High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)

Abstract

Kochia, a major weed species, has evolved resistance to four herbicide modes of action. Herbicide resistance appears to spread quickly, which could result in diminished standing genetic variation, reducing the ability of populations to adapt further. Here we used double digest restriction enzyme associated sequencing to determine the level of gene flow among kochia populations and whether selection for glyphosate resistance reduces genetic variation. Canadian Prairie populations show little to no genetic differentiation (F_ST = 0.01) and no correlation between genetic and geographic distance (r² = - 0.02 p = 0.56), indicating high gene flow and no population structure. There is some evidence that kochia populations are genetically depauperate compared to other weed species, but genetic diversity did not differ between glyphosate susceptible and resistant populations or individuals. The inbreeding coefficients suggest there are 23% fewer heterozygotes in these populations than expected with random mating, and no variation was found within the chloroplast. These results indicate that any alleles for herbicide resistance can be expected to spread quickly through kochia populations, but there is little evidence this spread will reduce the species' genetic variation or limit the species' ability to respond to further selection pressure.

Figure 1

Between population heat map with higher values as more intensely coloured with Nei’s genetic distance (D_ST; ranged from 0.01 to 0.05) below the diagonal and F_ST values (ranged from 0 to 0.08) above the diagonal. Values that were not considered statistically different from 0 (bootstrap p-value < 0.05) are coded in black.

Figure 2

Principal components analysis (PCA) using SNPs from 3248 variable loci with first and second axes account for 23.6% and 11.2% of the variation, respectively, but showing no clustering by EPSPS:ALS ratio (size), population (colour), or province (shape) indicating little to no population structure in this species.

Figure 3

UPGMA tree based on Prevosti’s Genetic distance (see scale at top of tree) for individuals from kochia populations in Alberta, Saskatchewan and Manitoba. Population of origin is represented by the coloured blocks at the tips, while EPSPS:ALS ratio is represented by the size of the bar. Red branches belong to individuals with an EPSPS:ALS ratios of 4 or greater, which are considered resistant to glyphosate, and blue dots indicate nodes with 80 or greater bootstrap support.

Figure 4

Locations of the kochia populations sampled in Alberta, Saskatchewan and Manitoba, Canada with north toward the top of the figure. Populations where glyphosate resistant individuals were detected in screens by Hall et al. and Beckie et al. are filled and contain a “R” in their label while those with no resistance detected in these screens are shown as empty and include an “S” in their labels.