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Gene copy number variation is a predominant mechanism used by organisms to respond to selective pressures from the environment. This often results in unbalanced structural variations that perpetuate as adaptations to sustain life. However, the underlying mechanisms that give rise to gene proliferation are poorly understood. Here, we show a unique result of genomic plasticity in Amaranthus palmeri : a massive, ~400-kb extrachromosomal circular DNA (eccDNA) that harbors the 5-ENOYLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE (EPSPS) gene and 58 other genes whose encoded functions traverse detoxification, replication, recombination, transposition, tethering, and transport. Gene expression analysis under glyphosate stress showed transcription of 41 of these 59 genes, with high expression of EPSPS , as well as genes coding for aminotransferases, zinc finger proteins, and several uncharacterized proteins. The genomic architecture of the eccDNA replicon is composed of a complex arrangement of repeat sequences and mobile genetic elements interspersed among arrays of clustered palindromes that may be crucial for stability, DNA duplication and tethering, and/or a means of nuclear integration of the adjacent and intervening sequences. Comparative analysis of orthologous genes in grain amaranth (Amaranthus hypochondriacus) and waterhemp (Amaranthus tuberculatus) suggests that higher order chromatin interactions contribute to the genomic origins of the A. palmeri eccDNA replicon structure. [ABSTRACT FROM AUTHOR]

BACKGROUND: Clethodim, an acetyl‐CoA carboxylase (ACCase)‐inhibiting herbicide, is one of the few postemergence chemical control options available to growers of Mississippi to manage glyphosate and/or other herbicide resistant Italian ryegrass populations. Recently, clethodim failed to adequately control Italian ryegrass populations across Mississippi. A sethoxydim, also an ACCase inhibitor, ‐resistant Italian ryegrass population from North Carolina was cross‐resistant to clethodim. This research characterized the magnitude and mechanisms of clethodim resistance in the Mississippi and North Carolina Italian ryegrass populations via whole‐plant herbicide dose response, cross resistance, and metabolism studies, and molecular analysis. RESULTS: Two clethodim‐resistant biotypes from Mississippi, MS24 and MS37, were 10‐ and 4‐fold resistant, respectively, relative to a susceptible (SUS1) biotype. A North Carolina biotype, NC21, was 40‐fold resistant to clethodim compared to SUS1. Two additional biotypes from North Carolina, NC22 and NC 23, recorded shoot dry weight reduction of only 17–30% of nontreated at the highest clethodim dose of 2.17 kg ha−1, (8×). The NC22 biotype was cross‐resistant to sethoxydim, fluazifop, quizalofop, and pinoxaden. Metabolic inhibitors such as piperonyl butoxide and 4‐chloro‐7‐nitrobenzofurazan did not affect resistance of MS37, MS51, and NC22 biotypes to fenoxaprop, clethodim, or pinoxaden. The MS37 biotype had three target site mutations, I2041N, C2088R, and G2096A. Another clethodim‐resistant biotype from Mississippi, MS51, had only the C2088R substitution. The NC22 and NC23 biotypes had I1781L, I2041N, and D2078G replacements. CONCLUSION: This study shows that the mechanism of resistance to clethodim in Italian ryegrass from Mississippi and North Carolina is due to target site modifications in the ACCase gene leading to broad cross‐resistance to other ACCase‐inhibiting herbicides. Published 2019. This article is a U.S. Government work and is in the public domain in the USA. [ABSTRACT FROM AUTHOR]

Abstract: BACKGROUND: Glyphosate resistance in Amaranthus palmeri, one of the most prevalent herbicide‐resistant weeds in the USA, is attributable to amplification and increased expression of the gene encoding the target site of glyphosate, 5‐enolpyruvylshikimate‐3‐phosphate synthase (EPSPS). The EPSPS gene and the surrounding 287 kilobases (kb) of amplified sequence are unique to glyphosate‐resistant plants and termed the EPSPS cassette. It has only been sequenced in one A. palmeri population from Mississippi. This research compares EPSPS cassettes in seven resistant and five sensitive populations from geographically distant locations within the USA, including Mississippi, Arizona, Kansas, Maryland, Delaware and Georgia. RESULTS: Polymerase chain reaction (PCR) products from 40 primer pairs specific to the cassette were similar in size and sequence in resistant populations. Several primer pairs failed to generate PCR products in sensitive populations. Regions of the cassette sequenced in the resistant populations were found to be nearly identical to those from Mississippi. Gene expression analysis showed that both EPSPS and another gene in the cassette, a reverse transcriptase, were elevated in all resistant populations tested relative to the sensitive populations. CONCLUSION: EPSPS cassettes from distant resistant populations were nearly homologous. Considering the complexity of the cassette, and the degree of similarity among some cassette sequences, the results are consistent with the hypothesis that glyphosate resistance probably evolved once and then rapidly spread across the USA. © 2017 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Gene amplification has been observed in many bacteria and eukaryotes as a response to various selective pressures, such as antibiotics, cytotoxic drugs, pesticides, herbicides, and other stressful environmental conditions. An increase in gene copy number is often found as extrachromosomal elements that usually contain autonomously replicating extrachromosomal circular DNA molecules (eccDNAs). Amaranthus palmeri, a crop weed, can develop herbicide resistance to glyphosate [N-(phosphonomethyl) glycine] by amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, the molecular target of glyphosate. However, biological questions regarding the source of the amplified EPSPS, the nature of the amplified DNA structures, and mechanisms responsible for maintaining this gene amplification in cells and their inheritance remain unknown. Here, we report that amplified EPSPS copies in glyphosate-resistant (GR) A. palmeri are present in the form of eccDNAs with various conformations. The eccDNAs are transmitted during cell division in mitosis and meiosis to the soma and germ cells and the progeny by an as yet unknown mechanism of tethering to mitotic and meiotic chromosomes. We propose that eccDNAs are one of the components of McClintock's postulated innate systems [McClintock B (1978) Stadler Genetics Symposium] that can rapidly produce soma variation, amplify EPSPS genes in the sporophyte that are transmitted to germ cells, and modulate rapid glyphosate resistance through genome plasticity and adaptive evolution. [ABSTRACT FROM AUTHOR]

The reniform nematode (Rotylenchulus reniformis) causes economic losses in cotton and soybean in the southeastern United States, and has the ability to reproduce on more than 300 plant species. Even when the host crop is protected through the use of nematicides or host plant resistance, the potential exists for other plants present in or near the field to support the reniform nematode population. Because of variations in weed susceptibility, nematode virulence, and environmental factors, determining the host status of weeds to local populations of the nematode is needed to provide management recommendations. To identify the most important weed and cover crop hosts for reniform nematodes in the Mississippi Delta, nematode infection was measured on 53 plant species in greenhouse and field surveys. Subsequent greenhouse and field tests were conducted to confirm the host status of nine of these plants. Sicklepod (Senna obtusifolia), spurred anoda (Anoda cristata), entireleaf morningglory (Ipomoea sp.), and velvetleaf (Abutilon theophrasti) were identified as excellent hosts for reniform nematode in this region, supporting nematode populations equivalent to or greater than those developing on susceptible cotton plants included in the tests. Purple (Cyperus rotundus) and yellow (C. esculentus) nutsedges were poor hosts for reniform nematode, despite all underground plant parts supporting nematode infection. Sicklepod, velvetleaf, and entireleaf morningglory were reported to be important hosts for reniform nematode in tests in Alabama and Georgia indicating that efforts to manage these weeds across a wider geographic region may be needed. [ABSTRACT FROM AUTHOR]