title: Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds.
abstract: BACKGROUND
  Forage quality of maize is influenced by both the content and structure of lignins in the cell wall. Biosynthesis of monolignols, constituting the complex structure of lignins, is catalyzed by enzymes in the phenylpropanoid pathway.
  
  
  RESULTS
  In the present study we have amplified partial genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (Zea mays L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD) possibly reflecting different levels of selection. Associations with forage quality traits were identified for several individual polymorphisms within the 4CL1, C3H, and F5H genomic fragments when controlling for both overall population structure and relative kinship. A 1-bp indel in 4CL1 was associated with in vitro digestibility of organic matter (IVDOM), a non-synonymous SNP in C3H was associated with IVDOM, and an intron SNP in F5H was associated with neutral detergent fiber. However, the C3H and F5H associations did not remain significant when controlling for multiple testing.
  
  
  CONCLUSIONS
  While the number of lines included in this study limit the power of the association analysis, our results imply that genetic variation for forage quality traits can be mined in phenylpropanoid pathway genes of elite breeding lines of maize.
authors.affiliation: Department of Genetics and Biotechnology, University of Aarhus, Research Center Flakkebjerg, 4200 Slagelse, Denmark. jepper.andersen@agrsci.dk
authors.forename: Jeppe Reitan
authors.initials: JR
authors.lastname: Andersen
authors.forename: Imad
authors.initials: I
authors.lastname: Zein
authors.forename: Gerhard
authors.initials: G
authors.lastname: Wenzel
authors.forename: Birte
authors.initials: B
authors.lastname: Darnhofer
authors.forename: Joachim
authors.initials: J
authors.lastname: Eder
authors.forename: Milena
authors.initials: M
authors.lastname: Ouzunova
authors.forename: Thomas
authors.initials: T
authors.lastname: Lübberstedt
mesh_terms: D001483:Base Sequence; D001947:Breeding; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D005819:Genetic Markers; D014644:Genetic Variation; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D010666:Phenylpropionates / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D003313:Zea mays / Q000145:classification / Q000235:genetics* / Q000378:metabolism*
chemical_list: D005819:Genetic Markers; D010666:Phenylpropionates; D010940:Plant Proteins