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Yeni O, Şen M, Hasançebi S, Turgut Kara N. Optimization of loop-mediated isothermal amplification assay for sunflower mildew disease detection. Sci Rep 2024; 14:23224. [PMID: 39369029 PMCID: PMC11455944 DOI: 10.1038/s41598-024-72228-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 09/04/2024] [Indexed: 10/07/2024] Open
Abstract
Loop-Mediated Isothermal Amplification (LAMP) represents a valuable technique for DNA/RNA detection, known for its exceptional sensitivity, specificity, speed, accuracy, and affordability. This study focused on optimizing a LAMP-based method to detect early signs of Plasmopara halstedii, the casual pathogen of sunflower downy mildew, a severe threat to sunflower crops. Specifically, a set of six LAMP primers (two outer, two inner, and two loop) were designed from P. halstedii genomic DNA, targeting the ribosomal Large Subunit (LSU). These primers were verified by in silico analysis and experimental validation using both target and non-target species' DNAs. Optimizations encompassing reaction conditions (temperature, time) and component concentrations (magnesium, Bst DNA polymerase, primers, and dNTP) were determined. Validation of these optimizations was performed by agarose gel electrophoresis. Furthermore, various colorimetric chemicals (Neutral Red, Hydroxynaphthol Blue, SYBR Safe, Thiazole Green) were evaluated to facilitate method analysis, and the real-time analysis has been optimized, presenting multiple approaches for detecting sunflower downy mildew using the LAMP technique. The analytical sensitivity of the method was confirmed by detecting P. halstedii DNA concentrations as low as 0.5 pg/μl. This pioneering study, establishing P. halstedii detection through the LAMP method, stands as unique in its field. The precision, robustness, and practicality of the LAMP protocol make it an ideal choice for studies focusing on sunflower mildew, emphasizing its recommended use due to its operational ease and reliability.
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Affiliation(s)
- Oğuzhan Yeni
- Institute of Science, Program of Molecular Biotechnology and Genetics, Istanbul University, Istanbul, Turkey
| | - Mutlu Şen
- Institute of Science, Program of Biotechnology and Genetics, Trakya University, Edirne, Turkey
| | - Semra Hasançebi
- Faculty of Engineering, Department of Genetics and Bioengineering, Trakya University, Ahmet Karadeniz Yerleskesi, Edirne, Turkey
| | - Neslihan Turgut Kara
- Faculty of Science, Department of Molecular Biology and Genetics, Istanbul University, Vezneciler, 34134, Istanbul, Turkey.
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2
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Qi LL, Talukder ZI, Ma GJ, Seiler GJ. Introgression and targeting of the Pl 37 and Pl 38 genes for downy mildew resistance from wild Helianthus annuus and H. praecox into cultivated sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:82. [PMID: 36952051 DOI: 10.1007/s00122-023-04316-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Two new downy mildew resistance genes, Pl37 and Pl38, were introgressed from wild sunflower species into cultivated sunflower and mapped to sunflower chromosomes 4 and 2, respectively Downy mildew (DM), caused by the oomycete pathogen Plasmopara halstedii (Farl.) Berl. & de Toni, is known as the most prevalent disease occurring in global sunflower production areas, especially in North America and Europe. In this study, we report the introgression and molecular mapping of two new DM resistance genes from wild sunflower species, Helianthus annuus and H. praecox, into cultivated sunflower. Two mapping populations were developed from the crosses of HA 89/H. annuus PI 435417 (Pop1) and CMS HA 89/H. praecox PRA-417 (Pop2). The phenotypic evaluation of DM resistance/susceptibility was conducted in the BC1F2-derived BC1F3 populations using P. halstedii race 734. The BC1F2 segregating Pop1 was genotyped using an Optimal GBS AgriSeq™ Panel consisting of 768 mapped SNP markers, while the BC1F2 segregating Pop2 was genotyped using a genotyping-by-sequencing approach. Linkage analysis and subsequent saturation mapping placed the DM resistance gene, designated Pl37, derived from H. annuus PI 435417 in a 1.6 cM genetic interval on sunflower chromosome 4. Pl37 co-segregated with SNP markers SPB0003 and C4_5738736. Similarly, linkage analysis and subsequent saturation mapping placed the DM resistance gene, designated Pl38, derived from H. praecox PRA-417 in a 0.8 cM genetic interval on sunflower chromosome 2. Pl38 co-segregated with seven SNP markers. Multi-pathotype tests revealed that lines with Pl37 or Pl38 are immune to the most prevalent and virulent P. halstedii races tested. Two germplasm lines, HA-DM15 with Pl37 and HA-DM16 with Pl38, were developed for use in sunflower DM-resistance breeding.
