Association mapping for maize stover yield and saccharification efficiency using a multiparent advanced generation intercross (MAGIC) population

Abstract

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 also to optimize crop breeding strategies in bioenergy grasses. A genome-wide association study (GWAS) was conducted using a subset of 408 Recombinant Inbred Lines (RILs) from a Multi-Parent Advanced Generation Intercross (MAGIC) Population in order to identify single nucleotide polymorphisms (SNPs) associated with yield and saccharification efficiency of maize stover. We identified 13 SNPs significantly associated with increased stover yield that corresponded to 13 QTL, and 2 SNPs significantly associated with improved saccharification efficiency, that could be clustered into 2 QTL. We have pointed out the most interesting SNPs to be implemented in breeding programs based on results from analyses of averaged and yearly data. Association mapping in this MAGIC population highlight genomic regions directly linked to traits that influence the final use of maize. Markers linked to these QTL could be used in genomic or marker-assisted selection programs to improve biomass quality for ethanol production. This study opens a possible optimisation path for improving the viability of second-generation biofuels.

Figure 1

Saccharification efficiency and stover yield values in RILs (combined and by years) and parent lines of the MAGIC population (Best Linear Unbiased Estimation).

Figure 2

GWAS of stover yield and saccharification efficiency in a maize MAGIC population. (a) Manhattan plot of the GWAS mixed linear model for Stover Yield. Single-nucleotide polymorphisms (SNPs) above the red horizontal line surpassed the p value threshold obtained by Bonferroni’s modification approach. (b) Quantile–quantile (Q–Q) plot of the GWAS mixed linear model for stover yield. (c) Manhattan plot of the GWAS mixed linear model for saccharification efficiency (SACC). Single-nucleotide polymorphisms (SNPs) above the red horizontal line surpassed the p value threshold obtained by the modification of Bonferroni approach (8.07E−06); (d) Q-Q plot of the GWAS mixed linear model for SACC.