Location: Sunflower and Plant Biology Research
2021 Annual Report
Objectives
OBJECTIVE 1: Develop and release sunflower germplasm and inbred lines with enhanced yield potential, desirable oil traits, or resistance to crop pests (insects and pathogens), along with effective molecular markers.
Subobjective 1A: Develop genetic markers for Phomopsis, rust, and downy mildew resistance.
Subobjective 1B: Characterize genetic and pathogenic variation in Phomopsis populations in North Central sunflower growing regions.
Subobjective 1C: Evaluate diverse interspecific germplasm for resistance to Phomopsis, rust, and downy mildew.
Subobjective 1D: Develop pre-breeding and advanced germplasm with novel traits or combinations of agronomically important traits.
OBJECTIVE 2: Identify and characterize traits associated with resistance to insect pests and improved sunflower-pollinator interactions, and evaluate their effectiveness in insect management systems.
Subobjective 2A: Evaluate susceptibility of sunflowers to insect pests and develop genetic markers for host plant resistance traits.
Subobjective 2B: Assess variation and develop genetic markers for traits associated with pollinator visitation.
Approach
The economic impact of sunflower production in the United States is at least $1.5 billion per year. In the primary sunflower production areas, sunflower must compete with genetically-modified crops like corn and soybean that can be easier to produce or have more consistent yields. To maintain its position as a valuable rotational crop and ensure a consistent supply of heart-healthy oil, both maximum yield and consistency of yield must be improved. Losses from diseases and insect pests, along with related costs of management, are primary challenges for improving sunflower yields. Proposed research aims to improve resistance to diseases and insect pests and combine these traits with herbicide resistance, improved oil content and quality to create a more competitive crop. Specific objectives are to: (1) develop genetic markers for resistance to three major sunflower pathogens, (2) understand genetic and pathogenic variation for a disease that has recently increased in incidence and severity, (3) search for new sources of disease resistance from crop wild relatives of cultivated sunflower, (4) identify and characterize traits that will provide resistance to insect pests or improve sunflower-pollinator interactions (which positively contribute to yields), and (5) combine desired traits for pest resistance with other important agronomic traits to create superior germplasm. Success in these objectives will allow higher, more consistent yields and reduce costs of production, contributing to a stable supply of oil and non-oil sunflowers that supports profitable farming.
Progress Report
Subobjective 1A: Develop genetic markers for Phomopsis, rust, and downy mildew resistance. A population derived from Phomopsis-susceptible (HA 89) and resistant (HA 378) parents was advanced to F5 generation; after further self-pollination, the resulting population of recombinant inbred lines (RIL) will permit mapping of Phomopsis resistance. Mapping of downy mildew resistance was conducted in two populations derived from the crosses of HA 89 with two wild annual sunflower accessions (PI 435378, PI 435432). Segregation for resistance in the 140 F2-derived F3 families (30 seedlings per each family tested) of two populations was evaluated using downy mildew race 734. Phenotypic data revealed that the downy mildew resistance in PI 435378 is controlled by two genes, while resistance in PI 435432 is controlled by one gene. Genetic mapping of the resistance gene in downy mildew differential line 803-1 is completed; the gene named Pl36 was mapped to sunflower chromosome 13.
Subobjective 1B: Characterize population structure and genetic variation within and among populations of Phomopsis helianthi in the Northern Great Plains. Isolation of DNA was completed for all Diaporthe samples across two years of pathogen sampling in three states. Of the 374 samples successfully processed (and Diaporthe species determined), DNA quantity and quality checks permitted 285 isolates to be submitted for genotyping-by-sequencing (GBS). Initial processing of the GBS data yielded 1,697 single nucleotide polymorphisms across 276 samples to be used for population genetic analyses. These analyses are currently underway. Two replications of stem lesion virulence tests for 20 Diaporthe helianthi isolates on a panel of sunflower lines with varying resistance responses were completed. The panel of sunflower lines was expanded to 15 lines to encompass the range of responses to stem lesion infection. Analyses of stem lesion responses to the 20 isolates indicates that some sunflower lines exhibit isolate-specific resistance while five lines were identified that exhibited broad-spectrum resistance to all tested isolates. These results demonstrate the importance of evaluating resistance to multiple isolates for this fungal pathogen and identify promising sources of broad-spectrum resistance.
Subobjective 1C: Evaluate diverse interspecific germplasm for resistance to Phomopsis, rust, and downy mildew. The third year of field screening of 120 interspecific germplasms in replicated trials at two locations for resistance genes for Phomopsis stem canker was completed. Preliminary results identified potential new sources based on four annual and three perennial sunflower crop wild relatives. Replicated greenhouse screening for new sources of downy mildew resistance genes for the most virulent races evaluated 75 promising interspecific germplasms. Four interspecific amphiploids based on perennial sunflower crop wild relatives showed 80 to 100% resistance, while two germplasms based on wild annual sunflower species had 100% resistance. Other lines were found to be segregating for downy mildew resistance (up to 40% resistant plants), allowing for further selection, gene identification, and development of mapping populations for marker-assisted breeding.