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Affiliation(s)
- L L Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA.
| | - Z I Talukder
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
| | - G J Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
- Ball Horticultural Company, 622 Town Road, West Chicago, IL, 60185, USA
| | - G J Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
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3
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Molinero-Ruiz L. Sustainable and efficient control of sunflower downy mildew by means of genetic resistance: a review. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3757-3771. [PMID: 35084515 DOI: 10.1007/s00122-022-04038-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
The breeding of sunflower (Helianthus annuus L.) for resistance to downy mildew (caused by the oomycete Plasmopara halstedii Farl. Berl. & de Toni) is reviewed in this work under the scope of its sustainability and efficiency. When sunflower turned into an oilseed crop, resistance to the disease was included in its initial breeding strategies. Subsequent development of genomic tools allowed a significant expansion of the knowledge on the diversity of its genetic resistance and its application to the genetic control of the disease. Simultaneously to genetic improvements, and as a consequence of the close interaction between the pathogen and its host plant, an enormous variety of pathotypes has been described in all the sunflower-growing areas worldwide. Thus, the genetic control of sunflower downy mildew is an active research field subjected to continuous evolution and challenge. In practice, genetic resistance constitutes the base tier of Integrated Pest Management against sunflower downy mildew. The second tier is composed of elements related to crop management: rotation, removal of volunteer plants, sowing date, tillage. Biological control alternatives and resistance inducers could also provide additional restraint. Finally, the top tier includes chemical treatments that should only be used when necessary and if the more basal Integrated Pest Management elements fail to keep pathogen populations under the economic threshold.
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Affiliation(s)
- L Molinero-Ruiz
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain.
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4
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Elameen A, de Labrouhe DT, Bret-Mestries E, Delmotte F. Spatial Genetic Structure and Pathogenic Race Composition at the Field Scale in the Sunflower Downy Mildew Pathogen, Plasmopara halstedii. J Fungi (Basel) 2022; 8:1084. [PMID: 36294648 PMCID: PMC9605284 DOI: 10.3390/jof8101084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022] Open
Abstract
Yield losses in sunflower crops caused by Plasmopara halstedii can be up to 100%, depending on the cultivar susceptibility, environmental conditions, and virulence of the pathogen population. The aim of this study was to investigate the genetic and phenotypic structure of a sunflower downy mildew agent at the field scale. The genetic diversity of 250 P. halstedii isolates collected from one field in southern France was assessed using single-nucleotide polymorphisms (SNPs) and single sequence repeats (SSR). A total of 109 multilocus genotypes (MLG) were identified among the 250 isolates collected in the field. Four genotypes were repeated more than 20 times and spatially spread over the field. Estimates of genetic relationships among P. halstedii isolates using principal component analysis and a Bayesian clustering approach demonstrated that the isolates are grouped into two main genetic clusters. A high level of genetic differentiation among clusters was detected (FST = 0.35), indicating overall limited exchange between them, but our results also suggest that recombination between individuals of these groups is not rare. Genetic clusters were highly related to pathotypes, as previously described for this pathogen species. Eight different races were identified (100, 300, 304, 307, 703, 704, 707, and 714), with race 304 being predominant and present at most of the sites. The co-existence of multiple races at the field level is a new finding that could have important implications for the management of sunflower downy mildew. These data provide the first population-wide picture of the genetic structure of P. halstedii at a fine spatial scale.
