About

Christina Cowger is a USDA Plant Pathologist and Adjunct Professor at NC State University, specializing in the biology, epidemiology, and population genetics of small grain pathogens. Her research aims to develop profitable and sustainable management practices for small grain diseases, working closely with breeders, extension personnel, and other groups across the eastern U.S. Her expertise includes pathogen adaptation to host resistance, host genotype diversity, and the epidemiological and disease management implications of pathogen population structure. Dr. Cowger's research involves laboratory, greenhouse, and field studies utilizing molecular techniques to investigate species identity, phylogeny, population structure, and pathogen life cycles, complemented by epidemiological modeling and classical field-plot research.

Research topics

• Biology
• Genetics
• Agronomy
• Mathematics
• Materials science
• Metallurgy
• Botany
• Animal science
• Horticulture
• Ecology
• Biotechnology
• Food science

Selected publications

• Identification of a novel powdery mildew resistance gene in a winter wheat cultivar

  Plant Disease · 2026-04-12

  article

  Wheat (Triticum aestivum) is an important staple crop that sustains over one-third of the global population. Powdery mildew, an economically important disease caused by Blumeria graminis f. sp. tritici (Bgt), significantly affects wheat production in many wheat-growing regions. Therefore, identification of novel powdery mildew resistance genes that can be easily used in wheat cultivar development is essential for meeting the needs of the increasing global human population. PI 606247 (formerly 'Samara') is a winter wheat cultivar developed in the Czech Republic in 1995 that exhibits resistance to representative U.S. Bgt isolates. An F7 recombinant inbred line (RIL) population derived from PI 606247 × Jagalene was evaluated for responses to Bgt isolate OKS(14)-B-3-1. Genetic analysis indicated that a single gene, designated PmSA, conditions powdery mildew resistance in PI 606247. Selective genotyping of a subset of RILs identified a set of SNPs co-segregating with powdery mildew resistance in the terminal region of chromosome arm 2BL. Linkage analysis using kompetitive allele specific PCR (KASP) markers located PmSA to a 14.43 Mb interval between 686.69 Mb and 701.12 Mb in the Chinese Spring IWGSC RefSeq v2.1 reference sequence. PmSA is a new powdery mildew resistance gene differing from the others in the terminal region of 2BL in genomic location, origin, and responses to a set of Bgt differential isolates. PmSA is valuable for enhancing powdery mildew resistance, and the KASP markers closely linked to PmSA can facilitate its rapid deployment in wheat cultivars via marker-assisted selection.

  PublisherDOI

• Chromosomal rearrangements and sequence similarity drive preferential allosyndetic introgression from a wild relative into wheat

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-02

  articleOpen access

  Abstract Recombination in polyploid genomes is generally constrained to homologous or homoeologous chromosomes; however, how chromosomal rearrangements influence recombination between chromosomes remains unclear. Here, we demonstrate that large-scale chromosomal rearrangements in the wild relatives of wheat are associated with recombination involving non-homoeologous chromosomes or arms during alien gene introgression under conditions that permit homoeologous recombination mediated by ph1b . Using a wheat chromosome 6A monosomic-induced 6AS•6CL Robertsonian translocation combined with ph1b -mediated recombination, we generated 17 independent recombinants carrying a new stem rust resistance gene, Sr69 , from Aegilops caudata chromosome arm 6CL. Unexpectedly, 94.1% (16 of 17) of recombinants resulted from exchanges with wheat group-7 chromosomes rather than with the homoeologous group-6 chromosome. Comparative sequence- and marker-based analyses identified a 67-Mb rearranged interval on Ae. caudata 6CL that corresponds to telomeric regions of the long arms of wheat group-7 chromosomes. Sequence similarity within this interval was quantitatively associated with recombination frequency, with higher similarity corresponding to more frequent translocations. Physical and optical mapping showed that recombination within the rearranged interval generated compensating 7A/6C, 7B/6C, and 7D/6C translocations, whereas recombination outside this region produced non-compensating 6A/6C exchanges. An independent case involving the powdery mildew resistance gene Pm7C showed a similar correspondence between a rearranged 7CL region and preferential introgression into wheat 7DS. Together, these results indicate that ph1b -mediated recombination involving structurally altered chromosomes is driven by local chromosomal structure and sequence similarity rather than strict homoeologous group identity. This provides a mechanistic basis for harnessing untapped beneficial genes from structurally rearranged alien genomes. Significance Statement Alien gene introgression is a powerful strategy for wheat improvement, typically relying on ph1b -mediated recombination between homoeologous chromosomes. The genomic basis and outcomes of introgression from structurally rearranged alien chromosomes remain unclear. Here, we show that ph1b -induced recombination can efficiently target wheat-allosyntenic blocks in rearranged alien genomes, preferentially transferring genes from structurally altered alien segments into their syntenic regions on wheat chromosomes of different homoeologous groups. Crossover formation is governed by extended sequence similarity within corresponding intervals rather than strict collinearity across entire homoeologous chromosomes. As many wild species exhibit extensive genome rearrangement, these findings and methodologies expand access to underexploited genetic diversity embedded within highly rearranged wild genomes for wheat improvement.

