New Lab Publications:
September, 21 - 2022
Detection and discovery of plant viruses in soybean by metagenomic sequencing
Manjula G. Elmore, Carol L. Groves, M. R. Hajimorad, Tracey P. Stewart, Mikaela A. Gaskill, Kiersten A. Wise, Edward Sikora, Nathan M. Kleczewski, Damon L. Smith, Daren S. Mueller & Steven A. Whitham.
Characterization of a foxtail mosaic virus vector for gene silencing and analysis of innate immune responses in Sorghum bicolor
Melissa Bredow, Martha Ibore Natukunda, Bliss M Beernink, Aline Sartor Chicowski, Maria G Salas-Fernandez & Steven A Whitham.
2022 Plant Health Conference held in Pittsburgh, Pennsylvania (August 6-10).
August, 24 - 2022
Aline and Ekkachai presented a poster at the meeting.
Aline Sartor Chicowski was selected for the 2022 Corteva DELTA Symposium and the 2022 DELTA research grant
August, 3 - 2022
Aline Sartor Chicowski was selected for the 2022 Corteva DELTA Symposium held in Indianapolis (Aug 1-3) at the Corteva world headquarters. Aline is also a recipient of the 2022 DELTA research grant.
Corteva "Developing Emerging Leaders and Talent in Agriculture" (DELTA) is a two-phased program encouraging diverse talent to apply their skills toward sustainable and reliable food production. This program includes a competitive research grant of $3000 for graduate students and postdocs, as well as participation in an annual symposium. The DELTA symposium provides not only a technical overview of the company but allows participants a chance to share their research, network, and develop soft skills that are essential to any industry career. Participants gain a better appreciation for the variety of roles within agriculture and are able to evaluate Corteva as a potential future employer.
2022 Plant Biology Conference held in Portland, Oregon (July 9-13, 2022).
July, 23 - 2022
Our lab had a graduate student and two postdocs attending the meeting. Shown in the picture (L-R): Dr. Ryan Lappe, Brianna Griffin, Aline Sartor Chicowski and Dr. Melissa Bredow.
Congratulations to Nuoya Xu! He successfully defended his master thesis.
July, 6 - 2022
New Publication: Impacts of RNA Mobility Signals on Virus-Induced Somatic and Germline Gene Editing
June, 9 - 2022
Bliss M. Beernink, Ryan R. Lappe, Melissa Bredow and Steven A. Whitham*
Viral vectors are being engineered to deliver CRISPR/Cas9 components systemically in plants to induce somatic or heritable site-specific mutations. It is hypothesized that RNA mobility signals facilitate entry of viruses or single guide RNAs (sgRNAs) into the shoot apical meristem where germline mutations can occur. Our objective was to understand the impact of RNA mobility signals on virus-induced somatic and germline gene editing in Nicotiana benthamiana and Zea mays. Previously, we showed that foxtail mosaic virus (FoMV) expressing sgRNA induced somatic mutations in N. benthamiana and Z. mays expressing Cas9. Here, we fused RNA mobility signals to sgRNAs targeting the genes encoding either N. benthamiana phytoene desaturase (PDS) or Z. mays high affinity potassium transporter 1 (HKT1). Addition of Arabidopsis thaliana Flowering Locus T (AtFT) and A. thaliana tRNA-Isoleucine (AttRNAIle) did not improve FoMV-induced somatic editing, and neither were sufficient to facilitate germline mutations in N. benthamiana. Maize FT homologs, Centroradialus 16 (ZCN16) and ZCN19, as well as AttRNAIle were found to aid somatic editing in maize but did not enable sgRNAs delivered by FoMV to induce germline mutations. Additional viral guide RNA delivery systems were assessed for somatic and germline mutations in N. benthamiana with the intention of gaining a better understanding of the specificity of mobile signal-facilitated germline editing. Potato virus X (PVX), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV) were included in this comparative study, and all three of these viruses delivering sgRNA were able to induce somatic and germline mutations. Unexpectedly, PVX, a potexvirus closely related to FoMV, expressing sgRNA alone induced biallelic edited progeny, indicating that mobility signals are dispensable in virus-induced germline editing. These results show that PVX, BSMV, and TRV expressing sgRNA all have an innate ability to induce mutations in the germline. Our results indicate that mobility signals alone may not be sufficient to enable virus-based delivery of sgRNAs using the viruses, FoMV, PVX, BSMV, and TRV into cell types that result in germline mutations.