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Affiliation(s)
- Abdelhameed Elameen
- NIBIO, Norwegian Institute of Bioeconomy Research, Division of Biotechnology and Plant Health, N-1431 Ås, Norway
| | | | | | - Francois Delmotte
- INRAE, Bordeaux Sciences Agro, ISVV, SAVE, 33140 Villenave d’Ornon, France
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Ma G, Song Q, Li X, Qi L. Genetic Insight into Disease Resistance Gene Clusters by Using Sequencing-Based Fine Mapping in Sunflower ( Helianthus annuus L.). Int J Mol Sci 2022; 23:9516. [PMID: 36076914 PMCID: PMC9455867 DOI: 10.3390/ijms23179516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Rust and downy mildew (DM) are two important sunflower diseases that lead to significant yield losses globally. The use of resistant hybrids to control rust and DM in sunflower has a long history. The rust resistance genes, R13a and R16, were previously mapped to a 3.4 Mb region at the lower end of sunflower chromosome 13, while the DM resistance gene, Pl33, was previously mapped to a 4.2 Mb region located at the upper end of chromosome 4. High-resolution fine mapping was conducted using whole genome sequencing of HA-R6 (R13a) and TX16R (R16 and Pl33) and large segregated populations. R13a and R16 were fine mapped to a 0.48 cM region in chromosome 13 corresponding to a 790 kb physical interval on the XRQr1.0 genome assembly. Four disease defense-related genes with nucleotide-binding leucine-rich repeat (NLR) motifs were found in this region from XRQr1.0 gene annotation as candidate genes for R13a and R16. Pl33 was fine mapped to a 0.04 cM region in chromosome 4 corresponding to a 63 kb physical interval. One NLR gene, HanXRQChr04g0095641, was predicted as the candidate gene for Pl33. The diagnostic SNP markers developed for each gene in the current study will facilitate marker-assisted selections of resistance genes in sunflower breeding programs.
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Affiliation(s)
- Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102-6050, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705-2350, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102-6050, USA
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102-2765, USA
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6
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Qi LL, Cai XW. Characterization and mapping of a downy mildew resistance gene, Pl36, in sunflower ( Helianthus annuus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:8. [PMID: 37309323 PMCID: PMC10248693 DOI: 10.1007/s11032-022-01280-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Downy mildew (DM) is one of the most serious diseases in sunflower-growing regions worldwide, often significantly reducing sunflower yields. The causal agent of sunflower DM, the oomycete pathogen Plasmopara halstedii, is highly virulent and aggressive. Studying regional disease spread and virulence evolution in the DM pathogen population is important for the development of new sunflower inbred lines with resistance to the existing DM pathogen. The sunflower line 803-1, as one of nine international differential hosts, has been used in the identification of P. halstedii virulent pathotypes in sunflower since 2000. The DM resistance gene in 803-1 was temporally designated Pl5 + based on allelic analysis but has not been molecularly characterized. In the present study, bulked segregant analysis and genetic mapping confirmed the presence of the Pl gene within a large gene cluster on sunflower chromosome 13 in 803-1, as previously reported. Subsequent saturation mapping in the gene target region with single nucleotide polymorphism (SNP) markers placed this gene at an interval of 3.4 Mb in the XRQ reference genome assembly, a location different from that of Pl5. Therefore, the Pl gene in 803-1 was re-designated Pl36 because it is not allelic with Pl5. Four SNP markers co-segregated with Pl36, and SNP SFW05743 was 1.1 cM proximal to Pl36. The relationship of eight Pl genes in the cluster is discussed based on their origin, map position, and specificity of resistance/susceptibility to DM infection. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01280-1.
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Affiliation(s)
- L. L. Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND 58102-2765 USA
| | - X. W. Cai
- USDA-Agricultural Research Service, Wheat, Sorghum and Forage Research Unit, 251 Filley Hall/Food Ind. Complex, Lincoln, NE 68583 USA
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New and High Virulent Pathotypes of Sunflower Downy Mildew ( Plasmopara halstedii) in Seven Countries in Europe. J Fungi (Basel) 2021; 7:jof7070549. [PMID: 34356928 PMCID: PMC8306969 DOI: 10.3390/jof7070549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
Downy mildew of sunflower, caused by Plasmopara halstedii (Farl.) Berl. et de Toni, is a relevant disease of this crop. High virulent pathotypes have been identified in several countries, while there are few data on the spread of P. halstedii pathotypes in some important sunflower-growing areas of Europe. The goal of this study was to give up-to-date information on the pathotype structure of P. halstedii in Hungary and provide some actual data on the virulence phenotype of the pathogen for six European countries. Infected leaves of different sunflower hybrids and volunteers were collected in seven countries (Hungary, Bulgaria, Serbia, Turkey, Greece, Romania, and Italy) between 2012 and 2019. A universally accepted nomenclature was used with a standardized set of sunflower differential lines for pathotype characterization of isolates. The virulence pattern of the isolates was determined by a three-digit code (coded virulence formula, CVF). A total of 109 P. halstedii isolates were characterized. As a result of our survey, 18 new P. halstedii pathotypes were identified in Europe. Two out of the eighteen pathotypes were detected from the Asian part of Turkey. The detailed distribution of pathotypes in Hungary is also discussed.
