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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

Abstract

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.

Keywords

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

References

  1. Beaulieu J, Doerksen T, Boyle B, Clément S, Deslauriers M, Beauseigle S, Blais S, Poulin PL, Lenz P, Caron S, Rigault P, Bicho P, Bousquet J, MacKay J (2011) Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression. Genetics 2:197–212CrossRefGoogle Scholar
  2. Berthet S, Demont-Caulet N, Pollet B, Bidzinsk P, Cézard L, Le Bris P, Borrega N, Hervé J, Blondet E, Balzergue S, Lapierre C, Jouanin L (2011) Disruption of LACCASE4 and 17 results in tissue-specific alterations to lignification of Arabidopsis thaliana stems. Plant Cell 23:1124–1137Google Scholar
  3. Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB (2004) Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc Natl Acad Sci USA 101:15255–15260CrossRefPubMedPubMedCentralGoogle Scholar
  4. Caicedo AL, Williamson S, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3:1745–1756CrossRefPubMedGoogle Scholar
  5. Cheng R, Ma JZ, Elston RC, Li MD (2005) Fine mapping functional sites or regions from case–control data using haplotypes of multiple linked SNPs. Ann Hum Genet 69:102–112CrossRefPubMedGoogle Scholar
  6. Chu YG, Su XH (2008) Research progress of single nucleotide polymorphisms in forest trees. Heredites 30:1272–1278Google Scholar
  7. Du QZ, Pan W, Tian JX, Li BL, Zhang DQ (2013) The UDP-glucuronate decarboxylase gene family in Populus: structure, expression, and association genetics. PLoS ONE 8:1–14CrossRefGoogle Scholar
  8. Dvornyk V, Sirvio A, Mikkonen M (2002) Low nucleotide diversity at the pall locus in the widely distributed Pinus sylvestris. Mol Biol Evol 19:179–188CrossRefPubMedGoogle Scholar
  9. Flint-Garcia SA, Thomsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Bio 54:357–374CrossRefGoogle Scholar
  10. Fu YX, Li WS (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709PubMedPubMedCentralGoogle Scholar
  11. Gehrig HH, Winter K, Cushman J, Borland A, Taybi T (2000) An improved RNA isolation method for succulent plant species rich in polyphenols and polysaccharides. Plant Mol Biol Report 18:369–376CrossRefGoogle Scholar
  12. González-Martínez SC, Wheeler NC, Ersoz E, Nelson DC, Neale DB (2007) Association genetics in Pinus taeda L.I. wood property traits. Genetics 175(1):399–409CrossRefPubMedPubMedCentralGoogle Scholar
  13. Guerra FP, Wegrzyn JL, Sykes R, Davis MF, Stanton BJ, Neale DB (2013) Association genetics of chemical wood properties in black poplar (Populus nigra). New Phytol 197:162–176CrossRefPubMedGoogle Scholar
  14. Guo M, Rupe MA, Zinselneier C, Habben J, Bewen BA, Smith OS (2004) Allelic variation of gene expression in maize hybrids. Plant Cell 16:1707–1716Google Scholar
  15. Guo Q, Wang BL, Wang BW, Li BL, Zhang DQ (2011) Isolation, expression and single nucleotide polymorphisms analysis of PtDREB2A in Populus tomentosa. Sci silvae sin 47:49–56Google Scholar
  16. Gupta K (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:46–485Google Scholar
  17. Harald C (2004) Laccases: structure, reactions, distribution. Micron 35(1–2):93–96Google Scholar
  18. Heuertz M, De Paoli E, Källman T, Larsson H, Jurman I, Morgante M, Lascoux M, Gyllenstrand N (2006) Multi-locus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce (Picea abies(L.) Karst). Genetics 174:2095–2105CrossRefPubMedPubMedCentralGoogle Scholar
  19. Hudson RR, Kreitman M, Aguade M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116:153–159PubMedPubMedCentralGoogle Scholar
  20. Ingvarsson PK (2005) Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L. Salicaceae). Genetics 169:945–953CrossRefPubMedPubMedCentralGoogle Scholar
  21. Jin L, Bao JS (2009) Progress on the trait-marker association analysis in plants. Mol Plant Breed 7:1048–1063Google Scholar
  22. Kado T, Yoshimaru H, Tsumura Y (2014) DNA variation in a conifer Cryptomeria japonica (Copressaceae sensu lato). Genetics 164:1547–1599Google Scholar
  23. Krutovsky KV, Neale DB (2005) Nucleotide diversity and linkage disequilibrium in cold-hardiness and wood quality-related candidate genes in douglas fir. Genetics 171:2029–2041CrossRefPubMedPubMedCentralGoogle Scholar
  24. Kuittinen H, Aguage M (2000) Nucleotide variation at the chalcone isomerase locus in Arabidopsis thaliana. Genetics 155:863–872PubMedPubMedCentralGoogle Scholar
  25. LaFayette PR, Eriksson KE, Dean JF (1999) Characterization and heterologous expression of laccase cDNAs from xylem tisssues yellow poplar (Liriodendron tulipifera). Plant Mol Biol 40:23–35CrossRefPubMedGoogle Scholar
  26. Lu SF, Li QZ, Wei HR, Chang MJ (2013) Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa. Plant Biol 110:10848–10853Google Scholar
  27. Ma C, Sun X (2008) Larch genetic improvement and its future development in China. World For Res 21:58–63Google Scholar
