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

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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).

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Abbreviations

IVDOM:

In vitro digestibility of organic matter

WSC:

Water soluble carbohydrates

NDF:

Neutral detergent fiber

DNDF:

Digestibility of neutral detergent fiber

Indel:

Insertion–deletion polymorphism

LD:

Linkage disequilibrium

PAL:

Phenylalanine Ammonia-Lyase

SNP:

Single nucleotide polymorphism

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Acknowledgments

We would like to thank KWS Saat AG (Einbeck) and the German ministry for education and science (BMBF) for financial support of the EUREKA project Cerequal.

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Authors and Affiliations

  1. Danish Institute of Agricultural Sciences, Research Center Flakkebjerg, 4200, Slagelse, Denmark

    Jeppe R. Andersen & Thomas Lübberstedt

  2. Department of Agronomy and Plant Breeding, Technical University of Munich, Am Hochanger 2, 85354, Freising-Weihenstephan, Germany

    Imad Zein & Gerhard Wenzel

  3. Bavarian State Research Center for Agriculture, Vöttinger Str. 38, 85354, Freising-Weihenstephan, Germany

    Birte Krützfeldt & Joachim Eder

  4. KWS Saat AG, Grimsehlstr. 31, 37555, Einbeck, Germany

    Milena Ouzunova

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  1. Jeppe R. Andersen
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  2. Imad Zein
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Correspondence to Thomas Lübberstedt.

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Communicated by H. H. Geiger.

Jeppe R. Andersen and Imad Zein contributed equally to the manuscript.

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Andersen, J.R., Zein, I., Wenzel, G. et al. High levels of linkage disequilibrium and associations with forage quality at a Phenylalanine Ammonia-Lyase locus in European maize (Zea mays L.) inbreds. Theor Appl Genet 114, 307–319 (2007). https://doi.org/10.1007/s00122-006-0434-8

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