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Gilley MA, Gulya TJ, Seiler GJ, Underwood W, Hulke BS, Misar CG, Markell SG. Determination of Virulence Phenotypes of Plasmopara halstedii in the United States. PLANT DISEASE 2020; 104:2823-2831. [PMID: 32955406 DOI: 10.1094/pdis-10-19-2063-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Downy mildew, caused by Plasmopara halstedii (Farl.) Berl. and de Toni, is an economically important disease in cultivated sunflowers, Helianthus annuus L. Resistance genes incorporated into commercial hybrids are used as an effective disease management tool, but the duration of effectiveness is limited as virulence evolves in the pathogen population. A comprehensive assessment of pathogen virulence was conducted in 2014 and 2015 in the U.S. Great Plains states of North Dakota and South Dakota, where approximately 75% of the U.S. sunflower is produced annually. The virulence phenotypes (and races) of 185 isolates were determined using the U.S. standard set of nine differentials. Additionally, the virulence phenotypes of 61 to 185 isolates were determined on 13 additional lines that have been used to evaluate pathogen virulence in North America and/or internationally. Although widespread virulence was identified on several genes, new virulence was identified on the Pl8 resistance gene, and no virulence was observed on the PlArg, Pl15, Pl17 and Pl18 genes. Results of this study suggest that three additional lines should be used as differentials and agree with previous studies that six lines proposed as differentials should be used in two internationally accepted differential sets. For effective disease management using genetic resistance, it is critical that virulence data be relevant and timely. This is best accomplished when pathogen virulence is determined frequently and by using genetic lines containing resistance genes actively incorporated into commercial cultivars.
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Affiliation(s)
- Michelle A Gilley
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | | | | | | | | | | | - Samuel G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
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Nisha N, Körösi K, Perczel M, Yousif AIA, Bán R. First Report on the Occurrence of an Aggressive Pathotype, 734, of Plasmopara halstedii Causing Sunflower Downy Mildew in Hungary. PLANT DISEASE 2020; 105:711-711. [PMID: 33044147 DOI: 10.1094/pdis-05-20-1054-pdn] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Downy mildew of sunflower (Helianthus annuus L.) is caused by Plasmopara halstedii (Farl.) Berl. et de Toni, leading to significant losses in crop production worldwide. The number of new and more aggressive pathotypes has increased rapidly over the last 10 years in Europe (Virányi et al. 2015, Bán et al. 2018), therefore, constantly monitoring the distribution of races is an important task. As part of regular surveys in June 2019, severe downy mildew was identified in some regions, appearing as chlorotic lesions along the veins of the adaxial side and white sporulation on the abaxial side of the leaves of severely stunted hybrids containing PI6 and PI7 resistance genes. The identification of the pathogen was performed microscopically based on morphological characteristics (average size of sporangia: 28x20 µm). Disease incidence (the ratio of diseased plants) ranged between 10 and 30% per field in three regions and resulted in moderate yield loss. Isolates (defined as a lesion per leaf) were collected from 4 to 8 infected leaves of each hybrid by region and stored at -70°C. Two, one and one isolates of P. halstedii were selected and characterized from the southeastern (Békés County), northern (Nógrád County) and northeastern (Borsod-Abaúj-Zemplén County) regions of Hungary, respectively. The pathotype of the four isolates was determined using the international standardized nomenclature method reviewed by Trojanová et al. (2017), including nine sunflower differential inbred lines (HA-304, RHA-265, RHA-274, PMI-3, PM-17, 803-1, HAR-4, QHP2 and HA-335). Zoosporangia from frozen sunflower leaves were washed off into bidistilled water and the concentration was adjusted to 3.5x104 sporangia/ml using a hemocytometer. Three-day-old seedlings