Omics Potential in Herbicide-Resistant Weed Management

Patterson, Eric; Saski, Christopher; Küpper, Anita; Beffa, Roland; Gaines, Todd A.

doi:10.3390/plants8120607

Cited by 22 publications

(18 citation statements)

References 99 publications

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“…2012 ). The availability of high-quality reference genomes in Amaranthus species would allow for more robust genomic and molecular studies within these species including elucidating the evolution of weedy traits such as herbicide resistance, which are often the result of very strong selection pressures exerted across vast geographic distances and under many different environments ( Korte and Farlow 2013 ; Patterson et al. 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri

Montgomery

Giacomini

Waithaka

et al. 2020

Genome Biology and Evolution

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Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. Here, we present the most contiguous draft assemblies of these three species to date. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact mapping information to assemble and order sequences of A. palmeri to near-chromosome-level resolution, with scaffold N50 of 20.1 Mb. To resolve the issues of heterozygosity and co-assembly of alleles in diploid species, we adapted the trio binning approach to produce haplotype assemblies of A. tuberculatus and A. hybridus. This approach resulted in an improved assembly of A. tuberculatus, and the first genome assembly for A. hybridus, with contig N50s of 2.58 and 2.26 Mb, respectively. Species-specific transcriptomes and information from related species were used to predict transcripts within each assembly. Syntenic comparisons of these species and Amaranthus hypochondriacus identified sites of genomic rearrangement, including duplication and translocation, while genetic map construction within A. tuberculatus highlighted the need for further ordering of the A. hybridus and A. tuberculatus contigs. These multiple reference genomes will accelerate genomic studies in these species to further our understanding of weedy evolution within Amaranthus.

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Section: Introductionmentioning

confidence: 99%

Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri

Montgomery

Giacomini

Waithaka

et al. 2020

Genome Biology and Evolution

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“…Even the list of the worst weeds in the world has not changed in the past 40 years, which should be highly unlikely, as the science is constantly changing. Research into weed genomics has room for improvement, and the development of weed genomics provides potential for greater understanding in how weed species evolve and the role polyploidy is playing and has played in weed evolution (Ravet et al, 2018;Patterson et al, 2019). The International Weed Genomics Consortium provides an outlet for collaborative research into weed genomics, with a growing genomics repository for weed species.…”

Section: Discussionmentioning

confidence: 99%

“…Despite this, barnyardgrass remains the only polyploid weed genome sequenced (Kyriakidou et al, 2018). There is an obvious need for a well-established weed genomics database; while there are still challenges to this undertaking, it is a necessary step that needs to be taken in order to advance the understanding of polyploidy in weeds, and weed genomics in general (Patterson et al, 2019).…”

Section: But Do Polyploids Make Better Weeds?mentioning

confidence: 99%

The Impact of Polyploidization on the Evolution of Weed Species: Historical Understanding and Current Limitations

2021

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Whole genome duplication via polyploidization is a major driver of diversification within angiosperms and it appears to confer the most benefit during times of rapid environmental change. Polyploidization offers expanded access to novel phenotypes that facilitate invasion of new environments and increased resistance to stress. These new phenotypes can arise almost immediately through the novel interactions among or between transcription factors of the duplicated genomes leading to transgressive traits, and general heterosis, or they can occur more slowly through processes like neofunctionalization, and subfunctionalization. These processes are characterized by the changes within homologs of the duplicated genomes, homoeologs. It has been proposed that redundant homoeologs are released from selective constraints and serve as an additional source of adaptive genetic variation, particularly in neo and meso-polyploids. Current practices in weed management create rapid environmental change through the use of chemicals, practices that are meant to cause the extirpation of the designated weed, and represent a strong recurrent selective event—a scenario that should favor polyploidy species. Here we ask the question, “Do polyploids make better weeds?” It is our conclusion that such a question is impossible to answer at this time due to the lack of resources and understanding in weed genomics. The growing contingent of research in weed genomics, however, driven by herbicide resistance evolution is rapidly improving our understanding of weed molecular biology and will aid in improving understanding of the impacts of ploidy levels on weed evolution and adaptation in the future.

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“…Earlier methods based on restriction site polymorphisms in PCR‐amplified internal transcribed spacer (ITS) regions have been useful for Amaranthus species identification but have only been validated against limited populations 29 . Recent developments in Omics provide a wealth of tools for the development of new markers 30 . These tools can be used to identify species diagnostic SNPs, which can then be genotyped through approaches such as KASP to provide a species identification 27 .…”

Section: Discussionmentioning

confidence: 99%

A needle in a seedstack: an improved method for detection of rare alleles in bulk seed testing through KASP

Brusa

Patterson

Gaines

et al. 2021

Pest Management Science

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BACKGROUND Amaranthus palmeri is an aggressive and prolific weed species with major impact on agricultural yield and is a prohibited noxious weed across the Midwest. Morphological identification of A. palmeri from other Amaranthus species is extremely difficult in seeds, which has led to genetic testing for seed identification in commercial seed lots. RESULTS We created an inexpensive and reliable genetic test based on novel, species‐specific, single nucleotide polymorphisms (SNPs) from GBS (Genotyping by Sequencing) data. We report three SNP‐based genetic tests for identifying A. palmeri alone or in a mixed pool of Amaranthus spp. Sensitivity ranged from 99.8 to 100%, specificity from 99.59 to 100%. Accuracy for all three tests is > 99.7%. All three are capable of reliably detecting one A. palmeri seed in a pool of 200 Amaranthus spp. seeds. The test was validated across 20 populations of A. palmeri, along with eight other Amaranthus species, the largest and most genetically diverse panel of Amaranthus samples to date. CONCLUSION Our work represents a marked improvement over existing commercial assays resulting in an identification assay that is (i) accurate, (ii) robust, (iii) easy to interpret and (iv) applicable to both leaf tissue and pools of up to 200 seeds. Included is a data transformation method for calling of closely grouped competitive fluorescence assays. We also present a comprehensive GBS dataset from the largest geographic panel of Amaranthus populations sequenced. Our approach serves as a model for developing markers for other difficult to identify species. © 2021 Society of Chemical Industry

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Omics Potential in Herbicide-Resistant Weed Management

Cited by 22 publications

References 99 publications

Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri

Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri

The Impact of Polyploidization on the Evolution of Weed Species: Historical Understanding and Current Limitations

A needle in a seedstack: an improved method for detection of rare alleles in bulk seed testing through KASP

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