Extensive DNA sequence variations in two lignin genes, Cinnamate 4-hydroxylase and Cinnamyl Alcohol Dehydrogenase from Acacia mangium and Acacia auriculiformis

M. S. Nur Fariza, S. L. Pang, Chee Yen Choong, R Wickneswari V Ratnam

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Abstract

This study examined DNA sequence variations of coding regions of Cinnamate 4-hydroxylase (C4H) and Cinnamyl Alcohol Dehydrogenase (CAD) in Acacia mangium and A. auriculiformis. cDNA fragments of C4H and CAD with size 1.5 and 1.3 kb, respectively were cloned into pGEM-T Easy Vector and were sequenced. Twenty eight Single Nucleotide Polymorphisms (SNPs) were identified in the coding region of C4H of which 8 caused changes in the amino acids or nonsynonymous mutations and 20 were synonymous mutations. Thirty two SNPs were detected in coding region of CAD. Of these, 12 were nonsynonymous mutations and 20 were synonymous mutations. Two A. mangium individuals (M20 and M22) and two A. auriculiformis individuals (A6 and A3) were used as parents for generating F1 mapping populations. Nucleotide sequence alignment of coding region of CAD detected 28 and 22 SNPs from A3×M22 parental combination and A6×M20 parental combination respectively. Nucleotide sequence alignment of coding region of C4H identified 6 and 23 SNPs for A3×M22 and A6×M20 parental combinations, respectively. For parental combination A3×M22, 11 nonsynonymous mutations were detected while for A6×M20 parental combination 23 nonsynonymous mutations were detected from CAD gene. Amino acid sequence alignment of C4H detected 4 amino acid variations from each parental combination. The putative SNPs can be developed as SNPs markers for Quantitative Trait Loci (QTL) detection. Selecting favourable alleles from progenies which produce desirable lignin profiles would be advantageous in tree breeding programmes for plantation establishment.

Original languageEnglish
Pages (from-to)687-690
Number of pages4
JournalJournal of Biological Sciences
Volume8
Issue number3
DOIs
Publication statusPublished - 2008

Fingerprint

Trans-Cinnamate 4-Monooxygenase
Acacia
Lignin
Single Nucleotide Polymorphism
Sequence Alignment
Genes
Mutation
Amino Acids
Quantitative Trait Loci
Breeding
cinnamyl alcohol dehydrogenase
Amino Acid Sequence
Complementary DNA
Alleles

Keywords

  • Acacia auriculiformis
  • Acacia mangium
  • Cinnamate 4-hydroxylase (C4H)
  • Cinnamyl alcohol dehydrogenase (CAD)
  • Single nucleotide polymorphism

ASJC Scopus subject areas

  • Cell Biology
  • Molecular Medicine

Cite this

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title = "Extensive DNA sequence variations in two lignin genes, Cinnamate 4-hydroxylase and Cinnamyl Alcohol Dehydrogenase from Acacia mangium and Acacia auriculiformis",
abstract = "This study examined DNA sequence variations of coding regions of Cinnamate 4-hydroxylase (C4H) and Cinnamyl Alcohol Dehydrogenase (CAD) in Acacia mangium and A. auriculiformis. cDNA fragments of C4H and CAD with size 1.5 and 1.3 kb, respectively were cloned into pGEM-T Easy Vector and were sequenced. Twenty eight Single Nucleotide Polymorphisms (SNPs) were identified in the coding region of C4H of which 8 caused changes in the amino acids or nonsynonymous mutations and 20 were synonymous mutations. Thirty two SNPs were detected in coding region of CAD. Of these, 12 were nonsynonymous mutations and 20 were synonymous mutations. Two A. mangium individuals (M20 and M22) and two A. auriculiformis individuals (A6 and A3) were used as parents for generating F1 mapping populations. Nucleotide sequence alignment of coding region of CAD detected 28 and 22 SNPs from A3×M22 parental combination and A6×M20 parental combination respectively. Nucleotide sequence alignment of coding region of C4H identified 6 and 23 SNPs for A3×M22 and A6×M20 parental combinations, respectively. For parental combination A3×M22, 11 nonsynonymous mutations were detected while for A6×M20 parental combination 23 nonsynonymous mutations were detected from CAD gene. Amino acid sequence alignment of C4H detected 4 amino acid variations from each parental combination. The putative SNPs can be developed as SNPs markers for Quantitative Trait Loci (QTL) detection. Selecting favourable alleles from progenies which produce desirable lignin profiles would be advantageous in tree breeding programmes for plantation establishment.",
keywords = "Acacia auriculiformis, Acacia mangium, Cinnamate 4-hydroxylase (C4H), Cinnamyl alcohol dehydrogenase (CAD), Single nucleotide polymorphism",
author = "{Nur Fariza}, {M. S.} and Pang, {S. L.} and Choong, {Chee Yen} and {V Ratnam}, {R Wickneswari}",
year = "2008",
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language = "English",
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pages = "687--690",
journal = "Journal of Biological Sciences",
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T1 - Extensive DNA sequence variations in two lignin genes, Cinnamate 4-hydroxylase and Cinnamyl Alcohol Dehydrogenase from Acacia mangium and Acacia auriculiformis

AU - Nur Fariza, M. S.

AU - Pang, S. L.

AU - Choong, Chee Yen

AU - V Ratnam, R Wickneswari

PY - 2008

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N2 - This study examined DNA sequence variations of coding regions of Cinnamate 4-hydroxylase (C4H) and Cinnamyl Alcohol Dehydrogenase (CAD) in Acacia mangium and A. auriculiformis. cDNA fragments of C4H and CAD with size 1.5 and 1.3 kb, respectively were cloned into pGEM-T Easy Vector and were sequenced. Twenty eight Single Nucleotide Polymorphisms (SNPs) were identified in the coding region of C4H of which 8 caused changes in the amino acids or nonsynonymous mutations and 20 were synonymous mutations. Thirty two SNPs were detected in coding region of CAD. Of these, 12 were nonsynonymous mutations and 20 were synonymous mutations. Two A. mangium individuals (M20 and M22) and two A. auriculiformis individuals (A6 and A3) were used as parents for generating F1 mapping populations. Nucleotide sequence alignment of coding region of CAD detected 28 and 22 SNPs from A3×M22 parental combination and A6×M20 parental combination respectively. Nucleotide sequence alignment of coding region of C4H identified 6 and 23 SNPs for A3×M22 and A6×M20 parental combinations, respectively. For parental combination A3×M22, 11 nonsynonymous mutations were detected while for A6×M20 parental combination 23 nonsynonymous mutations were detected from CAD gene. Amino acid sequence alignment of C4H detected 4 amino acid variations from each parental combination. The putative SNPs can be developed as SNPs markers for Quantitative Trait Loci (QTL) detection. Selecting favourable alleles from progenies which produce desirable lignin profiles would be advantageous in tree breeding programmes for plantation establishment.

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KW - Acacia auriculiformis

KW - Acacia mangium

KW - Cinnamate 4-hydroxylase (C4H)

KW - Cinnamyl alcohol dehydrogenase (CAD)

KW - Single nucleotide polymorphism

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