Investigation of genetic diversity of different accessions of resistance against Phytophthora capsici L. using SRAP and SSR markers

Year 2019, Volume: 36 Issue: 2, 124 - 134, 10.12.2019

Münevver Göçmen , Kazım Abak

https://doi.org/10.16882/derim.2019.557877

Cited By: 2

Abstract

Phytophthora capsici L. is one of the most important pathogens of pepper in the world.
Different genetic resources that resistant to P. capsici have been reported so far. Determination of the
phylogenetic relationships of resistant pepper genotypes is important for
transferring of resistance gene/genes to cultivated varieties. In this study,
12 pepper genotypes from different accessions of resistance and 4 susceptible
genotypes tested with P.
capsici were identified genetic relationship among genotypes using 144 SRAP
(Sequence Related Amplified Polymorphism) and 27 SSR (Simple Sequence Repeat)
primer combinations. 31 SRAP primers were polymorphic and yielded 254
polymorphic DNA fragments. Fifty SRAP primers were only monomorphic. However,
32 SRAP primers were not produced PCR products. Results showed that 16 pepper
genotypes were genetically separated from each other by SRAP primers. Twelve
SSR primers yielded total 36 DNA fragments, 33 of these were polymorphic (93%).
However 15 SSR primers only produced monomorphic DNA bands. Results showed that
Pepper genotypes PM-217 KM2-11, Perennial LS-279, PBC-178, Sera Demre, PBC 179
and KMAE-12 were not separated with SSR markers. When the SRAP and SSR
marker data were evaluated together, the results were more informative about the
genetic relationship of genotypes and clustering by origin. Findings indicated that the genotype CM 334 which is resistance resource
to P. capsici was genetically
different from PM 702, Perennial, PM-217, Taiwan's group called as PBC label
(1364, 1365, 178, 179 and 413) and KM211 selected from Kahramanmaraş pepper
populations.

Keywords

Pepper, Phytophthora capsici L., SRAP, SSR, Genetic relationship

Phytophthora capsici'ye dayanıklı bazı biber genotiplerinin SRAP ve SSR belirteçlerle genetik farklılıklarının belirlenmesi

Abstract

Dünyada biber yetiştiriciliğini sınırlayan en
önemli hastalıklardan birisi, kök boğazı yanıklığıdır. Bazı başka türlerde
olduğu gibi Capsicum annuum L. türüne
ait farklı genotiplerde de etmene karşı dayanıklılık kaynakları mevcuttur.
Dayanıklılık düzeyi farklı biber genotiplerinin genetik ilişkilerinin
belirlenmesi, dayanıklılık ile ilgili gen/genlerin kültür çeşitlerine
aktarılması açısından önemlidir. Bu çalışmada, P. capsici’ye karşı dayanıklılık düzeyi ve orijini farklı 12
dayanıklı ve 4 duyarlı biber genotipin filogenetik ilişkileri SRAP (Sequence
Related Amplified Polymorphism) ve SSR (Simple SequenceRepeat) moleküler
belirteçleriyle belirlenmiştir. Bunun için, 144 SRAP primer kombinasyonu ve 27
SSR primer çifti kullanılmıştır. Otuz iki SRAP primeri herhangi bir PCR ürünü
vermemiştir. Elli primer kombinasyonunda yalnızca monomorfik DNA bantı
oluşurken 31 primer kombinasyonu polimorfizm sağlamış toplam 254 DNA fragmenti
elde edilmiş, bunların, 99’u (%39) monomorfik, 155’i (%61) polimorfik DNAbandı
olarak değerlendirilmiştir. SRAP belirteçleri ile 16 biber genotipi birbirinden
genetik olarak ayrılmıştır. SSR primerinin 15’i monomorfik bant oluşturmasına
karşın 12 SSR primeri ile toplam 36 DNA bandı elde edilmiş bunların 33'ü (%93)
polimorfik olmuştur. SSR belirteç sistemi ile 16 biber genotipinin bazıları
(PM-217 KM2-11, Perennial LS-279, PBC-178, Sera Demre, PBC 179 KMAE-12)
birbirinden ayrılamamıştır. SRAP ve SSR belirteç verileri birlikte
değerlendirildiğinde, genotiplerin genetik ilişkisi, orijine göre kümelemesi
daha bilgi verici olmuştur. P. capsici’ye
karşı dayanıklılık genitörü olarak kullanılan CM 334'den, PM 702, Perennial,
PM-217, Tayvan'da temin edilen PBC grubu (1364, 1365, 178, 179 ve 413) ile
Kahramanmaraş biber populasyonundan selekte edilen KM211genotipleri genetik
olarak farklı gruplarda yer aldığı belirlenmiştir.

