Toward the identification of genes underlying maize QTLs for lignin content, focusing on colocalizations with lignin biosynthetic genes and their regulatory MYB and NAC transcription factors

The identification of genes controlling lignin content is of crucial importance for breeding maize with improved feeding value and yielding more bioenergy after fermentation into alcohol or methane. Up to now, the gene families mostly impacting observed variations in cell wall lignin content have not yet been identified. However, genes involved in monolignol biosynthesis and polymerization, and the MYB and NAC transcription factors that regulate their activities, are promising candidates. In order to test this hypothesis, colocalizations between genes of these families and QTLs for lignin content originating from nine RIL families were investigated, based on gene and QTL physical positions. Ninety-three lignin QTLs were thus collected which corresponded to 44 non-overlapping positions. Among these positions, 11 were jointly shared by three or four RIL progenies, while lignin QTLs were observed for only one progeny in 16 positions. In addition to the few genes described in maize, candidate genes involved in monolignol biosynthesis and regulation of secondary wall lignification were searched for as orthologs of genes with such functions from several species including Arabidopsis, eucalyptus, poplar, and rice. Altogether, 50 ZmMYB-, 49 ZmNAC-, and 95 monolignol-related genes were considered as putative candidates. ZmMYB genes were found colocalizing with lignin QTLs in 25 positions, ZmNAC in 22 positions, and both ZmMYB and ZmNAC genes were present together in 12 QTL positions. Finally, 74 % of ZmMYB and 63 % of ZmNAC putatively involved in secondary wall regulation colocalized with or were close to lignin QTLs. Similarly, 66 % of genes involved in monolignol biosynthesis colocalized with QTL positions, whereas fewer colocalizations were observed for laccases and peroxidases putatively involved in lignin polymerization. In addition, the maize ortholog of the EgMYB2/AtMYB46 secondary cell wall master regulator was not highlighted in this study, possibly indicating significant divergences in the regulation of lignification between grasses and dicotyledonous plants. In contrast, based on gene number and colocalizations with lignin QTLs, orthologs of EgMYB1/AtMYB4 genes seem to have a greater importance in maize and grasses than in dicotyledonous species during secondary wall biosynthesis and deposition.