Center for Quantitative Genetics and Genomics

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 qgg.au.dk Research Projects Current projects Center for Genomic Selection in Animals and Plants (GenSAP) Publications

Publications

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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.
Daetwyler, H. D., Capitan, A., Pausch, H., Stothard, P., van Binsbergen, R., Brøndum, R. F., Liao, X., Djari, A., Rodriguez, S. C., Grohs, C., Jung, S., Esquerré, D., Bouchez, O., Gollnick, N. S., Rossignol, M.-N., Klopp, C., Rocha, D., Fritz, S., Eggen, A. ... Hayes, B. J. (2014). Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genetics, 46(8), 858 - 865.
de los Campos, G., Sorensen, D. & Gianola, D. (2014). What is it?. Paper presented at 10th World Congress on Genetics Applied to Livestock Production (WCGALP), Vancouver, Canada.
Liu, A., Lund, M. S., Wang, Y., Guo, G., Dong, G., Madsen, P. & Su, G. (2017). Variance components and correlations of female fertility traits in Chinese Holstein population. Journal of Animal Science and Biotechnology, 8(1), Article 56. https://doi.org/10.1186/s40104-017-0189-x
Lopes, M. S., Bastiaansen, J. W. M., Janss, L., Bovenhuis, H. & Knol, E. F. (2014). Using SNP markers to estimate additive, dominance and imprinting genetic variance. Paper presented at 10th World Congress on Genetics Applied to Livestock Production (WCGALP), Vancouver, Canada. https://event.crowdcompass.com/wcgalp2014#/activity/l8lt5Q5qu9
van den Berg, I., Boichard, D., Guldbrandtsen, B. & Lund, M. S. (2016). Using Sequence Variants in Linkage Disequilibrium with Causative Mutations to Improve Across-Breed Prediction in Dairy Cattle: A Simulation Study. G3: Genes, Genomes, Genetics, 6(8), 2553-2561. https://doi.org/10.1534/g3.116.027730
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
Fang, L., Sahana, G., Ma, P., Su, G., Yu, Y., Zhang, S., Lund, M. S. & Sørensen, P. (2017). Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds. BMC Genomics, 18(1), 604. Article 604. https://doi.org/10.1186/s12864-017-4004-z
Edwards, D. (2015). Two molecular measures of relatedness based on haplotype sharing. BMC Bioinformatics, 16(383), 1-11. https://doi.org/10.1186/s12859-015-0802-y
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
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
Li, X., Lund, M. S., Janss, L., Wang, C., Ding, X., Zhang, Q. & Su, G. (2017). The patterns of genomic variances and covariances across genome for milk production traits between Chinese and Nordic Holstein populations. BMC Genetics, 18, Article 26. https://doi.org/10.1186/s12863-017-0491-9
Pertoldi, C., Bahrndorff, S., Kurbalija Novicic, Z. & Rohde, P. D. (2016). The Novel Concept of “Behavioural Instability” and Its Potential Applications. Symmetry, 8(11), 1-13. Article 135. https://doi.org/10.3390/sym8110135
Cai, Z., Petersen, B., Sahana, G., Madsen, L. B., Larsen, K., Thomsen, B., Bendixen, C., Lund, M. S., Guldbrandtsen, B. & Panitz, F. (2017). The first draft reference genome of the American mink (Neovison vison). Scientific Reports, 7(1), Article 14564. https://doi.org/10.1038/s41598-017-15169-z
Rohde, P. D., Madsen, L. S., Arvidson, S. M. N., Loeschcke, V., Demontis, D. & Kristensen, T. N. (2016). Testing candidate genes for attention-deficit/hyperactivity disorder in fruit flies using a high throughput assay for complex behavior. Fly, 10(1), 25-34. Article 1158365. https://doi.org/10.1080/19336934.2016.1158365
Xiang, T., Christensen, O. F. & Legarra, A. (2017). Technical note: Genomic evaluation for crossbred performance in a single-step approach with metafounders. Journal of Animal Science, 95(4), 1472-1480. https://doi.org/10.2527/jas2016.1155
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
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
Brøndum, R. F., Guldbrandtsen, B., Sahana, G., Lund, M. S. & Su, G. (2014). Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle. BMC Genomics, 15(728), 1-8. https://doi.org/10.1186/1471-2164-15-728
Meier, K., Thirstrup, J., Lund, M. S. & Sørensen, A. C. (2015). Stochastic simulation of breeding plans in mink: evaluation of genomic selection. In Book of Abstract of the 66th Annual Meeting of the European Federation of Animal Science (Vol. 21, pp. 390-390). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-816-2
Ostersen, T., Christensen, O. F., Madsen, P. & Henryon, M. (2016). Sparse single-step method for genomic evaluation in pigs. Genetics Selection Evolution, 48(1), Article 48. https://doi.org/10.1186/s12711-016-0227-8
Do, D. N., Janss, L., Jensen, J. & Kadarmideen, H. N. (2015). SNP annotation-based whole genomic prediction and selection: an application to feed efficiency and its component traits in pigs. Journal of Animal Science, 93(5), 2056-2063. https://doi.org/10.2527/jas.2014-8640
Gebreyesus, G., Lund, M. S., Janss, L., Poulsen, N. A., Larsen, L. B., Bovenhuis, H. & Buitenhuis, A. J. (2016). Short communication: Multi-trait estimation of genetic parameters for milk protein composition in the Danish Holstein. Journal of Dairy Science, 99(4), 2863-2866. https://doi.org/10.3168/jds.2015-10501
Li, X., Lund, M. S., Zhang, Q., Costa, C. N., Ducrocq, V. & Su, G. (2016). Short communication: Improving accuracy of predicting breeding values in Brazilian Holstein population by adding data from Nordic and French Holstein populations. Journal of Dairy Science, 99(6), 4574-4579. Article 74482. https://doi.org/10.3168/jds.2015-10609
