The population genomics of Conyza spp. in soybean macroregions suggest the spread of herbicide resistance through intraspecific and interspecific gene flow

Abstract

Herbicide-resistant Conyza spp. are a threat to many crops. These widespread weeds are closely related species and often cooccur. To characterize the origins of their resistance and the mechanisms underlying their spread, we assessed the genomic variation in glyphosate-resistant Conyza spp. in Brazil. Twenty populations were sampled from soybean fields across four macroregions (MRSs). A genotyping-by-sequencing study resulted in 2,998 single-nucleotide polymorphisms (SNPs) obtained for C. bonariensis (L.) and the closely related C. sumatrensis (Retz) E. Walker. Higher genomic diversity (π) and heterozygosity (H_O/H_E) and lower inbreeding coefficient (F_IS) values were detected in populations of Conyza spp. from MRS 1 (southern) than in those from other MRSs. Strong genomic structure clustered individuals into three groups (F_ST = 0.22; p value = 0.000) associated with the MRSs. Thus, resistance to glyphosate originated from independent selection in different MRSs across Brazil. Our dataset supports the occurrence of intraspecific gene flow in Brazil and identified individuals of C. bonariensis that did not group within species. These findings suggest that allelic introgressions within and among species have impacted the evolution and spread of resistance to glyphosate in Conyza spp. We discuss how to mitigate new resistance cases, particularly for the released stacked traits herbicide tolerance in soybeans.

Figure 1

The frequencies of plant mortality (%) in response to glyphosate grouped into two clusters for 314 individuals of Conyza bonariensis (ERIBO) or C. sumatrensis (ERISU) sampled in 20 soybean fields across four cropping macroregions in 2021 in Brazil. The data were evaluated 42 days after treatment. Dashed lines correspond to the cluster limits. K-clustering was defined by the elbow criterion, and the limits among clusters were defined by the K-means method.

Figure 2

Bar plots with the DAPC results for individuals of Conyza spp. sampled from 20 soybean fields across four cropping macroregions in 2021 in Brazil (202 individuals and 2998 SNPs included). Vertical bars represent individuals whose genotypes have been portioned into distinct clusters; (a) Bar plot of DAPC with ancestry coefficient for K = 2; (b) bar plot of K = 4; (c) bar plot of K = 6; and (d) bar plot of K = 8.

Figure 3

Principal component analysis (PCA) (202 individuals and 2,998 SNPs included). The separation between the Conyza spp. and soybean cropping macroregions in Brazil is shown. ERIBO refers to Conyza bonariensis, ERISU refers to Conyza sumatrensis, and MRS refers to the soybean cropping macroregion.

Figure 4

Neighbor-joining dendrograms based on Jaccard’s genetic similarity coefficient (202 individuals and 2998 SNPs included) showing potential interspecific hybridization. ERIBO refers to Conyza bonariensis, ERISU refers to Conyza sumatrensis, and MRS refers to the soybean cropping macroregion.