Original Paper

Theoretical and Applied Genetics

, Volume 114, Issue 2, pp 307-319

First online:

High levels of linkage disequilibrium and associations with forage quality at a Phenylalanine Ammonia-Lyase locus in European maize (Zea mays L.) inbreds

  • Jeppe R. AndersenAffiliated withDanish Institute of Agricultural Sciences, Research Center Flakkebjerg
  • , Imad ZeinAffiliated withDepartment of Agronomy and Plant Breeding, Technical University of Munich
  • , Gerhard WenzelAffiliated withDepartment of Agronomy and Plant Breeding, Technical University of Munich
  • , Birte KrützfeldtAffiliated withBavarian State Research Center for Agriculture
  • , Joachim EderAffiliated withBavarian State Research Center for Agriculture
  • , Milena OuzunovaAffiliated withKWS Saat AG
  • , Thomas LübberstedtAffiliated withDanish Institute of Agricultural Sciences, Research Center Flakkebjerg Email author 

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Abstract

Forage quality of maize is influenced by both the content and structure of lignin in the cell wall. Phenylalanine Ammonia-Lyase (PAL) catalyzes the first step in lignin biosynthesis in plants; the deamination of l-phenylalanine to cinnamic acid. Successive enzymatic steps lead to the formation of three monolignols, constituting the complex structure of lignin. We have cloned and sequenced a PAL genomic sequence from 32 maize inbred lines currently employed in forage maize breeding programs in Europe. Low nucleotide diversity and excessive linkage disequilibrium (LD) was identified at this PAL locus, possibly reflecting selective constrains resulting from PAL being the first enzyme in the monolignol, and other, pathways. While the association analysis was affected by extended LD and population structure, several individual polymorphisms were associated with neutral detergent fiber (not considering population structure) and a single polymorphism was associated with in vitro digestibility of organic matter (considering population structure).