Van den Berg, I., Boichard, D. & Lund, M. S. (2016). Sequence variants selected from a multi-breed GWAS can improve the reliability of genomic predictions in dairy cattle. Genetics Selection Evolution, 48, Article 83. https://doi.org/10.1186/s12711-016-0259-0
Sørensen, P., Edwards, S. M., Sarup, P. M. & Sorensen, D. A. (2014). Sequence-based partitioning of genomic variance using prior biological information. EAAP Book of Abstracts, 20, 167-167. http://www.wageningenacademic.com/eaap2014
Sarup, P. M., Jensen, J., Edwards, S. M., Ostersen, T., Sørensen, P. & Henryon, M. A. (2014). Separating Signal from Noise Estimating SNP-effects and Decomposing Genetic Variation to the Level of QTLs in Pure Breed Duroc Pigs. Paper presented at 10th World Congress on Genetics Applied to Livestock Production (WCGALP), Vancouver, Canada. https://event.crowdcompass.com/wcgalp2014/activity/8tN0Up65ZB
Zhang, Q., Guldbrandtsen, B., Bosse, M., Lund, M. S. & Sahana, G. (2014). Runs of homozygosity and distribution of functional variants in cattle genome. Paper presented at 10th World Congress on Genetics Applied to Livestock Production (WCGALP), Vancouver, Canada. https://event.crowdcompass.com/wcgalp2014#/activity/67ND0x1HWf
Zhang, Q., Guldbrandtsen, B., Bosse, M., Lund, M. S. & Sahana, G. (2015). Runs of homozygosity and distribution of functional variants in cattle genome. BMC Genomics, 16(542), 1-16. https://doi.org/10.1186/s12864-015-1715-x
Lund, M. S., van den Berg, I., Ma, P., Brøndum, R. F. & Su, G. (2016). Review: How to improve genomic predictions in small dairy cattle populations. Animal, 10(6), 1042-1049. https://doi.org/10.1017/S1751731115003031
Esfandyari, H., Henryon, M., Berg, P., Thomasen, J. R., Bjima, P. & Sørensen, A. C. (2017). Response to selection in finite locus models with non-additive effects. Journal of Heredity, 108(3), 318-327. https://doi.org/10.1093/jhered/esw123
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
Brøndum, R. F., Su, G., Janss, L., Sahana, G., Guldbrandtsen, B., Boichard, D. A. & Lund, M. S. (2015). Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction. Journal of Dairy Science, 98(6), 4107-4116. https://doi.org/10.3168/jds.2014-9005
Rohde, P. D. (2014). Psykofluer - bananfluer som model for psykiske  sygdomme. Aktuel Naturvidenskab, 5, 34-37.
Fé, D., Ashraf, B., Byrne, S., Czaban, A., Roulund, N., Lenk, I., Asp, T., Pedersen, M. G., Jensen, C. S., Janss, L. & Jensen, J. (2014). Prospects for introducing genomic selection info forage grass breeding. In Proceedings of the 25th General Meeting of the European Grassland Federation (pp. 830-832)
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.
Byrne, S., Cericola, F., Janss, L., Jensen, J., Fé, D., Ashraf, B., Czaban, A., Greve-Pedersen, M., Lenk, I., Jensen, C. S. & Asp, T. (2015). Partitioning SNPs Identified By GBS into Genome Annotation Classes and Calculating SNP-Explained Variances for Heading Date and Disease Resistance from the Resulting Genomic Relationship Matrices - Lolium perenne. In Final Program, Abstract & Exhibit Guide (pp. 290-290) https://pag.confex.com/pag/xxiii/webprogram/Paper15700.html
Liu, H., Sørensen, A. C. & Berg, P. (2014). Optimum contribution selection combined with weighting rare favourable alleles increases long-term genetic gain. Paper presented at 10th World Congress on Genetics Applied to Livestock Production (WCGALP), Vancouver, Canada. https://event.crowdcompass.com/wcgalp2014/activity/ppfvJcCuPy
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.
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
Sørensen, I. F., Edwards, S. M., Rohde, P. D. & Sørensen, P. (2017). Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster /631/208/721 /631/208/721 /631/208/729/743 /631/208/729/743 /119 /45 /45/43 article. Scientific Reports, 7(1), Article 2413. https://doi.org/10.1038/s41598-017-02281-3
van den Berg, I., Boichard, D. & Lund, M. S. (2015). Multi-breed GWAS and meta-analysis using sequences of five dairy cattle breeds improve QTL mapping. In Book of Abstract of the 66th Annual Meeting of the European Federation of Animal Science (Vol. 21, pp. 347-347). Wageningen Academic Publishers. http://www.wageningenacademic.com/doi/book/10.3920/978-90-8686-816-2
Gebreyesus, G., Lund, M. S., Buitenhuis, A. J., Bovenhuis, H., Poulsen, N. A. & Janss, L. (2017). Modeling heterogeneous (co)variances from adjacent-SNP groups improves genomic prediction for milk protein composition traits. Genetics Selection Evolution, 49(1), Article 89. https://doi.org/10.1186/s12711-017-0364-8
Gebreyesus, G., Lund, M. S., Janss, L., Bovenhuis, H. & Buitenhuis, A. J. (2016). Modeling heterogeneous co-variancas for genomic regions in prediction for milk protein compositions. In Book of Abstracts of the 67th Annual Meeting of the European Association for Animal Production Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-830-8
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
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
Liu, H., Henryon, M. & Sørensen, A. C. (2017). Mating strategies with genomic information reduce rates of inbreeding in animal breeding schemes without compromising genetic gain. Animal, 11(4), 547-555. https://doi.org/10.1017/S1751731116001786
Liu, H., Henryon, M. & Sørensen, A. C. (2015). Mating strategies using genomic information reduce rates of inbreeding. In Abstracts of the 66th Annual Meeting of the European Federation of Animal Science (Vol. 21, pp. 393-393). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-816-2
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
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

