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Dive into the research topics where Kevin M. Dorn is active.

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Featured researches published by Kevin M. Dorn.


Plant Journal | 2013

De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock

Kevin M. Dorn; Johnathon D. Fankhauser; Donald L. Wyse; M. David Marks

Field pennycress (Thlaspi arvense L.) has potential as an oilseed crop that may be grown during fall (autumn) and winter months in the Midwestern United States and harvested in the early spring as a biodiesel feedstock. There has been little agronomic improvement in pennycress through traditional breeding. Recent advances in genomic technologies allow for the development of genomic tools to enable rapid improvements to be made through genomic assisted breeding. Here we report an annotated transcriptome assembly for pennycress. RNA was isolated from representative plant tissues, and 203 million unique Illumina RNA-seq reads were produced and used in the transcriptome assembly. The draft transcriptome assembly consists of 33 873 contigs with a mean length of 1242 bp. A global comparison of homology between the pennycress and Arabidopsis transcriptomes, along with four other Brassicaceae species, revealed a high level of global sequence conservation within the family. The final assembly was functionally annotated, allowing for the identification of putative genes controlling important agronomic traits such as flowering and glucosinolate metabolism. Identification of these genes leads to testable hypotheses concerning their conserved function and to rational strategies to improve agronomic properties in pennycress. Future work to characterize isoform variation between diverse pennycress lines and develop a draft genome sequence for pennycress will further direct trait improvement.


DNA Research | 2015

A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop

Kevin M. Dorn; Johnathon D. Fankhauser; Donald L. Wyse; M. David Marks

Field pennycress (Thlaspi arvense L.) is being domesticated as a new winter cover crop and biofuel species for the Midwestern United States that can be double-cropped between corn and soybeans. A genome sequence will enable the use of new technologies to make improvements in pennycress. To generate a draft genome, a hybrid sequencing approach was used to generate 47 Gb of DNA sequencing reads from both the Illumina and PacBio platforms. These reads were used to assemble 6,768 genomic scaffolds. The draft genome was annotated using the MAKER pipeline, which identified 27,390 predicted protein-coding genes, with almost all of these predicted peptides having significant sequence similarity to Arabidopsis proteins. A comprehensive analysis of pennycress gene homologues involved in glucosinolate biosynthesis, metabolism, and transport pathways revealed high sequence conservation compared with other Brassicaceae species, and helps validate the assembly of the pennycress gene space in this draft genome. Additional comparative genomic analyses indicate that the knowledge gained from years of basic Brassicaceae research will serve as a powerful tool for identifying gene targets whose manipulation can be predicted to result in improvements for pennycress.


Weed Science | 2018

Gene Space and Transcriptome Assemblies of Leafy Spurge (Euphorbia esula) Identify Promoter Sequences, Repetitive Elements, High-Quality Markers, and a Full-Length Chloroplast Genome

David P. Horvath; Sagar Patel; Münevver Doğramacı; Wun S. Chao; James V. Anderson; Michael E. Foley; Brian E. Scheffler; Gerard Lazo; Kevin M. Dorn; Changhui Yan; Anna Childers; Michel Schatz; Shoshana Marcus

Abstract Leafy spurge (Euphorbia esula L.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects with E. esula have helped develop it as a model for studying many aspects of perennial plant development and response to abiotic stress. However, the lack of an assembled genome for E. esula has limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome for E. esula would enhance our understanding of signaling processes controlling plant development and responses to environmental stress and provide a better understanding of genetic factors impacting weediness traits, evolution, and herbicide resistance. A comprehensive transcriptome database would also assist in analyzing future RNA-seq studies and is needed to annotate and assess genomic sequence assemblies. Here, we assembled and annotated 56,234 unigenes from an assembly of 589,235 RNA-seq-derived contigs and a previously published Sanger-sequenced expressed sequence tag collection. The resulting data indicate that we now have sequence for >90% of the expressed E. esula proteincoding genes. We also assembled the gene space of E. esula by using a limited coverage (18X) genomic sequence database. In this study, the programs Velvet and Trinity produced the best gene-space assemblies based on representation of expressed and conserved eukaryotic genes. The results indicate that E. esula contains as much as 23% repetitive sequences, of which 11% are unique. Our sequence data were also sufficient for assembling a full chloroplast and partial mitochondrial genome. Further, marker analysis identified more than 150,000 high-quality variants in our E. esula L-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results, E. esula appears to have limited heterozygosity. This study provides a blueprint for low-cost genomic assemblies in weed species and new resources for identifying conserved and novel promoter regions among coordinately expressed genes of E. esula.


