title: Nucleotide diversity of the ZmPox3 maize peroxidase gene: relationships between a MITE insertion in exon 2 and variation in forage maize digestibility.
abstract: BACKGROUND
  Polymorphisms were investigated within the ZmPox3 maize peroxidase gene, possibly involved in lignin biosynthesis because of its colocalization with a cluster of QTL related to lignin content and cell wall digestibility. The purpose of this study was to identify, on the basis of 37 maize lines chosen for their varying degrees of cell wall digestibility and representative of temperate regions germplasm, ZmPox3 haplotypes or individual polymorphisms possibly associated with digestibility.
  
  
  RESULTS
  Numerous haplotypes with high diversity were identified. Frequency of nucleotide changes was high with on average one SNP every 57 bp. Nucleotide diversity was not equally distributed among site categories: the estimated pi was on average eight times higher for silent sites than for non-synonymous sites. Numerous sites were in linkage disequilibrium that decayed with increasing physical distance. A zmPox3 mutant allele, carrying an insertion of a transposable element in the second exon, was found in lines derived from the early flint inbred line, F7. This element possesses many structural features of miniature inverted-repeat transposable elements (MITE). The mutant allele encodes a truncated protein lacking important functional sites. An ANOVA performed with a subset of 31 maize lines indicated that the transposable element was significantly associated with cell wall digestibility. This association was confirmed using an additional set of 25 flint lines related to F7. Moreover, RT-PCR experiments revealed a decreased amount of corresponding mRNA in plants with the MITE insertion.
  
  
  CONCLUSIONS
  These results showed that ZmPox3 could possibly be involved in monolignol polymerisation, and that a deficiency in ZmPox3 peroxidase activity seemingly has a negative effect on cell wall digestibility. Also, genetic diversity analyses of ZmPox3 indicated that this peroxidase could be a relevant target for grass digestibility improvement using specific allele introgressions.
authors.affiliation: Centre de recherche en Biologie Forestière, Université Laval, Sainte-Foy, Québec, G1K 7P4, Canada. cguillet@rsvs.ulaval.ca
authors.forename: Carine
authors.initials: C
authors.lastname: Guillet-Claude
authors.forename: Christelle
authors.initials: C
authors.lastname: Birolleau-Touchard
authors.forename: Domenica
authors.initials: D
authors.lastname: Manicacci
authors.forename: Peter M
authors.initials: PM
authors.lastname: Rogowsky
authors.forename: Joan
authors.initials: J
authors.lastname: Rigau
authors.forename: Alain
authors.initials: A
authors.lastname: Murigneux
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Martinant
authors.forename: Yves
authors.initials: Y
authors.lastname: Barrière
mesh_terms: D001483:Base Sequence; D002473:Cell Wall / Q000378:metabolism*; D004251:DNA Transposable Elements; D004063:Digestion; D005091:Exons; D015870:Gene Expression; D014644:Genetic Variation; D007178:Inbreeding; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D005810:Multigene Family; D009154:Mutation; D010544:Peroxidases / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D003313:Zea mays / Q000201:enzymology* / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D010544:Peroxidases