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Articles by external partners

2018

Journal articles

Morgante, F., Huang, W., Maltecca, C., Mackay. T.F.C. 2018. Effect of genetic architecture on the prediction accuracy of quantitative traits in samples of unrelated individuals. Heredity 120: 500-514

Conference contributions

van den Berg, I., Hayes, B.J., Goddard, M.E. 2018. Using expression data to detect small QTL in dairy cattle. Proceedings of the 11th WCGALP, Auckland, New Zealand 2018

2017

Journal articles

van den Berg, I., Bowman, P.J., MacLeod, I.M., Hayes, B.J., Wang, T., Bolormaa, S., Goddard, M.E. 2017. Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect. Genetic Selection Evolution 49:70.

Conference contributions

van den Berg, I., MacLeod, I.M., Bowman, P.J., Wang, T., Goddard, M.E. 2017. Strategies to use whole genome sequence data for genomic prediction in dairy cattle. 22nd AAABG conference, Townsville, Australia.

van den Berg, I., Meuwissen, T.H.E., Macleod, I.M., Goddard, M.E. 2017. Predicting the effect of reference population on the accuracy of across and multi breed genomic prediction. 5th Annual GenSAP Meeting, Billund, Denmark. 15 – 16 November.

van den Berg, I., Hayes, B.J., Goddard, M.E. 2017. Using expression data to detect small QTL in dairy cattle. 5th Annual GenSAP Meeting, Billund, Denmark. 15 – 16 November.

Revised 19.03.2025
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Jette Odgaard Villemoes