  PublisherDOI

• Synthetic spike-in metabarcoding for plant pathogen diagnostics results in precise quantification of copy number within the genus <i>Fusarium</i>

  ISME Communications · 2025-01-01

  articleOpen accessSenior author

  Abstract Synthetic spike-in metabarcoding (SSIM) assays generate quantitative next-generation sequencing (NGS) data, but are marred by inconsistency and have seen limited adoption. Previous efforts to develop SSIM assays have focused on the ITS and 16S rRNA genes. This study marks the first use of SSIM as a diagnostic assay to identify and quantify plant-pathogenic species within the genus Fusarium and implements it using the single-copy TEF1 gene, which has relatively uniform G + C content and length. We identified variability between species in read quality score as a key source of bias that impacts SSIM to a lesser extent than other quantitative NGS approaches. SSIM was validated against another quantitative NGS assay that utilized qPCR (qMET) to calculate the total gene copy number. The comparison showed that SSIM was both precise (R2 &amp;gt; 0.93 for three Fusarium species) and proportional (slope ~1) in relation to qMET. Further, we applied SSIM to 24 wheat grain samples from Italy, revealing a diverse array of Fusarium species and associated mycotoxins, with SSIM demonstrating superior predictive accuracy for most toxin concentrations compared to qPCR. Our results underscore the utility of SSIM for pathogen-agnostic diagnostics, with important implications for food safety and management of mycotoxin contamination.

  PublisherOA PDFDOI

• Estimated Yield Reductions and Economic Losses on Wheat Caused by Disease from 2018 Through 2021

  Plant Health Progress · 2025-01-01 · 4 citations

  article

  Wheat ( Triticum aestivum L.) yield and economic losses caused by pathogens were estimated annually by plant pathologists from 29 U.S. states and Ontario, Canada, from 2018 through 2021. During this 4-year period, plant pathogens caused an estimated reduction of 560 million bushels, with an estimated loss value of US$2.9 billion. Annual losses ranged from 111 million bushels in 2018 to 188 million bushels in 2019. Based on the number of acres planted, the average per-acre loss caused by plant pathogens was US$18.10 across all years and state/province recording estimates. Fusarium head blight (caused by multiple species of Fusarium) was responsible for the greatest overall estimated reduction in yield, followed by stripe rust (caused by Puccinia striiformis) and leaf rust (caused by P. triticina). Although important disease management costs, such as pesticide application, were not considered, the results show the importance of continued plant disease education and research. Quantifying estimated losses associated with plant pathogens impacting wheat remains an important endeavor. Estimates provided by this group of experts are expected to be used as a guide to influence funding for plant disease research by directing Extension and research through both applied and basic efforts. Moreover, the continued effort to quantify plant diseases and their influence on yield losses, as well as the economics of managing plant diseases, will help inform the industries that influence plant disease management and shape on-farm disease management efforts.

  PublisherDOI

• Etiological Agents of Fusarium Crown Rot in Illinois Wheat

  Plant Disease · 2025-03-22 · 3 citations

  article

  The world is experiencing major changes in both climate and agronomic practices, which are intensifying the need to monitor plant diseases as they expand into new growing regions. Fusarium crown or foot rot is one disease of wheat and other cereals that has previously been the subject of economic concern and research primarily in arid to semiarid regions of the world. Many of the etiological agents involved in Fusarium crown rot (FCR) are cross-pathogenic in head tissues, causing the disease Fusarium head blight and increasing the risk for mycotoxin contamination of foods. During a survey of Fusarium head blight in the Midwestern U.S. state of Illinois in 2022, four soft red winter wheat fields displayed a high incidence of severe crown rot symptoms. The etiological agents of the observed symptoms were identified by translation elongation factor 1α sequencing, which revealed Fusarium graminearum, F. parabolicum, and F. acuminatum as the primary agents of FCR in Illinois wheat. The dominant Fusarium species varied across fields, with recovered isolates spanning five Fusarium species complexes, and a high diversity of likely secondary colonizers was also noted across fields. Lastly, no mycotoxins were detected in the screened wheat heads. Our results highlight the impact of local conditions in driving FCR and pathogen dynamics, even with relatively limited distances between fields. The identification of FCR agents in Illinois will serve as a resource for crop managers and breeders targeting effective control strategies in a changing agroecosystem.

