Research Project: Genetic Enhancement of Sunflower Yield and Tolerance to Biotic Stress

Location: Sunflower and Plant Biology Research

2019 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. Susceptible (HA 89) and resistant (HA 378) parents were crossed to develop a recombinant inbred line (RIL) population that will permit QTL mapping of Phomopsis resistance, and the resulting F1 hybrids were advanced to the F2 generation. Molecular mapping of a rust resistance gene derived from KP193 introduced from South Africa was completed. Individual F2 plants produced from a cross with KP193 were subjected to genotyping-by-sequence, self-pollinated, and the resulting 140 F2-derived F3 families were evaluated for rust resistance. Linkage analysis placed the rust resistance gene derived from KP193 to an interval of 2.7 cM on sunflower chromosome 13. Subobjective 1B: Characterize genetic and pathogenic variation in Phomopsis populations in North Central sunflower growing regions. The first year of Phomopsis isolate collection was completed. Stem lesion samples were collected from five sunflower fields per state in North Dakota, South Dakota, and Minnesota. Three of the fields in Minnesota were also used for hierarchical sampling of Phomopsis stalk lesions. Isolation of the fungal pathogen was successful for 200 stalk lesion samples and fungal DNA has been successfully extracted for all isolated fungal samples. The Diaporthe species isolated from stalk lesions has been determined for 164 samples by PCR with species-specific primers. Of samples for which the Diaporthe species has been identified, 148 were Diaporthe helianthi, providing further evidence that this species is the most common causal agent of Phomopsis stem canker in the region. Of the remaining 16 samples, 14 were identified as Diaporthe gulyae and 2 as the soybean stem canker species Diaporthe phaseolorum. DNA quantity and quality have been evaluated and samples are prepared to submit for genotyping-by-sequencing after completion of sampling in fall 2019. Subobjective 1C: Evaluate diverse interspecific germplasm for resistance to Phomopsis, rust, and downy mildew. To identify new sources of resistance genes for Phomopsis stem canker, the first year of testing was completed for 75 interspecific germplasms in replicated trials at two locations. Preliminary results identified potentially useful lines from diverse genetic backgrounds. Replicated greenhouse screening for new sources of rust and downy mildew resistance genes evaluated 100 interspecific germplasms against the most virulent races of both pathogens. Preliminary results for rust resistance identified three promising lines with high levels of resistance, while two lines were identified with very high levels of resistance to downy mildew. Subobjective 1D: Develop pre-breeding and advanced germplasm with novel traits or combinations of agronomically important traits. Nearly 3,000 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. Of these, several are candidates for release next year, including several Sclerotinia and Phomopsis resistant sunflower lines of both heterotic groups, and early maturing lines suitable for double cropping in the southern and central plains, and late planting in the northern plains. A plant release docket is being drafted for two lines with insect resistance, one to the red sunflower seed weevil and the other to banded sunflower moth. Both of these pests are common throughout the sunflower growing region, and the resistance will also come in a package that includes other traits like high oleic acid, disease resistance, and herbicide tolerance. Subobjective 2A: Evaluate susceptibility of sunflowers to insect pests and develop genetic markers for host plant resistance traits. A first year of testing was completed to examine susceptibility to red sunflower seed weevil for released inbred lines and putative sources of resistance to the weevil. On plants infested with 30 adult weevils each, results showed no significant variation among 16 released inbred lines, but an almost 70% reduction in seed damage for entry 14-121, an inbred line being developed for release. If 14-121 or other similarly effective material can be released, reductions in seed weevil damage of 50% or more are possible, and should be compatible with other management methods including insecticides. A first year of data was also collected on pericarp thickness in an association mapping population and data on pericarp strength from an additional biparental population. A second year of data collection for both seed weevil and pericarp traits is underway. Subobjective 2B: Assess variation and develop genetic markers for traits associated with pollinator visitation. Data on floret size, which determines nectar accessibility for pollinators, were collected from 270 inbred lines in a large association mapping population. Because of the importance of seed size as a market-defining trait, additional data on seed size were collected from most (246) of the same lines. Results show moderate correlations between floret and seed size in different market classes and heterotic groups, but suggest that selection for increased pollinator attraction (by reducing floret size) can be accomplished without decreasing seed size. Successful breeding for improved pollinator visitation through shortened florets should result in higher, more stable yields. Additional validation data are being collected and genetic markers for floret and seed size are being developed.

