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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2017

Contribution to journal

Liu, A., Wang, Y., Sahana, G., Zhang, Q., Liu, L., Lund, M. S. & Su, G. (2017). Genome-wide Association Studies for Female Fertility Traits in Chinese and Nordic Holsteins. Scientific Reports, 7(1), Article 8487. https://doi.org/10.1038/s41598-017-09170-9
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, 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
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
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
Fang, L., Sahana, G., Ma, P., Su, G., Yu, Y., Zhang, S., Lund, M. S. & Sørensen, P. (2017). Exploring the genetic architecture and improving genomic prediction accuracy for mastitis and milk production traits in dairy cattle by mapping variants to hepatic transcriptomic regions responsive to intra-mammary infection. Genetics Selection Evolution, 49, Article 44. https://doi.org/10.1186/s12711-017-0319-0
Fang, L., Sahana, G., Su, G., Yu, Y., Zhang, S., Lund, M. S. & Sørensen, P. (2017). Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle. Scientific Reports, 7, Article 45560. https://doi.org/10.1038/srep45560
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
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
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

2016

Contribution to conference

Sverrisdóttir, E., Janss, L., Byrne, S., Asp, T. & Lehmann Nielsen, K. (2016). Initiating genomic selection in tetraploid potato. Abstract from 13th Solanaceae Conference, Davis, United States.
Marete, A. G., Lund, M. S. & Boichard, D. A. (2016). Dissecting dairy complex traits beyond additive effects using genetic markers. Abstract from 19 thSéminaire des thésards du Département de Génétique Animale, Toulouse, France.
Gebreyesus, G., Lund, M. S., Janss, L., Bovenhuis, H. & Buitenhuis, A. J. (2016). Fine mapping and genomic prediction for detailed milk protein composition. Poster session presented at 5th International Conference on Quantitative Genetics , Madison, United States.

2016

Contribution to book anthology

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

2016

Contribution to journal

Zhang, Q., Guldbrandtsen, B., Calus, M. P. L., Lund, M. S. & Sahana, G. (2016). Comparison of gene-based rare variant association mapping methods for quantitative traits in a bovine population with complex familial relationships. Genetics Selection Evolution, 48(1), Article 60. https://doi.org/10.1186/s12711-016-0238-5
Zhang, Q., Guldbrandtsen, B., Thomasen, J. R., Lund, M. S. & Sahana, G. (2016). Genome-wide association study for longevity with whole-genome sequencing in 3 cattle breeds. Journal of Dairy Science, 99(9), 7289-7298. https://doi.org/10.3168/jds.2015-10697
Xiang, T., Christensen, O. F., Vitezica, Z. G. & Legarra, A. (2016). Genomic evaluation by including dominance effects and inbreeding depression for purebred and crossbred performance with an application in pigs. Genetics Selection Evolution, 48(1), 1-14. Article 98. https://doi.org/10.1186/s12711-016-0271-4
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
van den Berg, I., Boichard, D. & Lund, M. S. (2016). Comparing power and precision of within-breed and multibreed genome-wide association studies of production traits using whole-genome sequence data for 5 French and Danish dairy cattle breeds. Journal of Dairy Science, 99(11), 8932-8945. https://doi.org/10.3168/jds.2016-11073
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
Sarup, P. M., Jensen, J., Ostersen, T., Henryon, M. & Sørensen, P. (2016). Increased prediction accuracy using a genomic feature model including prior information on quantitative trait locus regions in purebred Danish Duroc pigs. BMC Genetics, 17(11), Article 11. https://doi.org/10.1186/s12863-015-0322-9
Sahana, G., Iso-Touru, T., Wu, X., Nielsen, U., de Koning, D.-J., Lund, M. S., Vilkki, J. & Guldbrandtsen, B. (2016). A 0.5-Mbp deletion on bovine chromosome 23 is a strong candidate for stillbirth in Nordic Red cattle. Genetics Selection Evolution, 48(1), Article 35. https://doi.org/10.1186/s12711-016-0215-z
Rohde, P. D., Krag, K., Loeschcke, V., Overgaard, J., Sørensen, P. & Kristensen, T. N. (2016). A Quantitative Genomic Approach for Analysis of Fitness and Stress Related Traits in a Drosophila melanogaster Model Population. International Journal of Genomics, 2016, 1-11. Article 2157494. https://doi.org/10.1155/2016/2157494
Rohde, P. D., Demontis, D., Castro Dias Cuyabano, B., Børglum, A. & Sørensen, P. (2016). Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes. Genetics (Print), 203(4), 1901-1913. https://doi.org/10.1534/genetics.116.189498
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
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
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
Michot, P., Chahory, S., Marete, A. G., Grohs, C., Dagios, D., Donzel, E., Aboukadiri, A., Deloche, M.-C., Allais-Bonnet, A., Chambrial, M., Barbey, S., Genestout, L., Boussaha, M., Danchin-Burge, C., Fritz, S., Boichard, D. & Capitan, A. (2016). A reverse genetic approach identifies an ancestral frameshift mutation in RP1 causing recessive progressive retinal degeneration in European cattle breeds. Genetics Selection Evolution, 48. https://doi.org/10.1186/s12711-016-0232-y
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
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
Laplat, F., Jensen, J. & Madsen, P. (2016). Genomic Prediction of Manganese Efficiency in Winter Barley. The Plant Genome, 9(2), 1-13. https://doi.org/10.3835/plantgenome2015.09.0085
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
Ehsani, A., Janss, L., Pomp, D. & Sørensen, P. (2016). Decomposing genomic variances in a mouse F2 population using information from GWA, GWE and eQTL analyses. Animal Genetics, 47(2), 165-173. https://doi.org/10.1111/age.12396
Edwards, S. M., Sørensen, I. F., Sarup, P., Mackay, T. F. C. & Sørensen, P. (2016). Genomic prediction for quantitative traits is improved by mapping variants to gene ontology categories in Drosophila melanogaster. Genetics, 203(4), 1871-1883. https://doi.org/10.1534/genetics.116.187161
Ashraf, B. H., Byrne, S., Fé, D., Czaban, A., Asp, T., Pedersen, M. G., Lenk, I., Roulund, N., Didion, T., Jensen, C. S., Jensen, J. & Janss, L. L. (2016). Estimating genomic heritabilities at the level of family-pool samples of perennial ryegrass using genotyping-by-sequencing. Theoretical and Applied Genetics, 129(1), 45-52. https://doi.org/10.1007/s00122-015-2607-9

