Population genomics of Digitaria insularis from soybean areas in Brazil

Abstract

BACKGROUND: Digitaria insularis is a weed species that has gained considerable importance in Brazil's soybean production areas that rely on glyphosate-resistant cultivars. Herbicide-resistant weed populations of this species have been reported in many regions in Brazil, first in the south, followed by later reports in the north. We hypothesized that the spread of herbicide-resistant D. insularis is facilitated by movement of agricultural machinery from the southern regions of Brazil.RESULTS: Population genomics revealed a weak or no genetic structure (F ST = [0; 0.16]), moderate expected heterozygosity (H E = 0.15; 0.44) and low inbreeding (F IS = [−0.1; 0.1]) in D. insularis populations. Our data supported the hypothesis that herbicide resistance gene flow predominantly occurred in a south-to-north direction based on a migration analysis. We also found evidence of local adaptation of resistant populations in the northern soybean-growing regions of Brazil. CONCLUSION: Evidence in our work suggests that gene flow of glyphosate-resistant D. insularis is associated with movement of agricultural machinery, although local selection pressure seems to play an important role in the evolution of herbicide resistance throughout the country. Our results suggest preventive practices such as equipment sanitation should be implemented to limit the spread of herbicide resistant D. insularis.

Genomic characterisation and dissection of the onset of resistance to acetyl CoA carboxylase-inhibiting herbicides in a large collection of Digitaria insularis from Brazil

“…Both genetic diversity parameters (PIC and H E ) indicated an overall high genetic diversity in the populations. The H E estimates in populations (0.56-0.64) are higher than the previously reported values for this species by GBS markers (0.15-0.45;Netto et al, 2021). This discrepancy is partly due to differences in the sample size, i.e., a smaller set analysed in the previous study and due to the fact that only glyphosate resistant and susceptible populations were investigated earlier (Gonçalves Netto et al, 2021).…”

“…The H E estimates in populations (0.56–0.64) are higher than the previously reported values for this species by GBS markers (0.15–0.45; Netto et al, 2021). This discrepancy is partly due to differences in the sample size, i.e., a smaller set analysed in the previous study and due to the fact that only glyphosate resistant and susceptible populations were investigated earlier ( Gonçalves Netto et al, 2021 ). A further comparison with other outcrossing weed species revealed higher genetic diversity in D. insularis as compared to Alopecurus myosuroides (average H E = 0.24) and Ipomoea purpurea (average H E = 0.24) and lower genetic diversity than Lolium multiflorum (average H E = 0.81) ( Délye et al, 2010 ; Kuester et al, 2015 ; Karn and Jasieniuk, 2017 ; Dixon et al, 2021 ).…”

“…Hitherto, limited knowledge exists on the genetic diversity and population genetic structure in D. insularis as is the case with most other weed species ( Gonçalves Netto et al, 2021 ). The information on the genetic diversity and population structure in D. insularis is important to increase our understanding of the genetic structure and gene flow across natural expansion area of this weed species.…”

A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae

“…Therefore, in addition to parallel evolution of adaptive traits in each local population, frequent gene flow among different habitats might have also occurred in D. ciliaris . Gene flow fostered by the outcrossing capability of D. ciliaris may have maintained genetic variation of each locally adapted population under adaptive selection, as hypothesized for herbicide-resistant populations of several weed species, including D. insularis (Kataoka and Kataoka 1991; Karn and Jasieniuk 2017; Gonçalves Netto et al . 2021; Brunharo and Tranel 2023).…”

“…The polyploidy of this reference genome and the limited number of reference genomes hamper efforts to perform genomic analyses of Digitaria species (Ravet et al . 2018; Gonçalves Netto et al . 2021).…”