with a radical of 1 to 1.5 cm long were immersed in the sporangial suspension and kept at 16°C overnight (Cohen and Sackston 1973). Inoculated seedlings were planted into trays containing clear moistened perlite (d = 4 mm) and grown in a growth chamber with a photoperiod of 12 h. The experiment was carried out twice with each isolate using 15 seeds/differential line with two replicates. Bidistilled water was sprayed on the plants 9 days after inoculation, and then trays were covered with a black polyethylene bag and maintained at 19°C overnight to induce sporulation. The first disease assessment was done based on cotyledons bearing white sporulation. Next, a second evaluation was performed 21 days after inoculation assessing stunting of the plants, chlorotic lesions on true leaves and damping-off. All 4 isolates examined caused disease on differential lines HA-304, RHA-265, RHA-274, PMI-3, PM-17 and HA-335, whereas the other lines showed no symptoms and signs of sunflower downy mildew. As a result, it was concluded that the presence of P. halstedii pathotype 734 was confirmed. This pathotype is likely widespread in Hungary as it could be detected from three different regions. Moreover, the possibility that pathotype 734 is present in Hungary has been raised before (Iwebor et al. 2018). This pathotype is already widespread in the USA and Russia and is considered to be highly aggressive, since it was able to infect hybrids with resistance genes PI6 and PI7 (Iwebor et al. 2018, Spring 2019). To our knowledge, this is the first report of pathotype 734 of P. halstedii in Hungary and Central Europe. Continuous monitoring and incorporation of new resistance genes into sunflower hybrids are essential steps in the future to control P. halstedii.
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Affiliation(s)
- Nisha Nisha
- Szent Istvan University, 72402, Department of Integrated Plant Protection, Institute of Plant Protection, Gödöllő, Hungary;
| | - Katalin Körösi
- Szent Istvan University, 72402, Department of Integrated Plant Protection, Institute of Plant Protection, Gödöllő, Hungary
- PlasmoProtect Ltd., Szarvas, Hungary;
| | | | - Ahmed Ibrahim Alrashid Yousif
- Szent Istvan University, 72402, Department of Integrated Plant Protection, Institute of Plant Protection, Gödöllő, Hungary;
| | - Rita Bán
- Szent Istvan University, 72402, Department of Integrated Plant Protection, Institute of Plant Protection, Gödöllő, Hungary
- PlasmoProtect Ltd., Szarvas, Hungary;
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Molecular dissection of resistance gene cluster and candidate gene identification of Pl 17 and Pl 19 in sunflower by whole-genome resequencing. Sci Rep 2019; 9:14974. [PMID: 31628344 PMCID: PMC6802088 DOI: 10.1038/s41598-019-50394-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/10/2019] [Indexed: 11/08/2022] Open
Abstract
Sunflower (Helianthus annuus L.) production is challenged by different biotic and abiotic stresses, among which downy mildew (DM) is a severe biotic stress that is detrimental to sunflower yield and quality in many sunflower-growing regions worldwide. Resistance against its infestation in sunflower is commonly regulated by single dominant genes. Pl17 and Pl19 are two broad-spectrum DM resistance genes that have been previously mapped to a gene cluster spanning a 3.2 Mb region at the upper end of sunflower chromosome 4. Using a whole-genome resequencing approach combined with a reference sequence-based chromosome walking strategy and high-density mapping populations, we narrowed down Pl17 to a 15-kb region flanked by SNP markers C4_5711524 and SPB0001. A prospective candidate gene HanXRQChr04g0095641 for Pl17 was identified, encoding a typical TNL resistance gene protein. Pl19 was delimited to a 35-kb region and was approximately 1 Mb away from Pl17, flanked by SNP markers C4_6676629 and C4_6711381. The only gene present within the delineated Pl19 locus in the reference genome, HanXRQChr04g0095951, was predicted to encode an RNA methyltransferase family protein. Six and eight SNP markers diagnostic for Pl17 and Pl19, respectively, were identified upon evaluation of 96 diverse sunflower lines, providing a very useful tool for marker-assisted selection in sunflower breeding programs.
