Journal of Forestry Research

, Volume 28, Issue 5, pp 891–901 | Cite as

Isolation, expression and single nucleotide polymorphisms (SNPs) analysis of LACCASE gene (LkLAC8) from Japanese larch (Larix kaempferi)

  • Changyong Liu
  • Yunhui Xie
  • Min Yi
  • Shougong Zhang
  • Xiaomei SunEmail author
Original Paper


Nucleotide diversity (π) and linkage disequilibrium (LD) analysis based on SNP marker could provide a sound basis for choosing an association analysis method. Japanese larch (Larix kaempferi) is an important timber coniferous tree species for pulping and papermaking, but its high lignin content has significantly restricted it application potential. In this study, the LACCASE gene, that plays an important regulatory role for lignin biosynthesis, was selected as research target. The full-length cDNA and genomic sequences of the encoding LkLAC8 gene were isolated from the LACCASE expressed sequence tags of the Japanese larch transcriptome database using the rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). The cDNA was determined to be 1940 bp, with an open reading frame (ORF, 1734 bp) that encoded a protein of 577 AA. This protein contains four highly specific Cu2+ binding sites and 11 glycosylation sites, thus belonging to the LACCASE family. The deduced protein sequence shared an 89% identity with the PtaLAC from Pinus taeda. A real-time PCR analysis showed that the LkLAC8 transcript was expressed predominantly in mature xylem, with moderate levels in the immature xylem, cambium and mature leaves, the lowest in the roots. Lastly, the genomic sequences of LkLAC8 in 40 individuals from six naturally distributed populations of Japanese larch were amplified, and a total of 201 SNPs (103 and 98 mutation types of transition and transversion, respectively) were detected; the frequency of the SNPs was 1/19 bp. Nucleotide diversity among the six populations ranged from 0.0034 to 0.0053, which suggested that there were no significant differences among the populations. The LD analysis showed that the LD level decayed rapidly within the increasing length of the LkLAC8 gene. These results implied that LD mapping and association analysis based on candidate gene may be feasible for the marker-assisted breeding of new germplasms with low lignin in Japanese larch.


Gene cloning LACCASE Larix kaempferi Linkage disequilibrium Real-time PCR Single nucleotide polymorphisms 


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Copyright information

© Northeast Forestry University and Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Changyong Liu
    • 1
    • 2
    • 3
  • Yunhui Xie
    • 1
    • 2
  • Min Yi
    • 4
  • Shougong Zhang
    • 1
    • 2
  • Xiaomei Sun
    • 1
    Email author
  1. 1.State Key Laboratory of Tree Genetics and Breeding, Research Institute of ForestryChinese Academy of ForestryBeijingChina
  2. 2.Research Institute of ForestryChinese Academy of ForestryBeijingChina
  3. 3.State Academy of Forestry AdministrationBeijingChina
  4. 4.School of Gardening and Landscape DesignJiangxi Agricultural UniversityNanchang CityChina

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