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Genomic Evaluation of Sunflower Broomrape (Orobanche Cumana) Germplasm by KASP Assay

  • Nilay Yonet , Yıldız Aydin , Goksel Evci und Ahu Altinkut Uncuoglu EMAIL logo
Veröffentlicht/Copyright: 5. Juli 2018
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Helia
Aus der Zeitschrift Helia Band 41 Heft 68

Abstract

Orobanche cumana Wallr. is a holoparasitic plant for only sunflower, hence it is called as sunflower broomrape. Yield loss created by O. cumana which is generally 50 % can reach to 100 %. In this study, it was planned to perform molecular characterization of O. cumana germplasm as nine locations of Thrace region obtained from Trakya Agricultural Research Institute by using Single Nucleotide Polymorphism (SNP) markers, widely used in plant breeding programs, in Competitive Allele Specific PCR (KASP) assay which is a fluorescent tagged allele specific PCR method based, economic, reliable and easily repeatable genotyping technology. Databases and literature were scanned to spot variations on O. cumana genome which is not known clearly. So far, four SSR (Simple Sequence Repeat) marker (Ocum-197, Ocum-006, Ocum-023 and Ocum-151) regions showing polymorphic pattern were used for searching possible SNPs. Primer pairs were designed for amplification of the regions possibly having SNPs and PCR amplifications with these primer pairs were performed and 1 candidate deletion was detected on the amplicon which was amplified by Ocum-197 SSR marker. Following, the deletion was converted to KASP primers and KASP assay was performed. The deletion marker, Del-197, has grouped the samples from nine locations in the resulting allelic discrimination plot and infestation was performed according to this grouping, As a conclusion, Del-197 is considered as a selective marker for the ability to rapidly assay allelic variation at DNA markers for O. cumana populations that have effects on infestation results were evaluated as races, F, G, H and I in Thrace region.

Acknowledgements

The authors would like to thank Dr Atilla Goknur from GGT Global Genetics for the help of the configuration of KASP assay and discussions of results. This study was performed with the support of Marmara University Research Foundation; Project ID: FEN-C-YLP-090217-0050.

References

Aly, R., 2007. Conventional and biotechnological approaches for control of parasitic weeds. Vitro Cellular & Developmental Biology Plant 43(4): 304–317.10.1007/s11627-007-9054-5Suche in Google Scholar

Antonova, T., 2014. The history of interconnected evolution of Orobanche cumana Wallr. and sunflower in the Russian Federation and Kazakhstan. Helia 37(61): 215–225.10.1515/helia-2014-0017Suche in Google Scholar

Antonova, T.S., Araslanova, N.M., Strelnikov, E.A., Ramazanova, S.A., Guchetl, S.Z., Chelyustnikova, T.A., 2013. Distribution of highly virulent races of sunflower broomrape (Orobanche cumana Wallr.) in the southern regions of the Russian Federation. Russian Agricultural Sciences 39(1): 46–50.10.3103/S1068367413010023Suche in Google Scholar

Bauer, F., Elbers, C.C., Adan, R.A.H., Loos, R.J.F., Onland-Moret, N.C., Grobbee, D.E., Van Vliet-Ostaptchouk, J.V., Vijmenga, C., Van Der Schouw, Y.T., 2009. Obesity genes identified in genome-wide association studies are associated with adiposity measures and potentially with nutrient-specific food preference. The American Journal of Clinical Nutrition 90(4): 951–959.10.3945/ajcn.2009.27781Suche in Google Scholar

Ben-Ari, G., Lavi, U., 2012. Marker-assisted selection in plant breeding (Chapter 11). In: Altman, A., Hasegawa, P.M. (eds) Plant Biotechnology and Agriculture, Elsevier Science & Technology, Atlanta, USA, pp. 163–184.10.1016/B978-0-12-381466-1.00011-0Suche in Google Scholar

Cortés, A.J., Chavarro, M.C., Blair, M.W., 2011. SNP marker diversity in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 123(5): 827–845.10.1007/s00122-011-1630-8Suche in Google Scholar

Duca, M., 2014. Current situation of sunflower broomrape in the Republic of Moldova. In: Proceedings 3rd International Symposium on Broomrape (Orobanche spp.) in Sunflower, Córdoba, Spain, pp. 44–50.Suche in Google Scholar

Fernández-Martinez, J.M., Pérez-Vich, B., Velasco, L., 2015. Sunflower broomrape (Orobanche cumana Wallr.). In: Martínez-Force, E., Turgut Dunford, N., Salas, J.J. (Eds.) Sunflower: Chemistry, Production, Processing, and Utilization, AOCS Press, Urbana, USA, pp. 129–156.10.1016/B978-1-893997-94-3.50011-8Suche in Google Scholar

Gascuel, Q., Bordat, A., Sallet, E., Pouilly, N., Carrere, S., Roux, F., Vincourt, P., Godiard, L., 2016. Effector polymorphisms of the sunflower downy mildew pathogen Plasmopara halstedii and their use to identify pathotypes from field isolates. PloS ONE 11(2): 1–19.10.1371/journal.pone.0148513Suche in Google Scholar

