QTL analysis of lignification and cell wall digestibility in the Bay-0 × Shahdara RIL progeny of Arabidopsis thaliana as a model system for forage plant

Abstract

Lignification and the complex relationships between lignins and polysaccharide or protein wall components are the basic cause of reduced digestibility in silage maize and other forage crops. Even if major genes of the lignin pathway are known in different species of forage plants, several QTL explaining a significant part of genetic variation either for lignin content or for cell wall digestibility in maize seem to have no colocalization with major genes of the lignin pathway, or their involvement is not yet entirely established. Cell wall and lignin contents, and cell wall digestibility, were thus investigated in an available Arabidopsis RIL progeny, using mature floral stems as organs representative of maize stalks and forage grass hays. Putative candidate genes underlying QTL were then looked for from genomic data available in Arabidopsis databases. Four QTL of cell wall digestibility were found on chromosomes 2, 4, and 5, but unlike previous observations in maize, these QTL were always associated with cell wall content QTL. Two QTL of lignin content in the cell wall were found on chromosome 3, without any colocalization with cell wall content or digestibility QTL. Only two putative candidate genes involved in the lignin monolignol pathway colocalized with found QTL. The PAL4 gene (At3g10340) and the CAD-C gene (At3g19450) positions were both located in the support interval of a QTL of KL/NDF on chromosome 3. However, laccases, peroxidases, and myb transcription factors were also found in the support interval of cell wall digestibility QTL. Genes involved in biosynthesis of polysaccharide and protein compounds of the cell wall were also found colocalizing with cell wall content QTL. The high differences between a floral stem of dicotyledons and a stalk of C4 monocotyledon, in anatomy, tissue patterning, lignin structure and specificity cross-linkage by hydroxycinnamic acids in grass cell walls could explain the difference observed between Arabidopsis and maize. However, the model plant Arabidopsis was proven as very efficient in evidencing genes of the lignin pathway from knocked-out genes, and such a RIL analysis should allow the evidencing of still unknown genes also involved in stem cell wall digestibility.