Moleküler Markerlar Kullanarak Çarliston ve Dolmalık Biber Hatlarında Genetik Çeşitliliğin Belirlenmesi

Öz

Hibrit çeşit ıslahında başarının sağlanması; genetik çeşitliliği yüksek bitki kaynağına, melezlenecek hatların homozigot olmasına ve melezlenecek hatların genetik olarak birbirinden uzak olmasına bağlıdır. Bu çalışmada, biber (Capsicum annum L.) saf hatları arasındaki genetik uzaklığın belirlenmesi ve ıslah programının etkinliğinin arttırılması amaçlanmıştır. Çalışmada 44 adet dolmalık ve 35 adet çarliston biber saf hatları arasındaki genetik uzaklık, SRAP (Sequence Related Amplified Polymorphism) markerı ile araştırılmıştır. Dendrogramlar UPGMA (unweighted pair-group method of mathematical averages method) yöntemine göre oluşturulmuştur. Test edilen 71 primer kombinasyonundan, çarliston biber hatlarında 50 kombinasyon polimorfizm göstermiş ve toplamda 123 adet polimorfik bant elde edilmiştir. Dolmalık biber hatlarında 24 SRAP primer kombinasyonu test edilmiş ve 15 kombinasyondan 25 polimorfik bant elde edilmiştir. UPGMA küme analizine göre biber hatları dolmalık biber ve çarliston biber olarak gruplara ayrılmıştır. Çarliston biber hatları arasındaki genetik benzerlik 0.62 ile 0.98 arasında değişirken, dolmalık biber hatları arasındaki genetik benzerlik 0.54 ile 1.00 arasında değişmiştir. Sonuç olarak, SRAP markerlarının biber saf hatlarının genetik uzaklıklarının belirlenmesinde başarılı bir şekilde kullanılarak ıslah programına yardımcı olacağı ifade edilebilir.

Anahtar Kelimeler

• Biber
• genetik akrabalık
• SRAP
• polimorfizm

Determination of Genetic Diversity in Banana and Bell Pepper Lines Using Molecular Markers

Abstract

Successful hybrid cultivar breeding is depend on the high genetic diversity of the plant sources, as well as the homozygous and genetically distant lines requiring hybridization. The aim of this study is to determine the genetic distance between the inbred lines of pepper (Capsicum annuum L.) in order to increase efficacy of the breeding program. In this study, the genetic distances between the inbred lines of 44 bell peppers and 35 banana peppers were investigated using the SRAP (Sequence Related Amplified Polymorphism) markers. Based on pattern scores, dendrograms were produced by the UPGMA (unweighted pair-group method of mathematical averages method). Out of the 71 primer combinations tested, 50 combinations revealed polymorphisms among the banana pepper lines, and a total of 123 polymorphic bands were obtained. In the bell pepper lines, 24 SRAP primer combinations were tested and 15 combinations had 25 polymorphic bands. Based on the UPGMA cluster analysis, the pepper lines divided into groups as bell peppers and banana peppers. While the genetic similarity among the banana pepper lines varied between 0.62 and 0.98, the genetic similarity among the bell pepper lines varied between 0.54 and 1.00. As a result, it can be stated that the SRAP markers can be used successfully for determining the genetic distances of the pepper inbred lines thus will help the breeding programme.