Gevezova, M., Dekalska, T., Stoyanov, K., Hristeva, T., Kostov, K., Batchvarova, R., Denev, I., 2012. Recent advances in broomrapes research. Journal of Bioscience and Biotechnology 1: 91–105.Suche in Google Scholar

Joel, D.M., 2000. The long-term approach to parasitic weeds control: Manipulation of specific developmental mechanisms of the parasite. Crop Protection 19(8): 753–758.10.1016/S0261-2194(00)00100-9Suche in Google Scholar

Kaya, Y., 2014. Current situation of sunflower broomrape in Turkey. In: Proceedings 3rd International Symposium on Broomrape (Orobanche spp.) in Sunflower, Córdoba, Spain, pp. 9–18.Suche in Google Scholar

Kaya, Y., Evci, G., Pekcan, V., Gucer, T., 2004. Determining new broomrape-infested areas, resistant lines and hybrids in Trakya region of Turkey. Helia 27(40): 211–218.10.2298/HEL0440211KSuche in Google Scholar

Kaya, Y., Evci, G., Pekcan, V., Yilmaz, M.I., 2012. The resistance breeding to broomrape parasite and other stress conditions in sunflower. In: Proceedings 41st Annual Meeting of ESNA, Stará Lesná, High Tatras, Slovak Republic.Suche in Google Scholar

Khera, P., Upadhyaya, H.D., Pandey, M.K., Roorkiwal, M., Sriswathi, M., Janila, P., Guo, Y., McKain, M.R., Nagy, E.D., Knapp, S.J., Leebens-Mack, J., Conner, J.A., Ozias-Akins, P., Varshney, R.K., 2013. Single nucleotide polymorphism-based genetic diversity in the reference set of peanut (Arachis spp.) by developing and applying cost-effective kompetitive allele specific polymerase chain reaction genotyping assays. The Plant Genome 6(3): 1–11.10.3835/plantgenome2013.06.0019Suche in Google Scholar

Khlestkina, E.K., Salina, E.A., 2006. SNP markers: Methods of analysis, ways of development, and comparison on an example of common wheat. Russian Journal of Genetics 42(6): 585–594.10.1134/S1022795406060019Suche in Google Scholar

Kumpatla, S.P., Buyyarapu, R., Abdurakhmonov, I.Y., Mammadov, J.A., 2012. Genomics-assisted plant breeding in the twenty-first century: Technological advances and progress (Chapter 7). In: Abdurakhmonov, I. (Eds.) Plant Breeding, InTech Publishers, London, UNITED KINGDOM, pp. 131–184.Suche in Google Scholar

Louarn, J., Boniface, M.C., Pouilly, N., Velasco, L., Pérez-Vich, B., Vincourt, P., Muños, S., 2016. Sunflower resistance to broomrape (Orobanche cumana) is controlled by specific QTLs for different parasitism stages. Frontiers in Plant Science 7(590): 1–14.10.3389/fpls.2016.00590Suche in Google Scholar PubMed PubMed Central

Miladinović, D., Jocić, S., Dedic, B., Cvejić, S., Dimitrijević, A., Imerovski, I., Malidža, G., 2014. Current situation of sunflower broomrape in Serbia. In: Proceedings 3rd International Symposium on Broomrape (Orobanche spp.) in Sunflower, Córdoba, Spain, pp. 33–38.Suche in Google Scholar

Mohamed, K.I., Papes, M., Williams, R., Benz, B.W., Peterson, A.T., 2006. Global invasive potential of 10 parasitic witchweeds and related Orobanchaceae. Ambio 35(6): 281–288.10.1579/05-R-051R.1Suche in Google Scholar

Molinero-Ruiz, L., Delavault, P., Pérez-Vich, B., Pacureanu-Joita, M., Bulos, M., Altieri, E., Domínguez, J., 2015. History of the race structure of Orobanche cumana and the breeding of sunflower for resistance to this parasitic weed: A review. Spanish Journal of Agricultural Research 13(4): 1–19.10.5424/sjar/2015134-8080Suche in Google Scholar

Molinero-Ruiz, L., García-Carneros, A.B., Collado-Romero, M., Raranciuc, S., Domínguez, J., Melero-Vara, J.M., 2014. Pathogenic and molecular diversity in highly virulent populations of the parasitic weed Orobanche cumana (sunflower broomrape) from Europe. Weed Research 54(1): 87–96.10.1111/wre.12056Suche in Google Scholar

Molinero-Ruiz, M.L., García-Ruiz, R., Melero-Vara, J.M., Domínguez, J., 2009. Orobanche cumana race F: Performance of resistant sunflower hybrids and aggressiveness of populations of the parasitic weed. Weed Research 49(5): 469–478.10.1111/j.1365-3180.2009.00708.xSuche in Google Scholar

Molinero-Ruiz, M.L., Melero-Vara, J.M., García-Ruiz, R., Domínguez, J., 2006. Pathogenic diversity within field populations of Orobanche cumana and different reactions on sunflower genotypes. Weed Research 46(6): 462–469.10.1111/j.1365-3180.2006.00517.xSuche in Google Scholar

