Genetic variation associated with PPO-inhibiting herbicide tolerance in sorghum

Abstract

Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum for tolerance to such residual herbicides would allow for increased sorghum production and the expansion of herbicide options for growers. In this study, we observed sorghum tolerance to residual fomesafen. To investigate the underlying tolerance mechanism a genome-wide association mapping study was conducted using field-collected sorghum biomass panel (SBP) data, and a greenhouse assay was developed to confirm the field phenotypes. A total of 26 significant SNPs (FDR<0.05), spanning a 215.3 kb region on chromosome 3, were detected. The ten most significant SNPs included two in genic regions (Sobic.003G136800, and Sobic.003G136900) and eight SNPs in the intergenic region encompassing the genes Sobic.003G136700, Sobic.003G136800, Sobic.003G137000, Sobic.003G136900, and Sobic.003G137100. The gene Sobic.003G137100 (PPXI), which encodes the PPO1 enzyme, one of the targets of PPO-inhibiting herbicides, was located 12kb downstream of the significant SNP S03_13152838. We found that PPXI is highly conserved in sorghum and expression does not significantly differ between tolerant and sensitive sorghum lines. Our results suggest that PPXI most likely does not underlie the observed herbicide tolerance. Instead, the mechanism underlying herbicide tolerance in the SBP is likely metabolism-based resistance, possibly regulated by the action of multiple genes. Further research is necessary to confirm candidate genes and their functions.

Fig 1. Field-based phenotypic variation.

Phenotypic distribution (A) and phenotypes (B and C) of herbicide injury in the sorghum biomass panel during the 2015 field season.

Fig 2. Manhattan plot for the genome-wide association mapping of herbicide injury observed in the field.

The threshold line is based on the Bonferroni corrected P-value. A total of twenty-six significant SNPs were detected on chromosome 3.

Fig 3. Linkage disequilibrium plot for the significant SNPs in the 215 kb region of chromosome 3.

The Manhattan plot is shown above and the linkage disequilibrium (LD) shown below. The Manhattan plot shows only the significant SNPs from the association analysis. The x-axis represents the physical location in base pairs. In the LD plot, the r² values between significant SNPs are shown. Red indicates high measures of LD, while yellow indicates low LD.