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Integration of Early Disease-Resistance Phenotyping Peng et al. Horticulture Research (2021) 8:108 Horticulture Research https://doi.org/10.1038/s41438-021-00543-w www.nature.com/hortres ARTICLE Open Access Integration of early disease-resistance phenotyping, histological characterization, and transcriptome sequencing reveals insights into downy mildew resistance in impatiens Ze Peng1,2, Yanhong He3,4, Saroj Parajuli 1,QianYou1, Weining Wang1, Krishna Bhattarai1, Aaron J. Palmateer5,6 and Zhanao Deng 1 Abstract Downy mildew (DM), caused by obligate parasitic oomycetes, is a destructive disease for a wide range of crops worldwide. Recent outbreaks of impatiens downy mildew (IDM) in many countries have caused huge economic losses. A system to reveal plant–pathogen interactions in the early stage of infection and quickly assess resistance/ susceptibility of plants to DM is desired. In this study, we established an early and rapid system to achieve these goals using impatiens as a model. Thirty-two cultivars of Impatiens walleriana and I. hawkeri were evaluated for their responses to IDM at cotyledon, first/second pair of true leaf, and mature plant stages. All I. walleriana cultivars were highly susceptible to IDM. While all I. hawkeri cultivars were resistant to IDM starting at the first true leaf stage, many (14/16) were susceptible to IDM at the cotyledon stage. Two cultivars showed resistance even at the cotyledon stage. Histological characterization showed that the resistance mechanism of the I. hawkeri cultivars resembles that in 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; grapevine and type II resistance in sunflower. By integrating full-length transcriptome sequencing (Iso-Seq) and RNA- Seq, we constructed the first reference transcriptome for Impatiens comprised of 48,758 sequences with an N50 length of 2060 bp. Comparative transcriptome and qRT-PCR analyses revealed strong candidate genes for IDM resistance, including three resistance genes orthologous to the sunflower gene RGC203, a potential candidate associated with DM resistance. Our approach of integrating early disease-resistance phenotyping, histological characterization, and transcriptome analysis lay a solid foundation to improve DM resistance in impatiens and may provide a model for other crops. Introduction fruits, and ornamental plants. DM is globally distributed Downy mildew (DM) is a destructive disease caused by and has high adaptability to new and changing envir- obligate parasitic oomycetes from the Peronosporaceae onmental conditions2. Most DM pathogens can infect family1. It has been a serious challenge for a wide range their host plant at the seedling stage, causing systemic of cultivated crops including row crops, vegetables, shoot infection, whereas infection at a more mature stage may develop into localized infection patches3.DM can affect the leaves, flowers, fruits, and shoots of hosts Correspondence: Zhanao Deng (zdeng@ufl.edu) 1 and cause great economic losses. It may lead to yield University of Florida, IFAS, Department of Environmental Horticulture, Gulf 4,5 Coast Research and Education Center, 14625 County Road 672, Wimauma, FL losses of up to 40–80% for different crops .Many 33598, USA fungicides have been developed to manage DM patho- 2 State Key Laboratory for Conservation and Utilization of Subtropical Agro- gens; however, due to genetic recombination, frequent Bioresources, South China Agricultural University, 510642 Guangzhou, China Full list of author information is available at the end of the article mutations, and asexual reproduction, new DM pathogen These authors contributed equally: Ze Peng, Yanhong He © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a linktotheCreativeCommons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Peng et al. Horticulture Research (2021) 8:108 Page 2 of 22 races with higher virulence levels emerge constantly, significant decrease of the wholesale values of impatiens resulting in fungicide resistance in DM pathogens and from ~$150 million in 2005 down to ~$65 million in thus severely hindering the effectiveness of fungicides 201525. IDM caused by P. obducens has become a major whose development could take many years and cost disease of I. walleriana. The infected plants exhibit hundreds of millions of dollars6,7. downward leaf curling, chlorotic and downy leaves, and DM pathogens are composed of at least 300 species leaves and flowers