Accomplishments
1. Discovery of a novel downy mildew resistance gene Pl35 derived from wild sunflowers. Downy mildew (DM) is an economically important disease in sunflower production worldwide. Although planting of fungicide-treated seed helps to manage this disease, incorporating genetic resistance is the most economical and sustainable strategy to prevent crop losses. ARS scientists in Fargo, North Dakota, transferred a new DM resistance gene from a wild sunflower species into both oilseed and confection sunflowers. The developed germplasms are resistant to most DM pathotypes identified in North America and genetic markers for this new DM resistance gene, located on chromosome 1, were validated in a large panel of sunflower lines collected worldwide. This new germplasm and markers will help plant breeders efficiently develop new downy mildew resistant sunflowers.

2. Cover crop mixes with or without sunflowers support different pollinator enhancement goals. Cover crops are single- or multiple-species mixtures grown in rotation with commodities that provide many ecosystem benefits, including reduced weed pressure and soil erosion, and improved soil health and pollinator habitat. ARS scientists in Mandan and Fargo, North Dakota, discovered that cover crop mixes including buckwheat provided the most flowers and bee visits over the longest time period. Mixes containing phacelia and buckwheat attracted high numbers of common bee species, while cover crops including sunflowers attracted more rare bees from the surrounding landscape. This information provides growers and conservation groups appropriate cover crop recommendations for attracting honey bees or bumble bees, by including phacelia, or supporting rare, wild bees by including sunflowers.

3. Potential use of naturalized sunflower crop wild relatives from Australia. Sunflower is a crop native to North America, but with wild relatives naturalized in Australia. However, it was not known whether the oil content and quality of these Australian populations changed during naturalization to differ from wild sunflowers in the United States. ARS scientists in Fargo, North Dakota, and their colleagues in Australia found naturalized wild annual sunflowers from Australia did not differ in oil content and quality from similar populations in the United States. While the oil content of the Australian populations was half that of the cultivated sunflower, the oil quality was similar. Because oil concentration can be rapidly increased to acceptable levels by backcrossing, sunflower breeders can use populations naturalized in Australia as sources for unique traits, such as disease resistance, salt tolerance, and insect resistance.

4. Cultivated sunflowers have significant resistance to an important insect pest. Cultivated sunflowers have significant resistance to an important insect pest. Resistance to banded sunflower moth, a seed-feeding pest of sunflowers and other insects has been considered absent in cultivated sunflowers. Recently, ARS scientists in Fargo, North Dakota, used sunflowers from both public (USDA) and private (commercial) sources to show that some public inbred lines (parents for hybrids) had only one-fifth as much insect-related damage as others. It was further discovered that when these less damaged inbred lines were used as parents, the hybrids also had less damage. Commercial hybrids tested also showed very low levels of seed damage from banded sunflower moth. Public and private breeders now know that selection for resistance to the banded sunflower moth is achievable, which allows growers of certain sunflower hybrids to make informed decisions on planting date and insecticide use.

5. Gene silencing in parental sunflower lines. The sunflower industry continuously produces new and improved hybrids to increase yields, add novel traits and broaden the crop’s relatively narrow genetic base. Producing sunflower hybrids requires crossing sterile female lines with fertility-restoring males, but in some combinations of crosses hybrid fertility is absent, suggesting that silencing genes may be responsible for these abnormalities. ARS scientists in Fargo, North Dakota, discovered the presence of silencing genes in certain hybrid combinations causing loss of fertility. Markers developed for identifying these silencing genes will improve efficiency of private- and public-sector sunflower breeding by allowing lines with silencing genes to be identified and eliminated.