Subobjective 1D: Develop pre-breeding and advanced germplasm with novel traits or combinations of agronomically important traits. Over 4,000 nursery rows of high yield, high oil, disease-insect, and herbicide-resistant sunflower experimental lines were grown in nurseries in Fargo, North Dakota, and Chile, with yield trials of experimental hybrids from these lines also grown at several locations throughout the sunflower growing region, including North Dakota, Minnesota, and Kansas. Of these, we are in the process of developing release dockets for several Sclerotinia and Phomopsis resistant sunflower lines of both heterotic groups, downy mildew resistant lines, and early maturing lines suitable for double cropping in the southern and central plains, and late planting in the northern plains.
Subobjective 2A: Evaluate susceptibility of sunflowers to insect pests and develop genetic markers for host plant resistance traits. Preliminary mapping was completed using one year of data on pericarp (hull) thickness from a 288-entry population. A second year of data from the same population showed high year-to-year correlation. The combined data from both years indicates six loci that contribute to sunflower hull thickness. When final QTL mapping is completed, marker-assisted selection should allow more efficient development of lines with greater oil content or reduced susceptibility to seed-feeding pests. Single-cross hybrids were made with the weevil-resistant parent HA 488 and several male lines for comparison to equivalent hybrids without known resistance to the red sunflower seed weevil.
Subobjective 2B: Assess variation and develop genetic markers for traits associated with pollinator visitation. A second year of sampling was completed to examine possible effects of genetic variation in floret size on the communities of wild bees foraging on sunflowers. While sunflowers with deeper or shallower florets were preferred by different bee species in North Dakota, the diversity of bee communities was not affected by floret size. The preference of some large-bodied, generalist bees (e.g., bumble bees) means that sunflower lines that are unattractive to other sunflower pollinators can still receive sufficient bee pollination to ensure high yields if the surrounding landscape supports these large-bodied, generalist bees. Lines from a population that varies for nectar quality (but equal floret size) were also planted and sampled to examine for any preference of wild bees for high sucrose nectar.
Accomplishments
1. Combined mapping of Sclerotinia head rot and Phomopsis stem canker disease resistance confirms shared genetic architecture. Phomopsis stem canker and Sclerotinia head rot are the two most serious diseases of sunflower, and are a recurring problem in the Northern Plains due to an increasing trend of wet conditions in late summers. ARS scientists in Fargo, North Dakota, along with researchers from University of Colorado, conducted genetic studies on a panel of domesticated sunflowers to identify regions of the genome associated with resistance to these two diseases. Several common genome regions were identified for both diseases, suggesting that several loci together may contribute to Phomopsis and Sclerotinia resistance in the same lines. This work provides germplasm resources and genetic markers that should improve breeding for disease resistance that ultimately benefits farmers with higher yields and simplified crop management.
2. Bee community composition, but not diversity, is influenced by floret size in cultivated sunflowers. Small-bodied bees that specialize in pollination of composite plants strongly prefer sunflowers with shallower florets, where nectar is more easily reached. ARS scientists in Fargo, North Dakota, showed that large-bodied generalists (such as bumble bees) foraged preferentially on sunflowers with deep florets. As a result, though different bee species foraged on lines with smaller or larger florets, the number of bee species pollinating various types of sunflowers appeared unchanged. Differences were seen, however, in the bee species present when the same lines were planted in May or June. Information on bee preference and bee availability over the growing season can be used to improve sunflower production in locations where inadequate pollination is believed to limit yields.
3. Marker assisted selection to pyramid rust and downy mildew genes. Sunflower rust and downy mildew are two of the most important global sunflower diseases due to new pathogen races continually evolving. Effective breeding strategies are needed to avoid the rapid breakdown of resistance mediated by race-specific genes for long-term management in sunflower. ARS scientists in Fargo, North Dakota, used marker-assisted selection to develop three breeding lines with resistance to rust (two genes) and downy mildew (one gene). The development of these germplasm lines will provide a broad spectrum of resistance to all known races of rust and downy mildew, allowing commercial sunflower breeders to more easily produce resistant hybrids and increase the durability of disease resistance in sunflower.
