., de Koning, D.-J., Boichard, D., Lund, M. S. & Sahana, G. (2017). A population scale discovery of large deletions in Holstein, Jersey and Nordic Red Cattle genome. Poster session presented at 36th International Society for Animal Genetics Conference, Dublin, Ireland. http://www.isag.us/Docs/Proceedings/ISAG2017_Proceedings.pdf?v3

Gebreyesus, G., Lund, M. S., Janss, L., Bovenhuis, H., Poulsen, N. A. & Buitenhuis, A. J. (2017). Genomic prediction for detailed milk protein composition traits. Poster session presented at 5th Annual GenSAP Meeting, 15-16 November 2017, Billund, Denmark.

Gebreyesus, G., Buitenhuis, A. J., Poulsen, N. A., Visker, M. H. P. W., Zhang, Q., van Valenberg, H. J. F., Sun, D. & Bovenhuis, H. (2017). Multi-population GWAS for the de novo synthesis of milk fatty acids. Poster session presented at 5th Annual GenSAP Meeting, 15-16 November 2017, Billund, Denmark.