bioRxiv | 2018

Transcriptome assembly and annotation of johnsongrass (Sorghum halepense) rhizomes identify candidate rhizome-specific genes

Nathan Ryder; Kevin M. Dorn; Mark Huitsing; Micah Adams; Jeff Ploegstra; Lee R. DeHaan; Steve R. Larson; Nathan L. Tintle

Abstract Rhizomes facilitate the wintering and vegetative propagation of many perennial grasses. Sorghum halepense (johnsongrass) is an aggressive perennial grass that relies on a robust rhizome system to persist through winters and reproduce asexually from its rootstock nodes. This study aimed to sequence and assemble expressed transcripts within the johnsongrass rhizome. A de novo transcriptome assembly was generated from a single johnsongrass rhizome meristem tissue sample. A total of 141,176 probable protein‐coding sequences from the assembly were identified and assigned gene ontology terms using Blast2GO. Estimated expression analysis and BLAST results were used to reduce the assembly to 64,447 high‐confidence sequences. The johnsongrass assembly was compared to Sorghum bicolor, a related nonrhizomatous species, along with an assembly of similar rhizome tissue from the perennial grain crop Thinopyrum intermedium. The presence/absence analysis yielded a set of 98 expressed johnsongrass contigs that are likely associated with rhizome development.


Plant Biotechnology Journal | 2018

Molecular tools enabling pennycress (Thlaspi arvense) as a model plant and oilseed cash cover crop

Michaela McGinn; Winthrop B. Phippen; Ratan Chopra; Sunil Bansal; Brice A. Jarvis; Mary E. Phippen; Kevin M. Dorn; Maliheh Esfahanian; Tara J. Nazarenus; Edgar B. Cahoon; Timothy P. Durrett; M. David Marks; John C. Sedbrook

Summary Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run‐off on otherwise barren farmland. We demonstrate that pennycress can serve as a user‐friendly model system akin to Arabidopsis that is well‐suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring‐type Spring 32‐10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter‐type pennycress, as well as predominantly a one‐to‐one correspondence with Arabidopsis genes, which makes translational research straightforward. We developed an Agrobacterium‐mediated floral dip transformation method (0.5% transformation efficiency) and introduced CRISPR‐Cas9 constructs to produce indel mutations in the putative FATTY ACID ELONGATION1 (FAE1) gene, thereby abolishing erucic acid production and creating an edible seed oil comparable to that of canola. We also stably transformed pennycress with the Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) gene, producing low‐viscosity acetyl‐triacylglycerol‐containing seed oil suitable as a diesel‐engine drop‐in fuel. Adoption of pennycress as a model system will accelerate oilseed‐crop translational research and facilitate pennycress’ rapid domestication to meet the growing sustainable food and fuel demands.


bioRxiv | 2017

Spring flowering habit in field pennycress (Thlaspi arvense) has arisen multiple independent times

Kevin M. Dorn; Evan Johnson; Erin Daniels; Donald L. Wyse; M. David Marks

- Pennycress (Thlaspi arvense L.) is currently being developed as a new cold-season oilseed crop. Like many Brassicaceae, pennycress can exhibit either a winter or spring annual phenotype. In Arabidopsis, mutations in negative regulators of flowering, including FLOWERING LOCUS C (FLC) and FRIGIDA can cause the transition to a spring annual habit. The genetics underlying the difference between spring and winter annual pennycress are currently unknown. - Using whole genome sequencing across wild spring annual pennycress accessions, co-segregation analyses, and comparative genomics approaches, we identify new alleles of TaFLC and explore their geographic distribution. - We report that loss of function mutations in TaFLC confer the spring annual phenotype in pennycress. We have also identified four natural alleles of TaFLC that confer a spring annual growth habit. The two spring annual FLC alleles present in European accessions were only identified in accessions collected in Montana, USA. - In pennycress, the spring annual habit has arisen several independent times. Accessions harboring the two European alleles were introduced to North America, likely after the species became a widespread on the continent. These findings provide new information on the natural history of the introduction and spread of the spring annual phenotype in pennycress.


