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1. Deciphering the Mechanism of Glyphosate Resistance in Amaranthus palmeri by Cytogenomics

   https://doi.org/10.1159/000521409  

   Koo, Dal-Hoe; Sathishraj, Rajendran; Friebe, Bernd; Gill, Bikram S. (February 2022, Cytogenetic and Genome Research)

   In agriculture, various chemicals are used to control the weeds. Out of which, glyphosate is an important herbicide invariably used in the cultivation of glyphosate-resistant crops to control weeds. Overuse of glyphosate results in the evolution of glyphosate-resistant weeds. Evolution of glyphosate resistance (GR) in Amaranthus palmeri (AP) is a serious concern in the USA. Investigation of the mechanism of GR in AP identified different resistance mechanisms of which 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification is predominant. Molecular analysis of GR AP identified the presence of a 5- to >160-fold increase in copies of the EPSPS gene than in a glyphosate-susceptible (GS) population. This increased copy number of the EPSPS gene increased the genome size ranging from 3.5 to 11.8%, depending on the copy number compared to the genome size of GS AP. FISH analysis using a 399-kb EPSPS cassette derived from bacterial artificial chromosomes (BACs) as probes identified that amplified EPSPS copies in GR AP exist in extrachromosomal circular DNA (eccDNA) in addition to the native copy in the chromosome. The EPSPS gene-containing eccDNA having a size of ∼400 kb is termed EPSPS-eccDNA and showed somatic mosacism in size and copy number. EPSPS-eccDNA has a genetic mechanism to tether randomly to mitotic or meiotic chromosomes during cell division or gamete formation and is inherited to daughter cells or progeny generating copy number variation. These eccDNAs are stable genetic elements that can replicate and exist independently. The genomic characterization of the EPSPS locus, along with the flanking regions, identified the presence of a complex array of repeats and mobile genetic elements. The cytogenomics approach in understanding the biology of EPSPS-eccDNA sheds light on various characteristics of EPSPS-eccDNA that favor GR in AP. 

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2. Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri

   https://doi.org/10.1073/pnas.1719354115  

   Koo, Dal-Hoe; Molin, William T.; Saski, Christopher A.; Jiang, Jiming; Putta, Karthik; Jugulam, Mithila; Friebe, Bernd; Gill, Bikram S. (March 2018, Proceedings of the National Academy of Sciences)

   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. 

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3. Case Study: Characterizing the Response of Young Glyphosate-Susceptible and Glyphosate-Resistant Amaranthus palmeri (Palmer Amaranth) after Being Sprayed with a Ten Percent Acetic Acid Solution to Control Growth

   https://doi.org/10.3390/IECPS2021-12009  

   Youngblood, Yolander; Carter, Ineceia; Montegut, Ayanna (December 2021, MDPI)

   In this case study, we investigated the responses of glyphosate-susceptible and glyphosate-resistant Amaranthus palmeri to an organic 10% acetic acid herbicide solution instead of the standard 20% acetic acid solution. We showed that, although both forms respond differently to glyphosate-based herbicides, both will respond in the same way to organic-based herbicides that contain acetic acid. After treatment with the 10% acetic acid solution, eighty-five percent (85%) of the glyphosate susceptible plants died within 24 h, while 100% of the glyphosate-resistant plants died within 24 h. Using a lower concentration may be better for the environment since there will be less buildup over time, and it is more cost-effective for the farmer. 

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4. Are Palmer’s Elm-Leaf Goldenrod and the Smooth Elm-Leaf Goldenrod Real? The Angiosperms353 Kit Provides Within-Species Signal in Solidago ulmifolia s. l.

   https://doi.org/10.1600/036364421X16370109698740  

   Beck, James B.; Markley, Morgan L.; Zielke, Mackenzie G.; Thomas, Justin R.; Hale, Haley J.; Williams, Lindsay D.; Johnson, Matthew G. (December 2021, Systematic Botany)

   Abstract— The genus Solidago represents a taxonomically challenging group due to its sheer number of species, putative hybridization, polyploidy, and shallow genetic divergence among species. Here we use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri , a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri. A multivariate analysis of both discrete and continuous morphological data revealed no clear distinction between S. ulmifolia var. palmeri and Solidago ulmifolia var. ulmifolia . Solidago ulmifolia var. palmeri ’s status was also assessed with a phylogenomic and SNP clustering analysis of data generated with the “Angiosperms353” probe kit. Neither analysis supported Solidago ulmifolia var. palmeri as a distinct taxon, and we suggest that this name should be discarded. The status of Solidago delicatula (formerly known as Solidago ulmifolia var. microphylla ) was also assessed. Both morphological and phylogenetic analyses supported the species status of S. delicatula and we suggest maintaining this species at its current rank. These results highlight the utility of the Angiosperms353 probe kit, both with herbarium tissue and at lower taxonomic levels. Indeed, this is the first study to utilize this kit to identify genetic groups within a species. 

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5. The contribution of sex chromosome conflict to disrupted spermatogenesis in hybrid house mice

   https://doi.org/10.1093/genetics/iyac151  

   Kopania, Emily E. K.; Watson, Eleanor M.; Rathje, Claudia C.; Skinner, Benjamin M.; Ellis, Peter J. I.; Larson, Erica L.; Good, Jeffrey M.; Barbash, ed., D. (October 2022, Genetics)

   Abstract Incompatibilities on the sex chromosomes are important in the evolution of hybrid male sterility, but the evolutionary forces underlying this phenomenon are unclear. House mice (Mus musculus) lineages have provided powerful models for understanding the genetic basis of hybrid male sterility. X chromosome–autosome interactions cause strong incompatibilities in M. musculus F1 hybrids, but variation in sterility phenotypes suggests a more complex genetic basis. In addition, XY chromosome conflict has resulted in rapid expansions of ampliconic genes with dosage-dependent expression that is essential to spermatogenesis. Here, we evaluated the contribution of XY lineage mismatch to male fertility and stage-specific gene expression in hybrid mice. We performed backcrosses between two house mouse subspecies to generate reciprocal Y-introgression strains and used these strains to test the effects of XY mismatch in hybrids. Our transcriptome analyses of sorted spermatid cells revealed widespread overexpression of the X chromosome in sterile F1 hybrids independent of Y chromosome subspecies origin. Thus, postmeiotic overexpression of the X chromosome in sterile F1 mouse hybrids is likely a downstream consequence of disrupted meiotic X-inactivation rather than XY gene copy number imbalance. Y chromosome introgression did result in subfertility phenotypes and disrupted expression of several autosomal genes in mice with an otherwise nonhybrid genomic background, suggesting that Y-linked incompatibilities contribute to reproductive barriers, but likely not as a direct consequence of XY conflict. Collectively, these findings suggest that rapid sex chromosome gene family evolution driven by genomic conflict has not resulted in strong male reproductive barriers between these subspecies of house mice. 

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