Genomics of Maize Stover Yield and Saccharification Efficiency Using a Multi-Parent Advanced Generation Intercross (MAGIC) Population

Abstract Background: Cellulosic ethanol derived from fast growing C4 grasses could become an alternative to finite fossil fuels. With the potential to generate a major source of lignocellulosic biomass, maize has gained importance as an outstanding model plant for studying the complex cell wall network, and as a model to optimize crop breeding strategies in bioenergy grasses. A genome-wide association study was conducted using a subset of 408 Recombinant Inbred Lines (RILs) from a Multiparent-Advanced Intercross (MAGIC) Population in order to identify single nucleotide polymorphisms (SNPs) associated with yield and saccharification efficiency of maize stover. Results: We identified 4 SNPs significantly associated with stover yield that corresponded to 4 QTL, and 16 SNPs significantly associated with saccharification efficiency, that could be clustered into 5 QTL. Markers linked to these QTL could be used in marker-assisted selection programs to improve ethanol production. In addition, we have pointed out genes that contain the significant SNPs or are physically close to them. Conclusions: Genes involved in nitrogen assimilation, organ growth, and stress tolerance could be good candidates attending to QTLs for stover yield. On the other hand, for saccharification efficiency we highlight genes implicated in biomass degradation, transcriptional control of monolignol biosynthesis, and lignin polymerization as probable candidate genes in the QTLs involved.