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11
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Cohen Y, Rubin AE, Galperin M. Novel synergistic fungicidal mixtures of oxathiapiprolin protect sunflower seeds from downy mildew caused by Plasmopara halstedii. PLoS One 2019; 14:e0222827. [PMID: 31545821 PMCID: PMC6756549 DOI: 10.1371/journal.pone.0222827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/09/2019] [Indexed: 01/11/2023] Open
Abstract
Plenaris (oxathiapiprolin) applied to sunflower seedlings was highly effective in controlling downy mildew incited by the oomycete Plasmopara halstedii. In vitro assays revealed strong suppression of zoospore release and cystospore germination of P.halstedii by Plenaris. Bion (acibenzolar-S-methyl) and Apron (mefenoxam) were partially effective when used singly, but performed synergistically when mixed with Plenaris. Seed treatment (coating) with Plenaris provided dose-dependent control of the disease whereas Bion and Apron provided partial or poor control. However, seeds treated with mixtures containing reduced rates of Plenaris and full rates of Bion and/or Apron provided complete control of the disease due to the synergistic interaction between these components. Such mixtures should be used for seed treatment in the field to minimize selection pressure imposed on the pathogen.
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Affiliation(s)
- Yigal Cohen
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
- * E-mail: ,
| | - Avia E. Rubin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Mariana Galperin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
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12
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Qi LL, Ma GJ, Li XH, Seiler GJ. Diversification of the downy mildew resistance gene pool by introgression of a new gene, Pl 35, from wild Helianthus argophyllus into oilseed and confection sunflowers (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2553-2565. [PMID: 31214741 DOI: 10.1007/s00122-019-03370-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/03/2019] [Indexed: 05/22/2023]
Abstract
We have mapped a new downy mildew resistance gene, Pl35, derived from wild Helianthus argophyllus to sunflower linkage group 1. New germplasms incorporating the Pl35 gene were developed for both oilseed and confection sunflower Sunflower downy mildew (DM), caused by the oomycete pathogen Plasmopara halstedii, is an economically important and widespread sunflower disease worldwide. Non-race-specific resistance is not available in sunflower, and breeding for DM resistance relies on race-specific resistance to control this disease. The discovery of the novel DM resistance genes is a long-term task due to the highly virulent and aggressive nature of the P. halstedii pathogen, which reduces the effectiveness of resistance genes. The objectives of this study were to: (1) transfer DM resistance from a wild sunflower species Helianthus argophyllus (PI 494576) into cultivated sunflowers; (2) map the resistance gene; and (3) develop diagnostic single-nucleotide polymorphism (SNP) markers for efficient targeting of the gene in breeding programs. The H. argophyllus accession PI 494576 previously identified with resistance to the most virulent P. halstedii race 777 was crossed with oilseed and confection sunflower in 2012. Molecular mapping using the BC2F2 and BC2F3 populations derived from the cross CONFSCLB1/PI 494576 located a new resistance gene Pl35 on linkage group 1 of the sunflower genome. The new gene Pl35 was successfully transferred from PI 494576 into cultivated sunflowers. SNP markers flanking Pl35 were surveyed in a validation panel of 548 diversified sunflower lines collected globally. Eleven SNP markers were found to be diagnostic for Pl35 SNP alleles, with four co-segregating with Pl35. The developed oilseed and confection germplasms with diagnostic SNP markers for Pl35 will be very useful resources for breeding of DM resistance in sunflower.