Review Publications
Ma, G.J., Seiler, G.J., Markell, S.G., Qi, L.L. 2019. Registration of three confection sunflower germplasms, HA-DM2, HA-DM3, and HA-DM4, resistant to downy mildew and rust. Journal of Plant Registrations. 13:103-108. https://dl.sciencesocieties.org/publications/jpr/pdfs/13/1/103.
Liu, Z., Zhang, L., Ma, G.J., Seiler, G.J., Jan, C.C., Qi, L.L. 2019. Molecular mapping of the downy mildew and rust resistance genes in a sunflower germplasm line TX16R. Molecular Breeding. 39:19. https://doi.org/10.1007/s11032-018-0921-z.
Mallinger, R.E., Bradshaw, J., Varenhorst, A.J., Prasifka, J.R. 2018. Native solitary bees provide economically significant pollination services to confection sunflowers (Helianthus annuusL.) (Asterales:Asteraceae) grown across the northern Great Plains. Journal of Economic Entomology. https://doi.org/10.1093/jee/toy322.
Talukder, Z.I, Ma, G., Hulke, B.S., Jan, C.-C., Qi, L. 2019. Linkage mapping and genome-wide association studies of the Rf gene cluster in sunflower (Helianthus annuus L.) and their distribution in world sunflower collections. Frontiers in Genetics. 10:216. https://doi.org/10.3389/fgene.2019.00216.
Seiler, G.J., Gulya, T., Kong, G., Thompson, S., Mitchell, J. 2018. Oil concentration and fatty acid profile of naturalized wild annual Helianthus annuus populations from Australia. Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-018-0686-6.
Reinert, S., Money, K., Rockstad, G.B., Kane, N., Van Tassel, D.L., Hulke, B.S. 2018. Two contrasting methods improve Silphium integrifolium Michx. germination rate to agronomically acceptable levels. Euphytica. 214:256. https://doi.org/10.1007/s10681-018-2236-x.
Liu, Z., Long, Y., Xu, S.S., Seiler, G.J., Jan, C.C. 2019. Unique fertility restoration suppressor genes for male-sterile CMS ANN2 and CMS ANN3 cytoplasms in sunflower (Helianthus annuus L.). Molecular Breeding. 39:22. https://doi.org/10.1007/s11032-018-0922-y.
Ma, G., Zhang, W., Liu, L., Chao, W.S., Gu, Y.Q., Qi, L., Xu, S.S., Cai, X. 2018. Cloning and characterization of the homoeologous genes for the Rec8-like meiotic cohesin in polyploid wheat. Biomed Central (BMC) Plant Biology. 18:224. https://doi.org/10.1186/s12870-018-1442-y.
Prasifka, J.R., Mallinger, R.E., Portlas, Z.M., Hulke, B.S., Fugate, K.K., Paradis, T., Hampton, M.E., Carter, C.J. 2018. Using nectar-related traits to enhance crop-pollinator interactions. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2018.00812.
Seiler, G.J. 2018. Chao-Chien Jan: Thirty-five years of dedicated research utilizing wild sunflower crop relatives for sunflower improvement. Helia. 41(68): 1-22. https://doi.org/10.1515/helia-2018-0005.
Talukder, Z.I., Long, Y., Seiler, G.J., Underwood, W., Qi, L. 2019. Introgression and monitoring of wild Helianthus praecox alien segments associated with Sclerotinia basal stalk rot resistance in sunflower using genotyping-by sequencing. PLoS One. 14(3):e0213065. https://doi.org/10.1371/journal.pone.0213065.
Mallinger, R., Franco Jr, J.G., Prischmann-Voldseth, D.A., Prasifka, J.R. 2018. Annual cover crops for managed and wild bees: Optimal plant mixtures depend on pollinator enhancement goals. Agriculture, Ecosystems and Environment. 273(1):107-116. https://doi.org/10.1016/j.agee.2018.12.006.
Hulke, B.S., Winkler-Moser, J.K. 2019. Registration of genetic stocks TOCO B1, TOCO R1, and TOCO R2 with high gamma- and delta-tocopherol and altered fatty acid composition in the seed oil. Journal of Plant Registrations. https://doi.org/10.3198/jpr2018.10.0070crgs.
Hulke, B.S., Markell, S.G., Kane, N.C., Matthew, F.M. 2019. Phomopsis stem canker of sunflower in North America: Correlation with climate and solutions through breeding and management. OCL - Oilseeds & fats, Crops and Lipids. 26:13. https://doi.org/10.1051/ocl/2019011.
Gao, L., Lee, J.S., Hubner, S., Hulke, B.S., Qu, Y., Rieseberg, L.H. 2019. Genetic and phenotypic analyses indicate that resistance to flooding stress is uncoupled from performance in cultivated sunflower. New Phytologist. 223((3):1657-1670. https://doi.org/10.1111/nph.15894.
Talukder, Z.I., Long, Y.M., Seiler, G.J., Underwood, W., Qi, L.L. 2019. Registration of oilseed sunflower germplasms HA-BSR6, HA-BSR7, and HA-BSR8 highly resistant to sclerotinia basal stalk rot and downy mildew. Journal of Plant Registrations. https://doi.org/10.3198/jpr2018.10.0071crg.