Molinero-Ruiz, M.L., Pérez-Vich, B., Pineda-Martos, R., Melero-Vara, J.M., 2008. Indigenous highly virulent accessions of the sunflower root parasitic weed Orobanche cumana. Weed Research 48(2): 169–178.10.1111/j.1365-3180.2007.00611.xSuche in Google Scholar

Nijman, I.J., Kuipers, S., Verheul, M., Guryev, V., Cuppen, E., 2008. A genome-wide SNP panel for mapping and association studies in the rat. BMC Genomics 9(95): 1–9.10.1186/1471-2164-9-95Suche in Google Scholar PubMed PubMed Central

Oueslati, A., Ollitrault, F., Baraket, G., Salhi-Hannachi, A., Navarro, L., Ollitrault, P., 2016. Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR. BMC Genetics 17(118): 1–14.10.1186/s12863-016-0426-xSuche in Google Scholar PubMed PubMed Central

Pariasca-Tanaka, J., Lorieux, M., He, C., McCouch, S., Thomson, M.J., Wissuwa, M., 2015. Development of a SNP genotyping panel for detecting polymorphisms in Oryza glaberrima/O. sativa interspecific crosses. Euphytica 201(1): 67–78.10.1007/s10681-014-1183-4Suche in Google Scholar

Piednoël, M., Aberer, A.J., Schneeweiss, G.M., Macas, J., Novak, P., Gundlach, H., Temsch, E.M., Renner, S.S., 2012. Next generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of Orobanchaceae. Molecular Biology of Evolution 29(11): 3601–3611.10.1093/molbev/mss168Suche in Google Scholar PubMed PubMed Central

Pineda-Martos, R., Velasco, L., Pérez-Vich, B., 2013. Identification, characterisation and discriminatory power of microsatellite markers in the parasitic weed Orobanche cumana. Weed Research 54(2): 120–132.10.1111/wre.12062Suche in Google Scholar

Plaza, L., Fernández, I., Juan, R., Pastor, J., Pujadas, A., 2004. Micromorphological studies on seeds of Orobanche species from the Iberian Peninsula and the Balearic Islands, and their systematic significance. Annals of Botany 94(1): 167–178.10.1093/aob/mch124Suche in Google Scholar PubMed PubMed Central

Rosso, M.L., Burleson, S.A., Maupin, L.M., Rainey, K.M., 2011. Development of breeder-friendly markers for selection of MIPS1 mutations in soybean. Molecular Breeding 28(1): 127–132.10.1007/s11032-011-9573-ySuche in Google Scholar

Semagn, K., Babu, R., Hearne, S., Olsen, M., 2014. Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): Overview of the technology and its application in crop improvement. Molecular Breeding 33(1): 1–14.10.1007/s11032-013-9917-xSuche in Google Scholar

Semagn, K., Bjørnstad, Å., Ndjiondjop, M.N., 2006. An overview of molecular marker methods for plants. African Journal of Biotechnology 5(25): 2540–2568.Suche in Google Scholar

Shi, Z., Liu, S., Noe, J., Arelli, P., Meksem, K., Li, Z., 2015. SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance. BMC Genomics 16(314): 1–12.10.1186/s12864-015-1531-3Suche in Google Scholar PubMed PubMed Central

Škorić, D., 2012. The genetics of sunflower. In: Škorić, D., Sakac, Z. (eds) Sunflower Genetics and Breeding, Serbian Academy of Sciences and Arts, Belgrade, SERBIA, pp. 1–163.Suche in Google Scholar

Škorić, D., Pacureanu, M., 2010. Sunflower breeding for resistance to broomrape (Orobanche cumana Wallr.). In: Proceedings of the International Symposium “Sunflower Breeding on Resistance to Diseases”, Krasnodar, Russia, pp. 19–30.Suche in Google Scholar

Sobrino, B., Brión, M., Carracedoa, A., 2005. SNPs in forensic genetics: A review on SNP typing methodologies. Forensic Science International 154: 181–194.10.1016/j.forsciint.2004.10.020Suche in Google Scholar PubMed

Tan, C.T., Assanga, S., Zhang, G., Rudd, J.C., Haley, S.D., Xue, Q., Ibrahim, A., Bai, G., Zhang, X., Byrne, P., Fuentealba, M.P., Liu, S., 2017. Development and validation of KASP markers for wheat streak mosaic virus resistance gene Wsm2. Crop Science 57(1): 340–349.10.2135/cropsci2016.04.0234Suche in Google Scholar

Vranceanu, A.V., Tudor, V.A., Stonescu, F.M., Pirvu, N. (1980). Virulence groups of broomrape (Orobanche cumana Wallr.) differential hosts and resistance sources and genes in sunflower. In: Proceedings of the 9th International Sunflower Conference, Torremolinos, Spain, pp. 74–82.Suche in Google Scholar

Received: 2017-08-17
Accepted: 2018-04-11
Published Online: 2018-07-05
Published in Print: 2018-07-26

© 2018 Walter de Gruyter GmbH, Berlin/Boston

Heruntergeladen am 29.10.2025 von https://www.degruyterbrill.com/document/doi/10.1515/helia-2017-0016/pdf
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