Whitham Lab celebrating Steve's birthday and recent publications.
May, 20 - 2022
Dr. Steven Whitham talks about CRISPR/Cas9 system on the "I See Dead Plants" podcast
May, 19 - 2022
A topic of science fiction not even a decade ago, genome editing technologies are now being used to research breeding efficiency and bacterial resilience in soybean. Get down to the molecular level in this episode of I See Dead Plants with Host Ed Zaworski and Iowa State University plant virology specialist Dr. Steven Whitham as they discuss the CRISPR/Cas9 system and its implications for the future of crop disease management research. Article discussed: “CRISPR/Cas9-Based Gene Editing Using Egg Cell-Specific Promoters in Arabidopsis and Soybean”.
Link for the episode: https://cropprotectionnetwork.org/podcast
Nuoya Xu was awarded a "Research Excellence Award"
May, 2 - 2022
Nuoya Xu, M. S. Student in Plant Biology (Interdepartmental Plant Biology Major) was recently awarded a "Research Excellence Award", which recognizes those graduate students with outstanding research accomplishments in a graduate program.
Aline Sartor Chicowski selected as a 2022 ASPB Recognition Travel Award Recipient
April, 29 - 2022
Aline Sartor Chicowski was recently selected as a 2022 ASPB Recognition Travel Award recipient. This award will cover all expenses at the American Society of Plant Biologists conference scheduled for July 9 - 13, 2022 in Portland, Oregon.
Aline is an Agronomist and a Ph.D. Candidate in Plant Pathology, with a minor in Genetics & Genomics, under Dr. Steven Whitham. Her projects aim to better understand the molecular mechanisms underlying fungal pathogenicity as well as soybean resistance against these organisms. Aline mainly works on the Soybean-Asian soybean rust (ASR) pathosystem, aiming to gain better insight into the molecular basis of the interactions of soybean and ASR, and thus potentially develop strategies to produce disease-resistant plants.
Dr. Steven Whitham named APS Fellow
April 1 - 2022
Steven Whitham, professor of plant pathology and microbiology, was named an APS fellow. He is one of 10 to receive this honor for the 2022 award year.
APS members are recognized with the fellow distinction for their “significant contributions” in research, teaching, administration, professional and public service and/or extension and outreach.
Whitham has been at Iowa State for more than 20 years. Since joining the university as a faculty member, Whitham has become known internationally for his cutting-edge research on the interactions between plant pathogens and their hosts.
He studies genes in plants and pathogens to determine the molecular basis for disease susceptibility and how viruses can be useful in plants. Whitham is also interested in finding ways to make plants more disease resistant and drought-resilient through testing various mutations in the plants.
Over the years, he’s collaborated with fellow researchers in other departments at Iowa State, including agronomy and horticulture, and mentored undergraduate and graduate students and post-doctoral scholars.
“I’ve worked with a lot of great teams, so that’s been a fun aspect,” Whitham said.
