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Frontiers of Agricultural Science and Engineering

Front. Agr. Sci. Eng.    2014, Vol. 1 Issue (1) : 77-84     https://doi.org/10.15302/J-FASE-2014010
RESEARCH ARTICLE |
Transcriptome resources and genome-wide marker development for Japanese larch (Larix kaempferi)
Wanfeng LI1,Suying HAN2,Liwang QI1,Shougong ZHANG1,*()
1. State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
2. State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
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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     
Corresponding Authors: Shougong ZHANG   
Issue Date: 22 May 2014
 Cite this article:   
Wanfeng LI,Suying HAN,Liwang QI, et al. Transcriptome resources and genome-wide marker development for Japanese larch (Larix kaempferi)[J]. Front. Agr. Sci. Eng. , 2014, 1(1): 77-84.
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http://journal.hep.com.cn/fase/EN/10.15302/J-FASE-2014010
http://journal.hep.com.cn/fase/EN/Y2014/V1/I1/77
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Wanfeng LI
Suying HAN
Liwang QI
Shougong ZHANG
Types of dataTotal sequencesTotal bases/bpMean length/bp
Illumina260749162607491600100
Roche 454591759211291630357
Sanger38742956198763
Total26670549
Assembled transcripts146786124640235849
Tab.1  Summary of transcriptome assembly
Fig.1  Representation of Gene Ontology (GO) classification in terms of ‘biologic processes’
Fig.2  Phylogenetic tree analysis from the orthologous data set across A. thaliana, L. kaempferi, P. abies, P. trichocarpa and V. vinifera
Marker informationSNPSSRInDel
Total number of identified markers463482475612434
Number of markers within annotated transcripts36422735208723
Number of transcripts with markers48578443810357
Number of annotated transcripts with markers3245332647035
Tab.2  Molecular markers identified from L. kaempferi
Fig.3  Summary analysis of single-nucleotide polymorphisms (SNPs) and single-nucleotide polymorphisms (SSRs). (a) Distribution of minor allele frequencies of SNPs identified in L. kaempferi. The x-axis represents the SNP sequence-derived minor allele frequency, while the y-axis represents the number of SNPs with a given minor allele frequency; (b) distribution of SNPs per transcript. The x-axis represents the number of SNPs per transcript, while the y-axis represents the number of transcripts with a given number of SNPs; (c) frequency of SSRs. The x-axis represents the SSR types and the y-axis represents the percentage of a given SSR type
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