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.
Highlights
Since the introduction of transgenic soybean, corn, and cotton in the mid-1990s, herbicide-resistant varieties of these crops have largely replaced conventional varieties in the United States (Coupe and Capel, 2016)
This study focuses on a GR population identified in a no-till cotton-wheat double crop system near Phoenix, Arizona (AZ), United States
Previous population genetics studies investigating the phylogeographic structure of pesticide resistant organisms reveal either a single origin (Raymond and Callaghan, 1991; Linda and Alan, 1997; Daborn et al, 2002) or, more frequently, redundant independent, parallel evolution events shaped by variations in selection pressure (Cavan et al, 1998; Anstead et al, 2005; Menchari et al, 2006; Chen et al, 2007; Pinto et al, 2007; Délye et al, 2010)
Summary
Since the introduction of transgenic soybean, corn, and cotton in the mid-1990s, herbicide-resistant varieties of these crops have largely replaced conventional varieties in the United States (Coupe and Capel, 2016). Amaranthus palmeri is a dioecious, annual species with prolific seed production, pollen-mediated gene flow due to obligate outcrossing, and high genetic variability (Franssen et al, 2001; Sellers et al, 2003; Ward et al, 2013). During the early 20th century, the species started to spread east and northeast, probably because of human mediated seed dispersal (Sauer, 1957; Ward et al, 2013). By 2009 the weed was ranked the most troublesome weed in cotton in the Southern United States (Webster and Nichols, 2012; Ward et al, 2013)
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