New Publication: Direct Agroinoculation of Maize Seedlings by Injection with Recombinant Foxtail Mosaic Virus and Sugarcane Mosaic Virus Infectious Clones
March 2, 2021
Published: February 27, 2021
Bliss M. Beernink*1, Katerina L. Holan*1, Ryan R. Lappe1, Steven A. Whitham1 * These authors contributed equally
Agrobacterium-based inoculation approaches are widely used for introducing viral vectors into plant tissues. This study details a protocol for the injection of maize seedlings near meristematic tissue with Agrobacterium carrying a viral vector. Recombinant foxtail mosaic virus (FoMV) clones engineered for gene silencing and gene expression were used to optimize this method, and its use was expanded to include a recombinant sugarcane mosaic virus (SCMV) engineered for gene expression. Gene fragments or coding sequences of interest are inserted into a modified, infectious viral genome that has been cloned into the binary T-DNA plasmid vector pCAMBIA1380. The resulting plasmid constructs are transformed into Agrobacterium tumefaciens strain GV3101. Maize seedlings as young as 4 days old can be injected near the coleoptilar node with bacteria resuspended in MgSO4 solution. During infection with Agrobacterium, the T-DNA carrying the viral genome is transferred to maize cells, allowing for the transcription of the viral RNA genome. As the gene expression replicates and systemically spreads throughout the plant, viral symptoms and phenotypic changes resulting from the silencing of the target genes lesion mimic 22 (les22) or phytoene desaturase (pds) can be observed on the leaves, or expression of green fluorescent protein (GFP) can be detected upon illumination with UV light or fluorescence microscopy. To detect the virus and assess the integrity of the insert simultaneously, RNA is extracted from the leaves of the injected plant and RT-PCR is conducted using primers flanking the multiple cloning site (MCS) carrying the inserted sequence. This protocol has been used effectively in several maize genotypes and can readily be expanded to other viral vectors, thereby offering an accessible tool for viral vector introduction in maize.
New Publication: CRISPR/Cas9-Based Gene Editing Using Egg Cell-Specific Promoters in Arabidopsis and Soybean
March 2, 2021
Published June 16, 2020
Na Zheng, Ting Li, Jaime D. Dittman, Jianbin Su, Riqing Li, Walter Gassmann, Deliang Peng, Steven A. Whitham, Shiming Liu and Bing Yang
CRISPR/Cas9-based systems are efficient genome editing tools in a variety of plant species including soybean. Most of the gene edits in soybean plants are somatic and non-transmissible when Cas9 is expressed under control of constitutive promoters. Tremendous effort, therefore, must be spent to identify the inheritable edits occurring at lower frequencies in plants of successive generations. Here, we report the development and validation of genome editing systems in soybean and Arabidopsis based on Cas9 driven under four different egg-cell specific promoters. A soybean ubiquitin gene promoter driving expression of green fluorescent protein (GFP) is incorporated in the CRISPR/Cas9 constructs for visually selecting transgenic plants and transgene-evicted edited lines. In Arabidopsis, the four systems all produced a collection of mutations in the T2 generation at frequencies ranging from 8.3 to 42.9%, with egg cell-specific promoter AtEC1.2e1.1p being the highest. In soybean, function of the gRNAs and Cas9 expressed under control of the CaMV double 35S promoter (2x35S) in soybean hairy roots was tested prior to making stable transgenic plants. The 2x35S:Cas9 constructs yielded a high somatic mutation frequency in soybean hairy roots. In stable transgenic soybean T1 plants, AtEC1.2e1.1p:Cas9 yielded a mutation rate of 26.8%, while Cas9 expression driven by the other three egg cell-specific promoters did not produce any detected mutations. Furthermore, the mutations were inheritable in the T2 generation. Our study provides CRISPR gene-editing platforms to generate inheritable mutants of Arabidopsis and soybean without the complication of somatic mutagenesis, which can be used to characterize genes of interest in Arabidopsis and soybean.
Iowa State Researchers Win Grant to Develop Plant Gene Editing Technique to Improve Switchgrass, Sorghum
September 10, 2020
August 25th, 2020
AMES, Iowa – Conventional approaches to plant genome editing still require transformation techniques that present roadblocks for many crops.
A new project supported by a two-year, $300,000 grant from the USDA Agriculture and Food Research Initiative, will explore the potential to employ viruses to overcome the usual tissue culture barriers that impede gene editing in sorghum and switchgrass.
The research is being led by Steve Whitham, a professor in plant pathology and microbiology at Iowa State University, along with co-investigators Maria Salas-Fernandez, associate professor in agronomy, and Shuizhang Fei, professor of horticulture.