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Affiliation(s)
- L L Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA.
| | - G J Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - X H Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - G J Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
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13
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Pecrix Y, Penouilh-Suzette C, Muños S, Vear F, Godiard L. Ten Broad Spectrum Resistances to Downy Mildew Physically Mapped on the Sunflower Genome. FRONTIERS IN PLANT SCIENCE 2018; 9:1780. [PMID: 30564260 PMCID: PMC6288771 DOI: 10.3389/fpls.2018.01780] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/15/2018] [Indexed: 05/12/2023]
Abstract
Resistance to downy mildew (Plasmopara halstedii) in sunflower (Helianthus annuus L.) is conferred by major resistance genes, denoted Pl. Twenty-two Pl genes have been identified and genetically mapped so far. However, over the past 50 years, wide-scale presence of only a few of them in sunflower crops led to the appearance of new, more virulent pathotypes (races) so it is important for sunflower varieties to carry as wide a range of resistance genes as possible. We analyzed phenotypically 12 novel resistant sources discovered in breeding pools derived from two wild Helianthus species and in eight wild H. annuus ecotypes. All were effective against at least 16 downy mildew pathotypes. We mapped their resistance genes on the sunflower reference genome of 3,600 Mb, in intervals that varied from 75 Kb to 32 Mb using an AXIOM® genotyping array of 49,449 SNP. Ten probably new genes were identified according to resistance spectrum, map position, hypersensitive response to the transient expression of a P. halstedii RXLR effector, or the ecotype/species from which they originated. The resistance source HAS6 was found to carry the first downy mildew resistance gene mapped on chromosome 11, whereas the other resistances were positioned on chromosomes 1, 2, 4, and 13 carrying already published Pl genes that we also mapped physically on the same reference genome. The new genes were designated Pl23-Pl32 according to the current nomenclature. However, since sunflower downy mildew resistance genes have not yet been sequenced, rules for designation are discussed. This is the first large scale physical mapping of both 10 new and 10 already reported downy mildew resistance genes in sunflower.
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Affiliation(s)
- Yann Pecrix
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Charlotte Penouilh-Suzette
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Felicity Vear
- INRA, Génétique, Diversité, Ecophysiologie des Céréales, UMR 1095, Clermont-Ferrand, France
- *Correspondence: Felicity Vear, Laurence Godiard,
| | - Laurence Godiard
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
- *Correspondence: Felicity Vear, Laurence Godiard,
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Ma GJ, Markell SG, Song QJ, Qi LL. Genotyping-by-sequencing targeting of a novel downy mildew resistance gene Pl 20 from wild Helianthus argophyllus for sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1519-1529. [PMID: 28432412 DOI: 10.1007/s00122-017-2906-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/07/2017] [Indexed: 05/20/2023]
Abstract
Genotyping-by-sequencing revealed a new downy mildew resistance gene, Pl 20 , from wild Helianthus argophyllus located on linkage group 8 of the sunflower genome and closely linked to SNP markers that facilitate the marker-assisted selection of resistance genes. Downy mildew (DM), caused by Plasmopara halstedii, is one of the most devastating and yield-limiting diseases of sunflower. Downy mildew resistance identified in wild Helianthus argophyllus accession PI 494578 was determined to be effective against the predominant and virulent races of P. halstedii occurring in the United States. The evaluation of 114 BC1F2:3 families derived from the cross between HA 89 and PI 494578 against P. halstedii race 734 revealed that single dominant gene controls downy mildew resistance in the population. Genotyping-by-sequencing analysis conducted in the BC1F2 population indicated that the DM resistance gene derived from wild H. argophyllus PI 494578 is located on the upper end of the linkage group (LG) 8 of the sunflower genome, as was determined single nucleotide polymorphism (SNP) markers associated with DM resistance. Analysis of 11 additional SNP markers previously mapped to this region revealed that the resistance gene, named Pl 20 , co-segregated with four markers, SFW02745, SFW09076, S8_11272025, and S8_11272046, and is flanked by SFW04358 and S8_100385559 at an interval of 1.8 cM. The newly discovered P. halstedii resistance gene has been introgressed from wild species into cultivated sunflower to provide a novel gene with DM resistance. The homozygous resistant individuals were selected from BC2F2 progenies with the use of markers linked to the Pl 20 gene, and these lines should benefit the sunflower community for Helianthus improvement.
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Affiliation(s)
- G J Ma
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - S G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Q J Song
- Soybean Genomics and Improvement Lab, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA
| | - L L Qi
- Red River Valley Agricultural Research Center, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA.
