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Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene

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Abstract

Cinnamyl alcohol dehydrogenase (CAD) is involved in the biosynthesis of lignin, a component of plant cell wall which negatively impacts paper pulp processing and biomass fermentation to ethanol. Transgenic poplars with depressed CAD activity show structural alterations of lignin. Natural CAD mutants have been identified in several plants; however, no natural CAD mutants have been identified in poplar. We surveyed the natural genetic variation in CAD4, a gene coding for CAD, in 360 poplar trees from Western Europe. We measured linkage disequilibrium (LD) between single-nucleotide polymorphisms (SNPs), performed neutrality tests and estimated diversity indexes, and investigated their dependence from sample size. We identified 45 SNPs, six of which caused an amino acid substitution. Our results suggest a short span of LD in Populus nigra CAD4 gene. We identified carriers of different nonsynonymous SNPs in CAD4; those subjects are candidate to be used in classical breeding programs to obtain carriers of different combinations of functional polymorphisms. We showed that use of small sample size might lead to biased estimates of LD, neutrality tests, and diversity indexes.

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Acknowledgments

The research leading to these results have received funding from the European Community’s Seventh Framework Program (FP7/2007-2013) under the grant agreement no. 211917 (ENERGYPOPLAR). The authors thank Marc Villard, Veronique Jorge, Vanina Guerin, and Catherine Bastien of the National Institute for Agricultural Research (INRA), Centre of Orleans, for providing samples, Wout Boerjian (VIB, Gent) for help in the planning of the study, and Martin Lascoux (University of Uppsala) for critical comments on the manuscript.

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Authors and Affiliations

  1. Institute of Applied Genomics, Udine, Italy

    Fabio Marroni, Sara Pinosio, Federica Cattonaro & Michele Morgante

  2. Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy

    Sara Pinosio, Giusi Zaina, Nicoletta Felice & Michele Morgante

  3. Department of Biomedical Sciences and Technologies, University of Udine, Udine, Italy

    Federico Fogolari

  4. IGA Technology Services, Udine, Italy

    Federica Cattonaro

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  1. Fabio Marroni
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  2. Sara Pinosio
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  3. Giusi Zaina
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  4. Federico Fogolari
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  5. Nicoletta Felice
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  6. Federica Cattonaro
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Correspondence to Fabio Marroni or Michele Morgante.

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Communicated by J. Wegrzyn

Electronic supplementary material

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Online Resource 1

GPS coordinates of study sample. Country of origin is shown together with latitude, longitude, and number of trees sampled at that coordinate (N). NA information not available (PDF 37 kb)

Online Resource 2

Primers used to sequence CAD4. F forward, R reverse, Position position of the first base of the primer relative to CAD4 consensus sequence (DOC 27 kb)

Online Resource 3

Summary statistics of identified SNPs. Position base pair position relative to the consensus sequence. SNP (1/2) alleles of the SNP (in alphabetical order). MA minor allele, MAF minor allele frequency, O(1/1) observed individuals with genotype 1/1, O(1/2) observed individuals with genotype 1/2, O(2/2) observed individuals with genotype 2/2. HWE p value of Fisher’s exact test for deviations from Hardy–Weinberg Equilibrium. Nonsynonymous SNPs are shown in bold (DOC 100 kb)

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Marroni, F., Pinosio, S., Zaina, G. et al. Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene. Tree Genetics & Genomes 7, 1011–1023 (2011). https://doi.org/10.1007/s11295-011-0391-5

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  • DOI: https://doi.org/10.1007/s11295-011-0391-5

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