Transcriptome resources and genome-wide marker development for Japanese larch (Larix kaempferi)

Abstract

While the differential responses of trees to changes in climatic and environmental conditions have been demonstrated as they age, the underlying mechanisms and age control of tree growth and development are complex and poorly understood particularly at a molecular level. In this paper, we present a transcriptome analysis of Larix kaempferi, a deciduous conifer that is widely-grown in the northern hemisphere and of significant ecological and economic value. Using high-throughput RNA sequencing, we obtained about 26 million reads from the stems of 1-, 2-, 5-, 10-, 25- and 50-year-old L. kaempferi trees. Combining these with the published Roche 454 sequencing reads and the expressed sequence tags (both mainly from Larix embryogenic cell cultures), we assembled 26670549 reads into 146786 transcripts, of which we annotated 79182 to support investigations of the molecular basis of tree aging and adaption, somatic embryogenesis and wood formation. Using these sequences we also identified many single-nucleotide polymorphisms, simple sequence repeats, and insertion and deletion markers to assist breeding and genetic diversity studies of Larix.

Keywords

Larix / transcriptome / age / wood formation / somatic embryogenesis / molecular marker

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (31200464 and 31330017), and the National High Technology Research and Development Program of China (2011AA100203 and 2013AA102704). The authors thank Dr. IC Bruce (Zhejiang University) and Dr. Yong Guo (Institute of Crop Science, Chinese Academy of Agricultural Sciences) for critical reading of the manuscript, and Dr. Tao Wu for sample collection.

Compliance with ethics guidelinesƒWanfeng Li, Suying Han, Liwang Qi, and Shougong Zhang declare that they have no conflict of interest or financial conflicts to disclose.‚‚This article does not contain any studies with human or animal subjects performed by the any of the authors.

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