Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Agronomy, Horticulture, and Plant Science

First Advisor

Febina Mathew


fungicides management, GWAS for resistance to D. helianthi and D. gulyae, Phomopsis stem canker, Sunflower, Vegetative and reproductive resistance


Phomopsis stem canker is a major threat to sunflower (Helianthus annuus L.) production worldwide and its prevalence has increased from 1.5% in 2001 to 61.0% in 2015 in the sunflower producing U.S. states of Colorado, Kansas, Minnesota, Nebraska, North Dakota, South Dakota, and Texas. The disease causes early senescence and lodging of sunflower plants resulting in yield losses up to 40% and oil content up to 25%. Several species of Diaporthe have been reported to cause Phomopsis stem canker. In the United States, Diaporthe helianthi Munyt.-Cvetk. et al. and D. gulyae Shivas et al., have been reported as predominant causal agents of Phomopsis stem canker in the sunflower producing areas of Minnesota, Nebraska, North Dakota, and South Dakota, where more than 80% of sunflower production takes place in the nation. Currently, there are sunflower commercial hybrids with partial resistance and foliar fungicides available to manage Phomopsis stem canker in the United States. However, there is limited information on their efficacy against the fungi causing Phomopsis stem canker. The objectives of this study were to (1) screen cultivated sunflower accessions for resistance to Diaporthe gulyae at vegetative and reproductive growth stages (2) perform genome-wide association mapping to identify the resistance loci in sunflower associated with Diaporthe helianthi and Diaporthe gulyae (3) evaluate fungicides efficacy against fungi causing Phomopsis stem canker. For the first objective, to determine if the sunflower growth stage affects the Phomopsis stem canker severity associated with D. gulyae, a total of 143 accessions screened for resistance to the fungus at V4 to V6 (four to six true leaves) and R4 to R6 (beginning of inflorescence to completion of flowering) using the mycelium contact inoculation method in the greenhouse. Disease severity was assessed 14 days postinoculation using a 0-to-5 rating scale, where 0 = no stem discoloration and 5 = lodged or dead plants and non-parametric statistics was used to determine the relative treatment effect (RTE) associated with disease severity. Twenty-seven, three, and two accessions had significantly lower relative treatment effect at V4 to V6 (ATS=17.06, df=1.43, p=1.86x10- 6), R4 to R6 (ATS=2.4, df=1.82, p=0.0095), and both growth stages compared to the susceptible check ‘HA 288’ based on 95% confidence intervals. For the second objective, disease phenotyping was conducted in the greenhouse using a diverse panel of 213 USDA cultivated sunflower accessions and one susceptible check (PI 552934). At four to six true leaves growth stages, six plants per accession were inoculated with a single isolate of D. helianthi or D. gulyae using the mycelium-contact inoculation method. Disease severity was assessed 15 days (D. gulyae) and 30 days (D. helianthi) post-inoculation using a 0 to 5 rating scale and non-parametric statistics was used to determine the RTE associated with disease severity. Out of 213 accessions, 39 were significant less susceptible to D. gulyae when compared to the susceptible check. Genome-wide association study identified 20 common loci associated with resistance to D. gulyae and D. helianthi as well as a total of 17 candidate genes associated with plant defense responses such as lectin receptor kinases. For the third objective, to evaluate the efficacy of foliar fungicides, a field experiment was carried out in 2019, 2020, and 2021, in Brookings, SD. Fourteen fungicides belonging to three FRAC (Fungicide Resistance Committee Action) groups: FRAC 3 DMI (DeMethylation Inhibitors), FRAC 7 (Succinate DeHydrogenase Inhibitors), and FRAC 11 (Quinone Outside Inhibitors) were sprayed at R1 (miniature floral head formation) growth stage of sunflower development. Significant differences in disease severity index (DSI) and yield were observed among treatments in 2019 and the treatment containing Mefentrifluconazole + Pyraclostrobin significantly reduced DSI by 26.88% and had a significant yield increase of 430.4 kg/ha greater than nontreated control, resulting in 372.97 kg/ha ($156.64/ha) for oil type and 384.7 kg/ha ($188.5/ha) for non-oil type profit using the oil type sunflower ($0.42/kg) and non-oil ($0.49/kg) prices in 2019. However, in 2020 and 2021, no significant differences were observed on yield, and there was a significant difference on DSI in 2021. Overall, the findings from this study provide information on parental materials with resistance to D. helianthi and D. gulyae, which will facilitate marker-assisted selection in future breeding and development of varieties and hybrids for resistance to the causal fungi. In addition, the information on foliar fungicides will help farmers to manage Phomopsis stem canker in sunflower.

Library of Congress Subject Headings

Sunflowers -- Disease and pest resistance.
Sunflowers -- Diseases and pests.
Sunflowers -- Genome mapping.
Canker (Plant disease)

Number of Pages



South Dakota State University



Rights Statement

In Copyright