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Abstract
Genomic variance was estimated using genomic relationship matrices based on different coverage depths to verify effects of coverage depth. Example traits were seed yield, rust score and heading date. A total of 995 F2 families were genotyped via GBS, resulting in allele frequency estimates at 1 million SNPs in each family, the coverage within family ranging from 0 to 60. Results from both real and simulated data show that genomic variance is overestimated at lower coverage depth. This overestimation is caused by inflated diagonals in the genomic relationship matrix based on sequence data. The estimate of environmental variance is independent of sequencing coverage.
We conclude that it is feasible to estimate genetic variance among F2 families using an NGS approach, which is promising for the application of genomic prediction and genomic selection
Original language | English |
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Title of host publication | Proceeding of Plant & Animal Genome XXII : The International Conference on the Status of Plant & Animal Genome Research |
Number of pages | 1 |
Place of publication | San Diego, USA |
Publication date | 11 Jan 2014 |
Pages | 157-157 |
Publication status | Published - 11 Jan 2014 |
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GenSAP : GenSAP - Center for Genomic Selection in Animal and Plants
Lund, M. S. (Project manager), Sørensen, P. (Project manager), Janss, L. (Project manager), Sørensen, A. C. (Project manager), Dybdahl Pedersen, L. (Project coordinator), Jensen, J. (Participant), Christensen, O. F. (Participant), Guldbrandtsen, B. (Participant), Asp, T. (Participant), Bendixen, C. (Participant), Su, G. (Participant), Madsen, P. (Participant), Brøndum, R. F. (Participant), Rasmussen, S. K. (Participant), Nielsen, K. L. (Participant), Goddard, M. (Participant), Meuwissen, T. (Participant), Mackay, T. (Participant), Boichard, D. (Participant), Zhang, Q. (Participant) & Gianola, D. (Participant)
Det Strategiske Forskningsråd, Programkomiteen for Sunhed, fødevarer og velfærd
01/01/2013 → 31/12/2018
Project: Research