4. Development of an improved, greenhouse-based method to evaluate sunflower resistance to Sclerotinia basal stalk rot. Evaluation of sunflower resistance to Sclerotinia basal stalk rot in field trials is time consuming and offers limited resolution for identifying resistance. ARS scientists in Fargo, North Dakota, and colleagues at North Dakota State University and Iowa State University developed and validated a new method to evaluate basal stalk rot resistance. The new method is time- and space-efficient and allows for testing multiple structured populations for genetic mapping in a single year as compared to the need for multi-year, multi-location studies using inoculated field trials. Results from the new method were strongly correlated with field observations and the new method improved identification of highly resistant genotypes. The newly developed method is being used to evaluate multiple mapping populations to improve the identification of genome regions that provide resistance to basal stalk rot.
5. Mapping of basal stalk rot resistance derived from wild sunflower species. Basal stalk rot is a serious fungal disease of sunflower in humid, temperate growing areas. Resistance to basal stalk rot is conferred by multiple genes and has been introduced from the wild silver-leaf sunflower into cultivated sunflower. ARS scientists in Fargo, North Dakota, and colleagues at North Dakota State University used a population made from crossing a cultivated sunflower with a silver-leaf sunflower to identify several genomic regions associated with basal stalk rot resistance. Of these, over half appeared to be associated with gene variants from the wild parent (silver-leaf sunflower). Identification of these new genetic markers will facilitate marker-assisted breeding of sunflowers with resistance to basal stalk rot.
6. Identification of downy mildew resistance genes in sunflower. Downy mildew is one of the most destructive and widely distributed diseases of sunflower worldwide. Resistance against downy mildew in sunflower is commonly regulated by single dominant genes. ARS scientists in Fargo, North Dakota, and colleagues at North Dakota State University confirmed the locations of four genes associated with downy mildew resistance. Diagnostic markers linked to each gene will enable efficient marker-assisted selection in sunflower breeding programs.
Review Publications
Schiffner, S., Hulke, B.S., Jungers, J., Smith, K., Van Tassel, D., Scheaffer, C. 2020. Silphium integrifolium seed and biomass responses to plant density and N fertilization. Agrosystems, Geosciences & Environment. 3:1-12. https://doi.org/10.1002/agg2.20118.
Reinert, S., Pogoda, C.S., Talukder, Z.I., Attia, Z., Collier-Zans, E.C., Gulya, T.J., Kane, N.C., Hulke, B.S. 2020. Genetic loci underlying quantitative resistance to necrotrophic pathogens Sclerotinia and Diaporthe (Phomopsis), and correlated resistance to both pathogens. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-020-03694-x.
Prasifka, J.R., Ferguson, B., Anderson, J.V. 2020. Fatty acid data and crop surveys indicate sources of red sunflower seed weevil, Smicronyx fulvus LeConte (Coleoptera: Curculionidae), populations and suggest strategies for management. Environmental Entomology. 50(1):154-159. https://doi.org/10.1093/ee/nvaa158.
Ma, G., Long, Y., Song, Q., Talukder, Z.I., Shamimuzzaman, M., Qi, L. 2021. Map and sequence-based chromosome walking towards cloning of the male fertility restoration gene Rf5 linked to R11 in sunflower. Scientific Reports. https://doi.org/10.1038/s41598-020-80659-6.
Talukder, Z.I., Underwood, W., Misar, C.G., Seiler, G.J., Liu, Y., Li, X., Cai, X., Qi, L. 2021. Unraveling the Sclerotinia basal stalk rot resistance derived from wild Helianthus argophyllus using a high-density SNP linkage map. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2020.617920.
Ma, G., Song, Q., Li, X., Qi, L. 2020. High-density mapping and candidate gene analysis of Pl18 and Pl20 in sunflower by whole-genome resequencing. International Journal of Molecular Sciences. 21(24):9571. https://doi.org/10.3390/ijms21249571.
Qi, L., Talukder, Z., Ma, G., Li, X. 2021. Discovery and mapping of two new rust resistance genes, R17 and R18, in sunflower using genotyping by sequencing. Theoretical and Applied Genetics. 134:2291-2301. https://doi.org/10.1007/s00122-021-03826-x.
Gilley, M.A., Gulya, T.J., Seiler, G.J., Underwood, W., Hulke, B.S., Misar, C.G., Markell, S.G. 2020. Determination of virulence phenotypes of Plasmopara halstedii in the United States. Plant Disease. 104:2823-2831. https://doi/10.1094/PDIS-10-19-2063-RE.
Underwood, W., Misar, C.G., Block, C., Gulya, T.J., Talukder, Z., Hulke, B.S., Markell, S. 2020. A greenhouse method to evaluate sunflower quantitative resistance to basal stalk rot caused by Sclerotinia sclerotiorum. Plant Disease. 105:464-472. https://doi.org/10.1094/PDIS-08-19-1790-RE.
Prasifka, J.R., Wallis, C.M. 2019. Concentrations of sunflower phenolics appear insufficient to explain resistance to floret- and seed-feeding caterpillars. Arthropod-Plant Interactions. 13:915-921. https://doi.org/10.1007/s11829-019-09706-y.