drop, all of which may result in com- belonging to different genera, such as Peronospora, plete losses of the aesthetic value of impatiens cultivars24. Pseudoperonospora, and Plasmopara, among which Per- Several studies reported the morphology, transmission onospora is the largest genus containing more than and hosts of P. obducens. This pathogen develops hyaline 260 species8. The common DM species infecting horti- and monopodial sporangiophores with apical branches cultural crops include Peronospora destructor (onion), that can produce ovoid and hyaline sporangia26. The Peronospora belbahrii (basil), Plasmopara viticola (grape), pathogen is readily transmitted by wind-blown or water- Pseudoperonospora cubensis (cucurbits), Plasmopara splashed sporangia from which the zoospores can be halstedii (sunflower), Peronospora effusa (spinach), and released and infect impatiens under suitable temperature Bremia lactucae (lettuce). To combat this disease, host and relative humidity27. Usually, 5–14 days after pathogen resistance to DM has been identified in several crops and infection, visible white downy symptoms could be a few resistance genes have been cloned. For example, the observed on the lower leaf surfaces27,28. The oospores sunflower genome contains more than 30 DM resistance could not be observed in fresh leaves and may survive genes distributed in the domesticated and wild species9. overwinter in plant debris26,27,29. Plasmopara obducens In lettuce, over 50 DM resistance genes have been iden- can infect a number of cultivated and wild Impatiens tified and genetically characterized, among which at least spp., including I. walleriana, I. balsamina, I. pallida, – 28 genes can provide high levels of resistance against I. carpensis, and I. glandulifera28,30 33. However, I. haw- DM10. In grapevine, 27 quantitative trait loci (QTLs) for keri appears to be highly resistant to this disease22. DM resistance have been identified from various Vitis Management of IDM can be achieved by using pre- species, of which the locus Rpv3 is a major determinant ventive fungicides. Several fungicides have been used to for DM resistance11. DM pathogens secrete apoplastic manage this disease in impatiens production facilities. and cytoplasmic effector molecules upon infection that Frequent applications of these fungicides have significantly can be recognized by the proteins encoded by plant increased the production costs and caused serious con- disease-resistance genes (R-genes), which are primarily cerns over pesticide pollution of the environment. More- comprised of nucleotide-binding site leucine-rich repeat over, few fungicides are available for use to manage this (NBS-LRR) genes. Many NBS-LRR clusters have been disease in the landscape (public or residential) and indoor identified in sunflower and lettuce genomic regions exhibitions where impatiens are grown34,35. Developing involved in DM resistance12,13. In Arabidopsis, some Toll/ and using disease-resistant cultivars have proven to be an interleukin-1 receptor NBS-LRR (TIR-NBS-LRR) genes effective, economic, and sustainable approach to managing such as RPP1 confer organ-specific resistance to downy devastating diseases in crops if genetic disease resistance mildew14. In spinach, NBS genes present at the RPF1 can be found or developed. For example, disease-resistant locus contribute to resistance to P. effusa15. cultivars have played an essential and critical role in Impatiens are one of the top-selling annual bedding controlling grapevine DM caused by P. viticola, which is in flowers in the United States. The genus Impatiens (family the same genus with the IDM pathogen P. obducens36.To Balsaminaceae) contains >1000 species that are widely develop disease-resistant cultivars, disease screening is distributed in different geographic and climatic regions, essential and most critical. First, germplasm accessions, as including tropical Africa, Southeast Asia, parts of Europe, many as possible, need to be screened to discover useful and North America16. Among these species, Impatiens sources of disease resistance. Then, large breeding popu- walleriana and Impatiens hawkeri are the most com- lations, generation after generation, need to be screened monly cultivated in the world. The popularity of impa- to identify the resistant progeny. Thus, effective and tiens in the floriculture industry is attributed to the flower efficient disease screening or resistance
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