QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data

Fuentes-Utrilla, P., Goswami, C. , Cottrell, J.E., Pong-Wong, R., Law, A., A'Hara, S.W., Lee, S.J. and Woolliams, J.A. (2017) QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data. Tree Genetics and Genomes, 13(2), 33. (doi: 10.1007/s11295-017-1118-z)

Abstract

Sitka spruce (Picea sitchensis (Bong.) Carr) is the most common commercial plantation species in Britain and a breeding programme based on traditional lines has been in operation since the early 1960s. Rotation lengths of 40-years have led breeders to adopt a process of indirect selection at younger ages based on traits well correlated with final selection, but still the generation interval is unlikely to reduce much below twenty years. Recent successful developments with genomic selection in animal breeding have led tree breeders to consider the application of this technology. In this study a RAD sequence assay was developed as a means of investigating the potential of molecular breeding in a non-model species. DNA was extracted from nearly 500 clonally replicated trees growing in a single full-sibling family at one site in Britain. The technique proved successful in identifying 132 QTLs for 5-year bud-burst and 2 QTLs for 6-year height. In addition, the accuracy of predicting phenotypes by genomic selection was strikingly high at 0.62 and 0.59 respectively. Sensitivity analysis with 200 offspring found only a slight fall in correlation values (0.54 and 0.38) although when the training population reduced to 50 offspring predictive values fell further (0.33 and 0.25). This proved an encouraging first investigation into the potential use of genomic selection in the breeding of Sitka spruce. The authors investigate how problems associated with effective population size and linkage disequilibrium can be avoided and suggest a practical way of incorporating genomic selection into a dynamic breeding programme.

• Item Type: Articles
• Additional Information: The research leading to these results received funding from the European Community’s Seventh Framework Programme (FP7/ 2007-2013) under the grant agreement No 211868 (Project Noveltree). John Woolliams and Andrew Law were supported by BBSRC Institute Strategic Grant funding (BBS/E/D/20211551, BBS/ E/D/20211554) and Edinburgh University, Scotland. Steve Lee and Joan Cottrell were supported by core funding from the Forestry Commission (GB). Pablo Fuentes-Utrilla was funded by a fellowship from the "Programa Nacional de Movilidad de Recursos Humanos del Plan Nacional de I-D+i 2008-2011^ of the Ministry of Education, Spain.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Goswami, Dr Cosmika
• Authors: Fuentes-Utrilla, P., Goswami, C., Cottrell, J.E., Pong-Wong, R., Law, A., A'Hara, S.W., Lee, S.J., and Woolliams, J.A.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: Tree Genetics and Genomes
• Publisher: Springer
• ISSN: 1614-2942
• ISSN (Online): 1614-2950
• Published Online: 04 February 2017
• Copyright Holders: Copyright © 2017 The Authors
• First Published: First published in Tree Genetics and Genomes 13(2): 33
• Publisher Policy: Reproduced under a Creative Commons License
• Data DOI: 10.7488/cfb6f594-4dc8-4928-a790-90dbc8bec2aa