EMBO Reports | 2017

A cooperative governance network for crop genome editing: The success of governance networks in other areas could help to find common ground for applying genome editing in agriculture

Nicholas R. Jordan; Kevin M. Dorn; Timothy M. Smith; Katie E Wolf; Patrick M. Ewing; Adria L. Fernandez; Alwyn Williams; You Lu; Jennifer Kuzma

Emerging biotechnologies, such as genome editing, may revolutionize agricultural development through rapid and precise genetic manipulation of a wide range of crop traits without having to transfer foreign DNA [1]. If so, these new genetic‐engineering (GE) technologies can help to generate crop varieties to address critical challenges in agricultural development, such as climate resilience or nutrient uptake, or diet‐related problems in nutrition and health in poorer countries. However, society must also be protected from potential harmful effects of genetically manipulated crops on the environment, human health, or social welfare. Governance of these crops must therefore balance agricultural developments with risk assessment and prevention of potential harm. > …genome editing is being used to improve the characteristics of major crop plants, but the governance of crop genome editing is poorly defined and developed Presently, genome editing is being used to improve the characteristics of major crop plants, but the governance of crop genome editing is poorly defined and developed. Influential groups concerned with the potential hazards of such crops view this situation with growing alarm, which has created tensions with the academic community and regulatory agencies [2]. Both the USA and the European Commission are currently reviewing the governance of crops produced by genome editing and other new technologies. On the US side, at least, the review process appears unlikely to result in governance approaches that will satisfy parties that are concerned with either over‐ or under‐regulation of such crops, and tension and conflicts about them are likely to heighten. We propose an alternative approach for governance of these crops that may help to defuse tensions and enable exploration of genome editing technologies’ potential while protecting society from harm: a cooperative governance network. Such networks have performed well in …


Annual Review of Plant Biology | 2016

Perennial Grain and Oilseed Crops

Michael B. Kantar; Catrin E. Tyl; Kevin M. Dorn; Xiaofei Zhang; Jacob M. Jungers; Joe M. Kaser; Rachel R. Schendel; James O. Eckberg; Mirko Bunzel; Nicholas R. Jordan; Robert M. Stupar; M. David Marks; James A. Anderson; Gregg A. Johnson; Craig C. Sheaffer; Tonya C. Schoenfuss; Baraem Ismail; George E. Heimpel; Donald L. Wyse


Crop Science | 2016

A Pipeline Strategy for Grain Crop Domestication

Lee R. DeHaan; David L. Van Tassel; James A. Anderson; Sean R. Asselin; Richard Barnes; Gregory J. Baute; Douglas J. Cattani; Steve W. Culman; Kevin M. Dorn; Brent S. Hulke; Michael B. Kantar; Steve R. Larson; M. David Marks; Allison J. Miller; Jesse Poland; Damián A. Ravetta; Emily Rude; Matthew R. Ryan; Donald L. Wyse; Xiaofei Zhang


Elementa: Science of the Anthropocene | 2016

Sustainable commercialization of new crops for the agricultural bioeconomy

Nicholas R. Jordan; Kevin M. Dorn; Patrick M. Ewing; Alwyn Williams; K.A. Anderson; L. Felice; K. Haralson; Jared J. Goplen; K. Altendorf; Adria L. Fernandez; Winthrop B. Phippen; John C. Sedbrook; M. Marks; K. Wolf; Donald L. Wyse; Gregg A. Johnson

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David P. Horvath

Agricultural Research Service

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James V. Anderson

Agricultural Research Service

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