Population Genetic Structure in Glyphosate-Resistant and -Susceptible Palmer Amaranth (Amaranthus palmeri) Populations Using Genotyping-by-sequencing (GBS)

Abstract

Palmer amaranth ( Amaranthus palmeri ) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri .

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

“…Husnot (F ST = 0.006–0.088 from microsatellites 48 ); and some population pairs of the obligate outcrossing species Amaranthus palmeri S. Watson in the USA (e.g. F ST = 0.052 for R-S pairs from Arizona from SNPs 49 ).…”

The power and potential of genomics in weed biology and management

“…With access to less expensive sequencing technologies, it becomes possible to generate orders of magnitude more data (tens of thousands of markers) for genotyping‐by‐sequencing and population genomics studies . These approaches will significantly increase the power to determine genetic structure, and associated gene flow and dispersal processes in weed populations.…”

“…65,66 With access to less expensive sequencing technologies, it becomes possible to generate orders of magnitude more data (tens of thousands of markers) for genotyping-by-sequencing and population genomics studies. 67 These approaches will significantly increase the power to determine genetic structure, and associated gene flow and dispersal processes in weed populations. Associated with this, the greater genome coverage achieved provides extra power to determine the areas of the genome that are under selection at landscape scales in weed populations, not just for resistance to herbicides, but for weedy traits in general.…”

The genetic architecture and genomic context of glyphosate resistance inAmaranthus tuberculatus

“…While increasingly the genetic repeatability of herbicide resistance is being investigated with genomic approaches (Flood et al, 2016;Küpper, Manmathan, et al, 2018;Leslie & Baucom, 2014;Molin, Wright, Lawton-Rauh, & Saski, 2017;Van Etten et al, 2019), traditional genome-wide association (GWA) approaches have yet to be applied to explicitly characterize the genetic architecture of herbicide resistance, and the repeatability of alleles implicated across populations (but for related approaches, see (Benevenuto et al, 2019;Van Etten et al, 2019)). In other systems, GWAS have been widely and successfully used to identify new candidate genes, characterize the architecture of key traits, make predictions about phenotypes in studied and novel populations, and inform breeding strategies through genomic selection (e.g.…”