Tree Genetics & Genomes

, Volume 7, Issue 5, pp 1011–1023 | Cite as

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

  • Fabio Marroni
  • Sara Pinosio
  • Giusi Zaina
  • Federico Fogolari
  • Nicoletta Felice
  • Federica Cattonaro
  • Michele Morgante
Original Paper

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.

Keywords

Cinnamyl alcohol dehydrogenase Functional variants Linkage disequilibrium Genetic variation Nucleotide diversity 

Supplementary material

11295_2011_391_MOESM1_ESM.pdf (37 kb)
Online Resource 1GPS 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)
11295_2011_391_MOESM2_ESM.doc (28 kb)
Online Resource 2Primers 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)
11295_2011_391_MOESM3_ESM.doc (100 kb)
Online Resource 3Summary 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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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Fabio Marroni
    • 1
  • Sara Pinosio
    • 1
    • 2
  • Giusi Zaina
    • 2
  • Federico Fogolari
    • 3
  • Nicoletta Felice
    • 2
  • Federica Cattonaro
    • 1
    • 4
  • Michele Morgante
    • 1
    • 2
  1. 1.Institute of Applied GenomicsUdineItaly
  2. 2.Department of Agriculture and Environmental SciencesUniversity of UdineUdineItaly
  3. 3.Department of Biomedical Sciences and TechnologiesUniversity of UdineUdineItaly
  4. 4.IGA Technology ServicesUdineItaly

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