Dataset Information

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.

SUBMITTER: Kupper A

PROVIDER: S-EPMC5788914 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

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

Küpper Anita A Manmathan Harish K HK Giacomini Darci D Patterson Eric L EL McCloskey William B WB Gaines Todd A TA

Frontiers in plant science 20180125

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 an ...[more]

PMID: 29422910

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Project description:Evolution of multiple herbicide resistance in Palmer amaranth across the United States is a serious challenge for its management. Recently, a Palmer amaranth population (KCTR; Kansas Conservation Tillage Resistant) from a long-term conservation tillage research project in Kansas, United States, was found uncontrolled by several commonly used herbicides. Importantly, this field did not have a history of repeated use of some of the herbicides for which the KCTR Palmer amaranth population showed lack of control. The objectives of this study were to confirm the evolution of multiple resistances and determine possible mechanism(s) of resistance in KCTR Palmer amaranth plants. In response to post-emergence application, 28-100% of KCTR Palmer amaranth survived field recommended rates of 2,4-D, ALS-, PS II-, EPSPS-, PPO-, HPPD-inhibitor herbicides, or tank- or pre-mixture of PS II- and HPPD-inhibitor herbicides, confirming evolution of six-way resistance in this Palmer amaranth population. However, this population was found susceptible to the PS I- and glutamine synthetase inhibitor herbicides. Chlorsulfuron-, imazethapyr-, and atrazine-resistant plants did not show any previously reported mutation in ALS and psbA genes, the target sites of these herbicides, respectively. However, the survivors of glyphosate treatment showed amplification of EPSPS gene (up to 88 copies). The KCTR plants pretreated with cytochrome P450 or GST inhibitors along with atrazine, 2,4-D, lactofen, or mesotrione had significantly less biomass accumulation than those treated with herbicides alone. Plants treated with P450 inhibitor followed by imazethapyr showed moderate reduction of biomass in KCTR which was statistically similar to a susceptible Palmer amaranth population treated with imazethapyr. These results suggest predominance of metabolic resistance possibly mediated by cytochrome P450 and GST enzyme activity that may have predisposed the KCTR Palmer amaranth population to evolve resistance to multiple herbicides. This is the first report of evolution of six-way resistance in a single Palmer amaranth population. Appropriate management strategies, including integration of cultural, and mechanical, and herbicide mixtures, are warranted to control such Palmer amaranth populations.

Project description:Weed infestations in agricultural systems constitute a serious challenge to agricultural sustainability and food security worldwide. Amaranthus palmeri S. Watson (Palmer amaranth) is one of the most noxious weeds causing significant yield reductions in various crops. The ability to estimate seed viability and herbicide susceptibility is a key factor in the development of a long-term management strategy, particularly since the misuse of herbicides is driving the evolution of herbicide response in various weed species. The limitations of most herbicide response studies are that they are conducted retrospectively and that they use in vitro destructive methods. Development of a non-destructive method for the prediction of herbicide response could vastly improve the efficacy of herbicide applications and potentially delay the evolution of herbicide resistance. Here, we propose a toolbox based on hyperspectral technologies and data analyses aimed to predict A. palmeri seed germination and response to the herbicide trifloxysulfuron-methyl. Complementary measurement of leaf physiological parameters, namely, photosynthetic rate, stomatal conductence and photosystem II efficiency, was performed to support the spectral analysis. Plant response to the herbicide was compared to image analysis estimates using mean gray value and area fraction variables. Hyperspectral reflectance profiles were used to determine seed germination and to classify herbicide response through examination of plant leaves. Using hyperspectral data, we have successfully distinguished between germinating and non-germinating seeds, hyperspectral classification of seeds showed accuracy of 81.9 and 76.4%, respectively. Sensitive and resistant plants were identified with high degrees of accuracy (88.5 and 90.9%, respectively) from leaf hyperspectral reflectance profiles acquired prior to herbicide application. A correlation between leaf physiological parameters and herbicide response (sensitivity/resistance) was also demonstrated. We demonstrated that hyperspectral reflectance analyses can provide reliable information about seed germination and levels of susceptibility in A. palmeri. The use of reflectance-based analyses can help to better understand the invasiveness of A. palmeri, and thus facilitate the development of targeted control methods. It also has enormous potential for impacting environmental management in that it can be used to prevent ineffective herbicide applications. It also has potential for use in mapping tempo-spatial population dynamics in agro-ecological landscapes.

Dataset Information

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

Publications

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

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