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Nucleotide sequence analysis of two lignin genes in Acacia auriculiformis × Acacia mangium hybrid for enhancement of wood pulp quality

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Abstract

There is large potential in the establishment of Acacia auriculiformis × Acacia mangium hybrid plantations through selection of high quality parents especially with characteristics favourable for some end products like pulp and fibre. Trees altered in their lignin profile with reduced amounts of lignin or increased extractable syringyl are desirable in the pulp and paper industry. Cinnamoyl-CoA reductase (CCR) and caffeic acid O-methyltransferase (COMT) are two enzymes likely to regulate lignin content and composition in the syringyl (S)- and guaiacyl (G)-related monolignols at specific branches of the lignin biosynthetic pathway. A goal of this study was to discover the genetic variation in CCR and COMT genes in Acacia species using single nucleotide polymorphisms (SNPs). In this study, two lignin genes, CCR (3,317 bp) and COMT (2,764 bp), were isolated from the Acacia hybrid, sequenced and analysed in silico. Southern blot analysis suggested that there are one to two copies of genes encoding CCR and COMT in the Acacia hybrid. Upon genotyping 480 individuals from natural populations of A. auriculiformis and A. mangium, six CCR SNPs were found in A. auriculiformis and five CCR SNPs in A. mangium. Three COMT SNPs were found in A. auriculiformis and one COMT SNP in A. mangium. A pair of CCR SNPs showed high linkage disequlibrium (LD) with r 2 value of 0.870 in an A. mangium population from Papua New Guinea. The SNPs will be further exploited through the candidate gene-based LD mapping to identify QTLs for the Acacia marker-assisted breeding. This is the first documentation of the isolation, cloning and re-sequencing of CCR and COMT genes in the Acacia hybrid and the natural populations of A. auriculiformis and A. mangium.

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Acknowledgments

This study was supported by e-Science Fund (02-01-02-SF0403) from the Ministry of Science, Technology and Innovation, Malaysia and OUP (UKM-OUP-KPB-33-166/2008 dan UKM-OUP-KPB-32-159/2009) from Universiti Kebangsaan Malaysia.

Data archiving statement

The CCR and COMT gene sequences have been deposited in the GenBank. AhgCCR1 GenBank accession number is HQ317734 and AhgCOMT1 GenBank accession number is HQ317735. The polymorphic SNPs identified in the assay have been deposited into dbSNP (Table 5).

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Authors and Affiliations

  1. School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia

    A. Sukganah, C. Y. Choong & R. Wickneswari

  2. The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK

    J. Russell

  3. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    D. Neale

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  1. A. Sukganah
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  2. C. Y. Choong
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  3. J. Russell
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  4. D. Neale
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  5. R. Wickneswari
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Correspondence to R. Wickneswari.

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Communicated by D. Neale

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Sukganah, A., Choong, C.Y., Russell, J. et al. Nucleotide sequence analysis of two lignin genes in Acacia auriculiformis × Acacia mangium hybrid for enhancement of wood pulp quality. Tree Genetics & Genomes 9, 1369–1381 (2013). https://doi.org/10.1007/s11295-013-0640-x

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