Keywords

Biber, kök boğazı yanıklığı, SRAP, SSR, Genetik ilişki

References

• Abak, K. (1982). Biberlerde kökboğazı yanıklığına dayanıklılığın kalıtımı üzerinde araştırmalar. A.Ü. Ziraat Fakültesi, Bahçe Bitkileri Bölümü, Doçentlik Tezi, Ankara.
• Alcantara, T.P., & Bosland, P.W. (1994). An inexpensive disease screening technique for foliar blight of chile pepper seedlings. HortScience, 29:1182-1183.
• Ares, J.L.A., Martinez, A.R.,& Paz, J.P. (2005). Resistance of pepper germplasm to Phytophthora capcisi isolates collected in northwest Spain. Spain Journal of Agriculture Research, 3:429-436.
• Babadoost, M., & Pavon, C. (2013). Survival of oospores of Phytophthora capsici in soil. Plant Diseases, 97:1478-1483.
• Barchenger, D. W., Lamour, K.H., & Bosland, P. W. (2018). Challenges and strategies for breeding resistance in Capsicum annuum to the multifarious pathogen, Phytophthora capsici. The Journal Frontiers in Plant Science, 9:1-19.
• Bozokalfa, M.K., Aşcıoğul, T.K., & Eşiyok, D. (2017). Biber genotiplerinin genetik çeşitliliklerinin SRAP belirteçleri kullanılarak belirlenmesi. Anadolu Tarım Bilimleri Dergisi, 321-329.
• Buso G.S.C., Amaral Z.P.S., Machad F.R.B., Bem L., Ferreıra M.E. (2003). Variedade genética e análise filogenética de espécies brasileiras de pimenta e pimentão (Capsicum spp). Congresso Brasıleıro De Melhoramento De Plantas: 2.
• Curtis, M. R. (2014). QTL Mapping of Phytophthora capsici resistance and horticultural traits in pepper (Capsicum annuum) recombinant in bred line population. MS Thesis,University of California, Davis, CA.
• Çakır,C., Göçmen, M., & Devran, Z. (2001). Investigation of genetic variation of root rot (Phytophthora capcisi Leon) isolates of pepper (Capsicum annuum L.) obtained from the west mediterranean region by RAPD-PCR amplification. XIth Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, p:265-269.
• Dato, D.D., Parisi, M., Cardi, T., & Tripodi, P. (2015). Genetic diversity and assessment of markers linked to resistance and pungency genes in Capsicum germplasm. Euphytica, 204: 103-119
• Dice, L.R. (1945). Measures of the amount of ecologic association between species. Ecology, 26:297-302.
• Du, X., Wang, D., &Gong, Z. (2010). Comparison of RSAP,SRAP and SSR markers for genetic analysis in hot pepper. Indian Journal Horticulture, 67(4):505-512.
• Göçmen, M. (2006). Biberlerde Phytophthora capsici'ye karşı dayanıklılıkta genotip x izolat interaksiyonu ve farklı dayanıklılık kaynaklarının karakterizasyonu. Doktora Tezi, Çukurova Üniversitesi, Adana.
• Göçmen, M., & Abak, K. (2010).Genetics of resistance of the Kahramanmaraş pepper KM2-11 genotype to Phytophthora capsici isolates. Proceedings of the XIVth EUCARPIA Meeting on Genetics and Breeding of Capsicum & Eggplant, p:236-242.
• Ilbi, H. (2003). RAPD markers assisted varietal identification and genetic purity test in pepper, Capsicum annuum. Scientia Horticulturae, 97:211–218.
• Hwang, B.K., Kim, Y.J., & Kim, C.H. (1995). Differential interactions of Phytophthora capsici isolates with pepper genotypes at various plant growth stages. European Journal of Plant Pathology, 102:311-316.
• Hildebrand, C.E., Torney, D.C., & Wagner, R.P. (1992). Mapping the genome. Informativeness of polymorphic DNA markers. Los Alamos Science, 20:100-102.
• Jiang, L., Sanogo, S., & Bosland, P.W. (2015). Using recombinant inbred lines to monitor changes in the race structure of Phytophthora capsici in chile pepper in New Mexico. Plant Health Programme, 16:235-240
• Kwon, Y.S., Lee, J.M., Yi, G.B., Ti, S.I., Kim, K.M., Soh, E.H.,, Bae, K.M., Park, E.K., Song I.N., & Kim, B.D. (2005). Use of SSR markers to complement tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Molecules and Cells, 19(3): 428-435
• Lee, J.M., Nahm, S.H., Kim, Y.M., & Kim, B.D. (2004). Characterization and molecular genetic mapping of microsatellite loci in pepper. Theoretical and Applied Genetics, 108: 619-27.
• Lee, S.J., Park, Y.J., Kim, H.T., & Kim, B.S. (2010). The race differentiation of Phytophthora capsici in Korea. Research in Plant Disease, 16:153-157.
• Lefebvre, V., Goffinet, B., Chauvet, J.C., Caromel, B., Signoret, P., Brand, R., & Palloix, A. (2001). Evaluation of genetic distances between pepper inbred lines for cultivar protection purposes: comparison of AFLP, RAPD and phenotypic data. Theoretical and Applied Genetics, 102: 741-50.