2015

Contribution to conference

Janss, L. (2015). Experiences in Bioinformatics. Abstract from ADSA-ASAS Joint Annual Meeting 2015, Orlando, Florida, United States. http://www.jtmtg.org/JAM/2015/index.asp
Janss, L., Sverrisdóttir, E. & Lehmann Nielsen, K. (2015). Genomic analysis in tetraploid potato using genotyping-by-sequencing. Abstract from XVI Meeting of the EUCARPIA , Wageningen, Netherlands.
Sverrisdóttir, E., Janss, L., Byrne, S. & Lehmann Nielsen, K. (2015). Initiating Genomic Selection in Tetraploid Potato. Poster session presented at 12th Solanaceae Conference, Bordeaux, France.
Cericola, F., Fé, D., Janss, L., Byrne, S., Fé, D., Czaban, A., Asp, T., Pedersen, M. G., Roulund, N., Jensen, C. S., Lenk, I. & Jensen, J. (2015). Genomic Selection Using Genotyping-By-Sequencing Data with Different Coverage Depth in Perennial Ryegrass. Poster session presented at Plant and Animal Genome Conference XIII, San Diego, United States. https://pag.confex.com/pag/xxiii/webprogram/Paper15890.html

2015

Contribution to book anthology

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
Meier, K., Lund, M. S. & Sørensen, A. C. (2015). A simulation study of a future infrastructure supporting genomic selection in mink. In Proceedings of NJF fur animal seminar 485 (pp. 221-230)
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
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
Cericola, F., Fé, D., Janss, L., Byrne, S., Fé, D., Czaban, A., Asp, T., Pedersen, M. G., Roulund, N., Jensen, C. S., Lenk, I. & Jensen, J. (2015). Genomic Selection Using Genotyping-By-Sequencing Data with Different Coverage Depth in Perennial Ryegrass. In Final Program, Abstract & Exhibit Guide (pp. 290-290) https://pag.confex.com/pag/xxiii/webprogram/Paper15890.html
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

2015

Contribution to journal

Zhang, Q., Calus, M. P. L., Guldbrandtsen, B., Lund, M. S. & Sahana, G. (2015). Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genetics, 16(88), 1-16. https://doi.org/10.1186/s12863-015-0227-7
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
Sørensen, P., de los Campos, G., Morgante, F., F C Mackay, T. & Sorensen, D. (2015). Genetic control of environmental variation of two quantitative traits of Drosophila melanogaster revealed by whole-genome sequencing. Genetics (Print), 201(2), 487-497. https://doi.org/10.1534/genetics.115.180273
Morgante, F., Sorensen, P., Sorensen, D. A., Maltecca, C. & Mackay, T. F. C. (2015). Genetic Architecture of Micro-Environmental Plasticity in Drosophila melanogaster. Scientific Reports, 5, Article 9785. https://doi.org/10.1038/srep09785
Lopes, M. S., Bastiaansen, J. W. M., Janss, L., Knol, E. F. & Bovenhuis, H. (2015). Estimation of Additive, Dominance, and Imprinting Genetic Variance Using Genomic Data. G3: Genes, Genomes, Genetics (Bethesda), 5(12), 2629-2637. https://doi.org/10.1534/g3.115.019513

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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