Their grant is part of a $3.4 million multi-institution investment in 12 projects nationwide that are part of a USDA Ag Innovation through Gene Editing Initiative.
The Iowa State researchers plan to use plant viruses, such as Foxtail mosaic virus, as vehicles for delivering guide RNAs in sorghum and switchgrass. The guide RNAs are part of CRISPR gene editing systems that can direct changes in genetic sequences to modify the functions of genes. The goal is to create controlled techniques to introduce the guide RNA from compatible plant viruses into cells of the target plants, inducing desirable gene edits that can be inherited.
“We believe we can develop this new tool to simplify and accelerate gene editing applications in sorghum and switchgrass, which will enable more rapid progress in improving agricultural traits related to yield, stress and disease resistance and nutrient use efficiency,” said Whitham.
Sorghum is important for grain and forage production and both sorghum and switchgrass are important feedstocks for bioenergy production due to their ability to fix large amounts of carbon and convert it into biomass. Both species can be transformed by traditional gene-editing technologies, but successful transformation is restricted to only certain genotypes and the process is lengthy.
As a perennial crop, switchgrass is an especially time-consuming plant to breed using conventional technologies, said Fei. He foresees the research being used to enhance traits such as delayed flowering or increased tillering for more stems per plant, which could increase yields and improve economics for producers.
“Sorghum is also one of the most difficult crops to transform through conventional practices,” Salas-Fernandez said. “It is a big bottleneck for breeding. If we can succeed at this, heritable edits can be transferred to the next generation, which would avoid a lot of steps in what is now a very long process and make sorghum more competitive as a biofuel.”
Project leader Whitham emphasized the ‘proof of concept’ nature of the new grant.
“This support is for technology development to see if it can work. We’re optimistic and have a good start, but we have a lot of work ahead to develop and demonstrate this as a practical tool.”
Katerina Holan awarded USDA NIFA AFRI grant
June 26, 2020
Congratulations to Katerina Holan, Whitham lab Graduate Assistant, on being awarded a USDA-NIFA AFRI grant.
Kat's project is titled "Identification and characterization of candidate secreted effector proteins in the rust pathogen Puccinia sorghi". This competitive grant has been awarded to cover her stipend and tuition as well as some supplies and travel costs. The overall goal of her project is to identify and characterize the role members of the rust effector family Cluster 112 have in modulating plant immunity in the maize-P. sorghi pathosystem.
AFRI, with its broad funding portfolio, addresses every facet of agriculture, including food production, farming and ranching, renewable energy, aquaculture, nutrition, forestry, food safety, rural communities, farm efficiency and profitability, and traditional and innovative breeding techniques. AFRI advances fundamental sciences as well as translational research and development in support of agriculture and coordinates research opportunities to build on these new discoveries. In addition, AFRI-awarded programs deliver this science to communities through extension programs, which allows the public to make informed decisions that impact their daily lives.
The Agriculture and Food Research Initiative (AFRI) solicits applications from scientists each year. The application process offers funding for single-function and integrated agricultural research, education, and extension efforts that address key problems of local, regional, national, and global importance in sustaining conventional and organic food and agriculture systems.
Bliss Beernink to present in the Virtual Maize Genetics Meeting 2020
June 25, 2020
Bliss Beernink, Whitham Lab Graduate Research Assistant, was rewarded a travel grant from the Crop Bioengineering Center (CBC) to present her research on "protein expression and gene editing in maize using foxtail mosaic virus vectors". The 2020 Maize Genetics Meeting was to be held on the beautiful island of Hawaii in March. When the Pandemic hit the USA, the Board and Committee of the MGM chose to cancel. We were pleased when they announced a Virtual Meeting for June 25-26, 2020. Bliss is one of 25 researchers that have been selected to give an oral presentation at the virtual meeting. The conference will take place on Zoom and invitations have been sent to the registrants of the original meeting and members of the Maize Genetics Cooperation. Registrants will be treated to talks that help them "learn the most current scientific and technical advances in maize genetics".
Please see Maize Genetics for more information.