Genome‐wide quantitative trait loci detection for biofuel traits in switchgrass (Panicum virgatum L.)

Abstract

Lignocellulosic biomass is composed of complex structures of cellulose, hemicellulose, lignin, and other biochemical and structural components of cell wall. Because of its obligatory outcrossing nature, broad adaptation, and extensive genetic variation, both biomass production and cell wall composition traits could be improved for biofuel production. Among the cell wall components, lignin has been found to be a major inhibitor of the conversion process of cellulosic

Syntenic Cell Wall QTLs as Versatile Breeding Tools: Intraspecific Allelic Variability and Predictability of Biomass Quality Loci in Target Plant Species

“…In addition to evaluating the level and relevance of the intraspecific genetic variability of SQTLs in diverse species, another aim of this study was to assess the validity of SQTLs for predicting genomic loci associated with biomass quality traits in novel plant populations and species. This aspect was studied by assessing the degree of colocalization between the SQTLs previously detected in Miscanthus sinensis and Panicum virgatum [ 1 ] and cell wall related QTLs mapped by genome-wide association analysis (GWAS) in a Miscanthus sinensis collection and QTLs mapped by other researchers in an F1 progeny of a biparental cross of two switchgrass lines diverging for cell wall quality traits [ 21 ]. These populations represent respectively a different intraspecific population than the one from which QTLs used for SQTLs mapping came from (miscanthus), and a separate species than the ones from which initial QTLs have been selected at the moment of SQTLs detection (thus, a hypothetical novel, under-domesticated, species; switchgrass).…”

“…An analogous procedure to the one just described for miscanthus was performed in switchgrass to test the colocalization between the 56 cell wall-related QTLs identified by Ali, Serba, Walker, Jenkins, Schmutz, Bhamidimarri, and Saha [ 21 ] ( Supplementary Table S5 ), and the 254 SQTLs previously detected in switchgrass and conserved across Poaceae ( Supplementary Table S6 ). In switchgrass, it was shown that 53 SQTLs (20.8% of all the switchgrass SQTLs) (partially) colocalize with the 56 cell wall QTLs, while 33 QTLs (59%) colocalize for >50% of their length with SQTLs ( Figure 7 ).…”

“…For switchgrass, the most relevant cell wall genes found in colocalizing regions between SQTLs and QTLs from Ali, Serba, Walker, Jenkins, Schmutz, Bhamidimarri, and Saha [ 21 ] are summarized in Figure 7 and Table 2 . Among others, these include a homolog of the arabidopsis FRAGILE FIBRE 1 locus ( FRA1 ; IV_6NG323500) and a homolog of the arabidopsis KOR gene (IV_1NG408000).…”

“…Moreover, an IRX gene involved in xylan synthesis (IV_5NG144100), and two MYB42 / MYB85 genes important for lignin biosynthesis (IV_2NG449200 and IV_6NG352900). All these genes are retained in QTLs from Ali, Serba, Walker, Jenkins, Schmutz, Bhamidimarri, and Saha [ 21 ] that are associated to traits for which the genes themselves appear highly functionally relevant ( Table 2 ). Moreover, synteny analysis of these genes showed that, as for miscanthus, they are highly syntenic, even if synteny is again mostly restricted to Poaceae ( Figure 8 C,D).…”

“…A total of 56 QTLs related to cell wall traits in switchgrass were retrieved from the results of Ali, Serba, Walker, Jenkins, Schmutz, Bhamidimarri, and Saha [ 21 ] ( Supplementary Table S5 ). Colocalization between these QTLs and the switchgrass SQTLs was analyzed with an analogous procedure to miscanthus.…”