  PublisherDOI

• Virulence and molecular characterization of <i>Blumeria graminis</i> isolates from wheat fields across Ontario

  Canadian Journal of Plant Pathology · 2025-04-02

  article
  PublisherDOI

• Wheat Disease Loss Estimates from the United States and Canada — 2024

  2025-03-24 · 3 citations

  report
  PublisherDOI

• Genetic mapping of resistance to <i>Fusarium</i> head blight in soft red winter wheat line NC13‐20076

  Crop Science · 2025-03-01

  articleOpen access

  Abstract Fusarium head blight (FHB) infection causes yield loss, quality degradation, and the production of damaging mycotoxins in common wheat ( Triticum aestivum L). Marker analysis suggests that NC13‐20076 does not possess previously identified FHB resistance quantitative trait loci (QTL) screened for in eastern winter wheat germplasm. A doubled haploid population of 168 lines from the cross of GA06493‐13LE6 and NC13‐20076 was phenotyped in inoculated nurseries in six environments. Heading date, plant height, and visual ratings of Fusarium damage on heads were recorded in the field; percent Fusarium damaged kernels (FDK) and deoxynivalenol (DON) accumulation were recorded post‐harvest. Interval and multiple QTL mapping were performed on each environment‐by‐trait combination. Plant height and heading date QTL were identified on chromosomes 4A, 5A, 6A, and 7B, and peak markers were used as covariates in mapping of disease response traits. Disease response QTL were identified on chromosomes 1A, 2A, 2B, 3A, 3B, 4A, 5A, 7A, and 7D. The largest percent variance (PV) QTL identified for FHB visual ratings (10.8%) and DON accumulation (10.1%) were found on chromosome 5A ( QFvr.nc‐5A , QDon.nc‐5A ). The largest PV (10.3%) QTL identified for FDK were found on 1A ( QFdk.nc‐1A ). Disease response QTL for multi‐environment scans of visual ratings, FDK, and DON accumulation accounted for 4.0%–10.8%, 4.1%–10.3%, and 4.9%–10.1% of the total variance, respectively. The present results indicate that NC13‐20076 contains several FHB response QTL, which overlap with previously identified QTL and demonstrate the importance of NC13‐20076 as a readily accessible source of FHB resistance.

  PublisherOA PDFDOI

• Wheat Disease Loss Estimates from the United States and Ontario, Canada — 2023

  2024-07-11 · 1 citations

  report
  PublisherDOI

• Registration of ‘GA09436‐16LE12’: A new soft red winter wheat cultivar adapted to the US southeast region

  Journal of Plant Registrations · 2024-12-04

  articleOpen accessSenior author

  Abstract Soft red winter wheat ( Triticum aestivum L.; SRWW) is a major crop in the US southeast (SE) region. However, growing successful wheat crop is challenged by many stresses resulting in substantial losses in yield and quality. To alleviate these challenges, developing new cultivars with high yield potential with resistance to major pests in the region and good quality is warranted. This constitutes the major goal of the SRWW breeding programs ate the University of Georgia (UGA) and the regional institutions including the southern universities GRAINS (SUNGRAINS) programs. ‘GA09436‐16LE12’ (Reg. no. CV‐1209, PI 700011) SRWW cultivar was among the adapted wheat developed and released by the UGA College of Agricultural and Environmental Sciences in 2019. While GA09436‐16LE12 is generally adapted to the US SE region, it specifically well fit to the Georgia environments. It has high yield, very good resistance to most dominant diseases including leaf (caused by Puccinia triticina Erikss.) and stripe (caused by P. striiformis Westend.) rusts; powdery mildew (caused by Erisyphe graminis ); and Soil‐borne wheat mosaic virus . GA09436‐16LE12 has improved Fusarium head blight (caused by Fusarium graminearum Schwabe) which is reflected in lower levels of Deoxynivalenol toxin and Fusarium damaged kernels levels. It also showed moderate field resistance to Hessian fly [ Mayetiola destructor (Say)] although it is susceptible to the biotypes B, C, O, and L. GA09436‐16LE12 has good grain volume weight and good milling and baking quality as a SRWW.

  PublisherOA PDFDOI

Frequent coauthors

• Ryan Parks

  University of North Carolina at Greensboro

  73 shared

• Evsey Kosman

  Tel Aviv University

  58 shared

• Roi Ben‐David

  Agricultural Research Organization

  54 shared

• A. Dinoor

  Hebrew University of Jerusalem

  53 shared

• Beat Keller

  University of Zurich

  53 shared

• Thomas Wicker

  University of Zurich

  50 shared

• P. S. Ojiambo

  North Carolina State University

  40 shared

• Gina Brown‐Guedira

  Agricultural Research Service

  35 shared

Labs

• Structural Pest Management Training & Research FacilityPI