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Open Access Research article

Near-saturated and complete genetic linkage map of black spruce (Picea mariana)

Bum-Yong Kang14, Ishminder K Mann1, John E Major3 and Om P Rajora12*

Author Affiliations

1 Forest Genetics and Biotechnology Group, Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, NS, B3 H 4J1, Canada

2 Current Address: Canada Research Chair in Forest and Conservation Genomics and Biotechnology, Canadian Genomics and Conservation Genetics Institute, Faculty of Forestry and Environmental Management, PO Box 44000, 28 Dineen Drive, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada

3 Natural Resources Canada, Canadian Forest Service - Atlantic Forestry Centre, PO Box 4000, 1350 Regent Street, Fredericton, NB, E3B 5P7, Canada

4 Current Address: Division of Pulmonary, Allergy, and Critical Care Medicine, Emory University School of Medicine and Atlanta Veterans Affairs Medical Center, 1670 Clairmont Road, Decatur, GA 30033, USA

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BMC Genomics 2010, 11:515  doi:10.1186/1471-2164-11-515

Published: 24 September 2010

Abstract

Background

Genetic maps provide an important genomic resource for understanding genome organization and evolution, comparative genomics, mapping genes and quantitative trait loci, and associating genomic segments with phenotypic traits. Spruce (Picea) genomics work is quite challenging, mainly because of extremely large size and highly repetitive nature of its genome, unsequenced and poorly understood genome, and the general lack of advanced-generation pedigrees. Our goal was to construct a high-density genetic linkage map of black spruce (Picea mariana, 2n = 24), which is a predominant, transcontinental species of the North American boreal and temperate forests, with high ecological and economic importance.

Results

We have developed a near-saturated and complete genetic linkage map of black spruce using a three-generation outbred pedigree and amplified fragment length polymorphism (AFLP), selectively amplified microsatellite polymorphic loci (SAMPL), expressed sequence tag polymorphism (ESTP), and microsatellite (mostly cDNA based) markers. Maternal, paternal, and consensus genetic linkage maps were constructed. The maternal, paternal, and consensus maps in our study consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal map had 816 and the paternal map 743 markers distributed over 12 linkage groups each. The consensus map consisted of 1,111 markers distributed over 12 linkage groups, and covered almost the entire (> 97%) black spruce genome. The mapped markers included 809 AFLPs, 255 SAMPL, 42 microsatellites, and 5 ESTPs. Total estimated length of the genetic map was 1,770 cM, with an average of one marker every 1.6 cM. The maternal, paternal and consensus genetic maps aligned almost perfectly.

Conclusion

We have constructed the first high density to near-saturated genetic linkage map of black spruce, with greater than 97% genome coverage. Also, this is the first genetic map based on a three-generation outbred pedigree in the genus Picea. The genome length in P. mariana is likely to be about 1,800 cM. The genetic maps developed in our study can serve as a reference map for various genomics studies and applications in Picea and Pinaceae.