  28. McCaig BC, Meagher RB, Dean JF (2005) Gene structure and molecular analysis of the Laccase-like multicopper oxidase (LMCO) gene family in Arabidopsis thaliana. Planta 221:619–636CrossRefPubMedGoogle Scholar
  29. Mohamad SB, Ong AL, Ripen AM (2008) Evolutionary trace analysis at the ligand binding site of laccase. Bioinformation 2:369–372CrossRefPubMedPubMedCentralGoogle Scholar
  30. Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9:325–330CrossRefPubMedGoogle Scholar
  31. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York Google Scholar
  32. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3:1289–1299CrossRefGoogle Scholar
  33. Nowotny P, Kwon JM, Goate AM (2001) SNP analysis to dissect human traits. Curr Opin Neurobiol 11:637–641CrossRefPubMedGoogle Scholar
  34. Olivier M (2004) From SNPs to function: the effect of sequence variation on gene expression. Physiol Genomics 16:182–183 Google Scholar
  35. Paques LE (2004) Roles of European and Japanese larch in the genetic control of growth, architecture and wood quality traits in interspecific hybrids (Larix x eurolepis Henry). Ann Forest Sci 61:25–33CrossRefGoogle Scholar
  36. Pot D, McMillan L, Echt C, Le Provost G, Garnier-Géré P, Cato S, Plomion C (2005) Nucleotide variation in genes involved in wood formation in two pine species. New Phytol 167:101–112CrossRefPubMedGoogle Scholar
  37. Ranocha P, Dougall MC, Hawkins G, Sterjiades S (1999) Biochemical characterization, molecular cloning and expression of laccases-a divergent gene family in poplar. Eur J Biochem 159:1–2Google Scholar
  38. Reinhammar B (1984) Laccase. In: Lontie R (ed) Copper proteins and copper enzymes, vol 3. CRC Press Inc, Boca Raton, pp 1–35Google Scholar
  39. Richardson A, Duncan J, Mcdougall GJ (2000) Oxidase activity in lignifying xylem of a taxonomically diverse range of trees: identification of a conifer Laccase. Tree Physiol 20:1039–1047CrossRefPubMedGoogle Scholar
  40. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497Google Scholar
  41. Salisbury BA, Pungliya M, Choi JY, Jiang RH, Sun XJ, Stephens JC (2003) SNP and haplotype variation in the human genome. Mutat Res 526:53–61CrossRefPubMedGoogle Scholar
  42. Sato Y, Wuli B, Sederoff R (2001) Molecular cloning and expression of eight laccase cDNAs in loblolly pine (Pinus taeda). J Plant Res 114:147–155CrossRefGoogle Scholar
  43. Schuetz M, Smith R, Ellis B (2013) Xylem tissue specification, patterning, and differentiation mechanisms. Exp Botany 64:11–31CrossRefGoogle Scholar
  44. Sun XM, Zhang SG, Li SY, Hou YM (2005) Multi traits selection of open pollinated Larix kaempferi families for pulpwood purpose. Sci silvae sin 41:48–54Google Scholar
  45. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedPubMedCentralGoogle Scholar
  46. Takata K, Kurinobu S, Akio K, Yasue K, Tamai Y, Kisanuki M (2005) Bibliography on Larix kaempferi (Larix kaempferi (Lamb.) Carr.). Eurasian J For Res 8:111–126Google Scholar
  47. Tenaillon M, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98:9161–9166CrossRefPubMedPubMedCentralGoogle Scholar
  48. Tian JX, Du QZ (2012) Allelic variation in PtGA20Ox associates with growth and wood properties in Populus spp. PLoS ONE 12:1–11Google Scholar
  49. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276Google Scholar
  50. Witayakran S (2008) Laccase in organic synthesis and its applications. Doctor Degree, Georgia Institute of Technology United StatesGoogle Scholar
  51. Yasushi S, Ross W, Whetten (2006) Characterization of two laccases of loblolly pine (Pinus taeda) expressed in tobacco BY-2 cells. J Plant Res 119:581–588Google Scholar
  52. Yi M (2014) Polymorphic single nucleotide polymorphisms (SNP) loci within wood quality-related candidate genes are associated with growth and wood properties in Larix kaempferi. Chinese Academy of Forestry, BeijingGoogle Scholar
  53. Yi M, Zhang SG, Xie YH, Sun XM (2013) Isolation and single nucleotide polymorphisms analysis of caffeic acid O-methyltransferase gene (LkCOMT) from Larix kaempferi. For Res 26:52–59Google Scholar
  54. Yoshida KT, Naito S, Takada G (1994) cDNA cloning of regeneration-specific genes in rice by differential screening of randomly amplified cDNAs using RAPD primers. Plant Cell Physiol 35:1003–1009PubMedGoogle Scholar
  55. Zhang DQ, Zhang ZY (2005) Single nucleotide polymorphisms (SNPs) discovery and linkage disequilibrium (LD) in forest trees. For Stud China 7:1–14CrossRefGoogle Scholar
  56. Zhang DQ, Xu BH, Yang XH, Zhang ZY, Li BL (2011) The sucrose synthase gene family in Populus: structure, expression and evolution. Tree Genet Genomes 7:443–456CrossRefGoogle Scholar
  57. Zhao Q, Nakashima Jin, Fang Chen F (2013) Laccase is necessary and non-redundant with peroxidase for lignin polymerization during vascular development in Arabidopsis. Plant Cell 25:3976–3987CrossRefPubMedPubMedCentralGoogle Scholar
  58. Zollner S, Wen X, Pritchard JK (2005) Association mapping and fine mapping with tree LD. Bioinformatics 21:3168–3170CrossRefPubMedPubMedCentralGoogle Scholar

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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