• Lefebvre V., Pflieger S., Thabuis A., Caranta C., Blattes A., Chauvet, J.C., Daubèze A.M. & Palloıx, A. (2002). Towards the saturation of the pepper linkage map by alignment of three intraspecific mapsincluding known-function genes. Genome, 45: 839-854.
• Li, G., & Quiros, C.F., (2001). Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theoretical Applied Genetic, 103:455-461.
• McGregor, C., Waters, V., Nambeesan, S., MacLean, D., Candole, B. L., & Conner, P. (2011). Genotypic and phenotypic variation among pepper accessions resistant to Phytophthora capsici. HortScience, 46: 1235-1240.
• Morgante, M., Hanafey, M., & Powell, W. (2002).Microsatellites are preferentially associated with non-repetitive DNA in plant genomes. Nature Genetics, 30: 194-200.
• Oelke, LM., Bosland, PW., & Steiner, R. (2003). Differentiation of race specific resistance to phytophthora root rot and foliar blight in Capsicum annuum. The Journal of the American Society for Horticultural Science,128:213- 218.
• Ortega, RG., Palazon-Espanol, C., & Cuartero-Zueco, J. (1991). Genetics of resistanceto Phytophthora capsici in the pepper line ‘SCM-334’. Plant Breeding,107:50-55.
• Palloıx, A., Daubeze, A.M., &Pochard, E. (1988). Phytophthora root rot of pepper. Influence of host genotype and pathogen strain on the ınoculum density- disease severity relationships. Journal Phytopathology,123:25-33.
• Palloıx, A., Daubeze, A.M., Phaly, T. & Pochard, E. (1990). Breeding transgressive lines of pepper for resistance to Phytophthora capsici ina recurrent selection system. Euphytica, 51:141-150.
• Paran, I., Afterdoot, E., &Shifriss, C. (1998).Variation in Capsicum annuum revealed by RAPD and AFLP markers. Euphytica, 99:167-173.
• Pochard, E., & Daubezea, M. (1980). Recherches et evalution des composantes d’une resistance polygenique:la resistance du piment a Phytophthora capsici. Annual. Amelior. Plantes, 30(4):377-398.
• Pochard, E., Molot, P. M. & Dominguez, G. (1983). Etude de deux nouvelles sources de resistance a P.capsici chez le piment:confirmation de existence trois composantes distinctes dans la resistance. Agronomie, 3:333-342.
• Portis, E., Nagy, I., Sasvari, Z., Stage,l A., Barchi, L., & Lanteri, S. (2007). The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping. Plant Science, 172:640-648.
• Quirin, E.A., Ogundiwin, E.A., Prince, J.P., Mazourek, M., Briggs, M.O.,& Chlanda, T.S. (2005). Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2, a major QTL for resistance to Phytophthora capsici Leon. in pepper. Theoretical and Applied Genetics,110:605-612.
• Ren, Y., Zhang, Y., Yin, J., & Wang, D. (2008). Parent grouping of 31 elite inbred lines in hot pepper(Capsicum annuum L.). Hereditas, 30: 237-45.
• Rodriguez, JM., Berke, T., Engle, L. & Nienhuis, J. (1999).Variation among and within Capsicum species revealed by RAPD markers. Theoretical Applied Genetic, 99:147-156.
• Rohlf, F.J. (2000). NTSYSpc, numerical taxonomy and multivariate analysis system version 2.10e. Exeter Software, Setauket.
• Smith, J.S.C., Chin, E.C.L., Shu, H., Smith, O.S., Wall, S.J., Senior, M.L., Mitchel, S.E., Kresorich, S., & Tiegle, J. (1997). An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics, 95(1-2):163-173.
• Stuthman, D.D., Leonard, J.J.,& Miller-Garvin, J. (2007). Breeding crops for durable resistance to disease. Advances in Agronomy, 95:319-367.
• Tam, S.M., Mhiri, C., Vogelaar, A., Kerkveld, M., Pearce, S.R., & Grandbastien, M.A. (2005). Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon- based SSAP, AFLP and SSR. Theoretical and Applied Genetics, 110: 819-31.
• Thabuis, A., Palloix, A., Pflieger S., Daubèze, A.M., Caranta, C., & Lefebvre, V.(2003). Comparative mapping of Phythophtoraresistance loci in pepper germplams: evidence for conserve resistance loci across Solanaceae and for a large genetic diversity. Theoretical and Applied Genetics, 106:1473-1485.
• Thabuis, A., Lefebvre, V., Bernard, G., Daubeze, A. M., Phaly, T., &Pochard, E. (2004). Phenotypic and molecular evaluation of a recurrent selection program from a polygenic resistance to Phytophthora capsici in pepper. Theoretical and Applied Genetics, 109:342-351.
• TUİK (2016). Biber Üretim İstatistikleri http://www.tuik.gov.tr. Erişim tarihi: 19 Aralık 2018.