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.
Highlights
Abbreviations Multi-Parent Advanced Generation Intercross (MAGIC) Multi-Parent Advanced Generetion InterCross genome-wide association study (GWAS) Genome wide association study single nucleotide polymorphisms (SNPs) Single nucleotide polymorphism QTL Quantitative Trait Loci linkage disequilibrium (LD) Linkage disequilibrium SACC Saccharification efficiency Recombinant Inbred Lines (RILs) Recombinant inbred line CI Confidence interval
Lignocellulosic biomass from maize stover is composed of 33.1% hemicellulose, 39.4% cellulose, and 14.9% lignin[3]
We identified genomic regions and genes putatively associated with saccharification efficiency and stover yield using this MAGIC population
Summary
A subset of 408 RILs of the MAGIC population together with the eight founders were evaluated for saccharification efficiency of maize stover after alkaline pre-treatment and for stover yield. The analyses of variance showed that differences among founder inbreds were significant for stover yield but not for saccharification efficiency. RIL means differed significantly for both traits without showing year x environment interaction. Reliable associations between some SNPs and stover yield are expected since, in the Q-Q plot, lower p values significantly differ from those expected under no significant association. Fifteen SNPs were significantly associated with the traits under study in the two-year combined analysis, 13 of them being significant in 2016 and nine in 2017 (Table 2). The genes containing or physically close (within the SNP confidence interval (CI) when CI ≤ 1 Mbp) to SNPs significantly associated with traits were identified and characterized according to the maize B73 reference genome assembly, version 4 (Supplementary Table S2). No candidate genes for stover yield and saccharification efficiency could be highlighted
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