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Qi LL, Talukder ZI, Hulke BS, Foley ME. Development and dissection of diagnostic SNP markers for the downy mildew resistance genes Pl Arg and Pl 8 and maker-assisted gene pyramiding in sunflower (Helianthus annuus L.). Mol Genet Genomics 2017; 292:551-563. [PMID: 28160079 DOI: 10.1007/s00438-017-1290-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/09/2017] [Indexed: 12/17/2022]
Abstract
Diagnostic DNA markers are an invaluable resource in breeding programs for successful introgression and pyramiding of disease resistance genes. Resistance to downy mildew (DM) disease in sunflower is mediated by Pl genes which are known to be effective against the causal fungus, Plasmopara halstedii. Two DM resistance genes, Pl Arg and Pl 8 , are highly effective against P. halstedii races in the USA, and have been previously mapped to the sunflower linkage groups (LGs) 1 and 13, respectively, using simple sequence repeat (SSR) markers. In this study, we developed high-density single nucleotide polymorphism (SNP) maps encompassing the Pl arg and Pl 8 genes and identified diagnostic SNP markers closely linked to these genes. The specificity of the diagnostic markers was validated in a highly diverse panel of 548 sunflower lines. Dissection of a large marker cluster co-segregated with Pl Arg revealed that the closest SNP markers NSA_007595 and NSA_001835 delimited Pl Arg to an interval of 2.83 Mb on the LG1 physical map. The SNP markers SFW01497 and SFW06597 delimited Pl 8 to an interval of 2.85 Mb on the LG13 physical map. We also developed sunflower lines with homozygous, three gene pyramids carrying Pl Arg , Pl 8 , and the sunflower rust resistance gene R 12 using the linked SNP markers from a segregating F2 population of RHA 340 (carrying Pl 8 )/RHA 464 (carrying Pl Arg and R 12 ). The high-throughput diagnostic SNP markers developed in this study will facilitate marker-assisted selection breeding, and the pyramided sunflower lines will provide durable resistance to downy mildew and rust diseases.
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Affiliation(s)
- L L Qi
- Northern Crop Science Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA.
| | - Z I Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - B S Hulke
- Northern Crop Science Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA
| | - M E Foley
- Northern Crop Science Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA
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16
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Qi LL, Foley ME, Cai XW, Gulya TJ. Genetics and mapping of a novel downy mildew resistance gene, Pl(18), introgressed from wild Helianthus argophyllus into cultivated sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:741-752. [PMID: 26747047 DOI: 10.1007/s00122-015-2662-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/14/2015] [Indexed: 05/20/2023]
Abstract
A novel downy mildew resistance gene, Pl(18), was introgressed from wild Helianthus argophyllus into cultivated sunflower and genetically mapped to linkage group 2 of the sunflower genome. The new germplasm, HA-DM1, carrying Pl(18) has been released to the public. Sunflower downy mildew (DM) is considered to be the most destructive foliar disease that has spread to every major sunflower-growing country of the world, except Australia. A new dominant downy mildew resistance gene (Pl 18) transferred from wild Helianthus argophyllus (PI 494573) into cultivated sunflower was mapped to linkage group (LG) 2 of the sunflower genome using bulked segregant analysis with 869 simple sequence repeat (SSR) markers. Phenotyping 142 BC1F2:3 families derived from the cross of HA 89 and H. argophyllus confirmed the single gene inheritance of resistance. Since no other Pl gene has been mapped to LG2, this gene was novel and designated as Pl (18). SSR markers CRT214 and ORS203 flanked Pl(18) at a genetic distance of 1.1 and 0.4 cM, respectively. Forty-six single nucleotide polymorphism (SNP) markers that cover the Pl(18) region were surveyed for saturation mapping of the region. Six co-segregating SNP markers were 1.2 cM distal to Pl(18), and another four co-segregating SNP markers were 0.9 cM proximal to Pl(18). The new BC2F4-derived germplasm, HA-DM1, carrying Pl(18) has been released to the public. This new line is highly resistant to all Plasmopara halstedii races identified in the USA providing breeders with an effective new source of resistance against downy mildew in sunflower. The molecular markers that were developed will be especially useful in marker-assisted selection and pyramiding of Pl resistance genes because of their close proximity to the gene and the availability of high-throughput SNP detection assays.
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Affiliation(s)
- L L Qi
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA.
| | - M E Foley
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
| | - X W Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - T J Gulya
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
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