Keywords

• Pepper
• genetic relationship
• SRAP
• polymorphism

References

1. Aktas, H., Abak, K., & Sensoy, S. (2009). Genetic diversity in some Turkish pepper (Capsicum annuum L.) genotypes revealed by AFLP analyses. African Journal of Biotechnology, 8(18). https://www.ajol.info/index.php/ajb/article/view/62388
2. Alvares Bianchi, P., Renata Almeida da Silva, L., André da Silva Alencar, A., Henrique Araújo Diniz Santos, P., Pimenta, S., Pombo Sudré, C., Erpen-Dalla Corte, L., Simões Azeredo Gonçalves, L., Rodrigues, R. (2020). Biomorphological characterization of Brazilian Capsicum Chinense Jacq. germplasm. Agronomy, 10(3), 447. https://doi.org/10.3390/agronomy10030447
3. Bozokalfa, M. K., Aşcıoğlu, T. K., & Eşiyok, D. (2017). Genetic diversity of pepper genotypes as assessed by SRAP markers. Anadolu Journal of Agricultural Sciences, 32(3), 321. https://doi.org/10.7161/omuanajas.284511
4. Carvalho, S. I. C., Ragassi, C. F., Bianchetti, L. B., Reifschneider, F. J. B., Buso, G. S. C., & Faleiro, F. G. (2014). Morphological and genetic relationships between wild and domesticated forms of peppers (Capsicum frutescens L. and C. chinense Jacquin). Genetics and Molecular Research, 13(3), 7447-7464. http://dx.doi.org/10.4238/2014.September.12.11
5. Carvalho, S. I. C., Ragassi, C. F., Oliveira, L. B., Amaral, Z. D. S., Faleiro, F. G., Reifschneider, F. J. B., & Buso, G. S. C. (2015). Transferability of microsatellite markers of Capsicum annuum L. to C. frutescens L. and C. chinense Jacq. Embrapa Hortaliças-Artigo em periódico indexado (ALICE). http://dx.doi.org/10.4238/2015.July.17.1
6. Doyle, J. J., Doyle, J. L. (1990). Isolation of plant DNA from fresh tissue. Focus, 12, 13-15.
7. FAOSTAT, (2022). http://www.fao.org/faostat/en/#data/QC/visualize. [Access date: March 25, 2022).
8. Finger, F. L., Lannes, S. D., Schuelter, A. R., Doege, J., Comerlato, A. P., Gonçalves, L. S. A., Ferreira, F. R. A., Clovis, L. R., & Scapim, C. A. (2010). Genetic diversity of Capsicum chinensis (Solanaceae) accessions based on molecular markers and morphological and agronomic traits. Genetics and Molecular Research, 9(3), 1852-1864. https://doi.org/10.4238/vol9-3gmr891

9. Geleta, L. F., Labuschagne, M. T., & Viljoen, C. D. (2005). Genetic variability in pepper (Capsicum annuum L.) estimated by morphological data and amplified fragment length polymorphism markers. Biodiversity Conservation 14(10), 2361-2375. https://doi.org/10.1007/s10531-004-1669-9
10. Göçmen, M. (2019). Phytophthora capsici'ye dayanıklı bazı biber genotiplerinin SRAP ve SSR belirteçlerle genetik farklılıklarının belirlenmesi [Investigation of genetic diversity of different accessions of resistance against Phytophthora capsici L. using SRAP and SSR markers]. Derim, 36(2), 124-134. https://doi.org/10.16882/derim.2019.557877
11. Grover, A., & Sharma, P. C. (2016). Development and use of molecular markers: past and present. Critical reviews in biotechnology, 36(2), 290-302. https://doi.org/10.3109/07388551.2014.959891
12. Ibiza, V. P., Blanca, J., Cañizares, J., & Nuez, F. (2012). Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region. Genetic resources and crop evolution, 59(6), 1077-1088. https://doi.org/10.1007/s10722-011-9744-z
13. Kumar. S., Singh, V., Singh, M., Rai, S., Kumar, S., Rai, S.K., & Rai, M. (2007). Genetics and distribution of fertility restoration associated RAPD markers in inbreds of pepper (Capsicum annuum L.). Scientia horticulturae, 111(3), 197-202. https://doi.org/10.1016/j.scienta.2006.10.021
14. Lee. H. Y., Ro, N. Y., Jeong, H. J., Kwon, J. K., Jo, J., Ha, Y., Jung, A., Han, J. W., Venkatesh, J., & Kang, B. C. (2016). Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm. BMC genetics, 17(1), 142. https://doi.org/10.1186/s12863-016-0452-8
15. 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(5), 741-750. https://doi.org/10.1007/s001220051705
16. 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 and applied genetics, 103(2-3), 455-461. https://doi.org/10.1007/s001220100570
17. Moreira, A. F. P., Ruas, P. M., de Fátima Ruas, C., Baba, V. Y., Giordani, W., Arruda, I. M., Rodrigues, R., & Gonçalves, L. S. A. (2018). Genetic diversity, population structure and genetic parameters of fruit traits in Capsicum chinense. Scientia Horticulturae, 236, 1-9. https://doi.org/10.1016/j.scienta.2018.03.012
18. Moses, M., Umaharan, P., & Dayanandan, S. (2014). Microsatellite based analysis of the genetic structure and diversity of Capsicum chinense in the Neotropics. Genetic resources and crop evolution, 61(4), 741-755. https://doi.org/10.1007/s10722-013-0069-y
19. Pacheco‐Olvera, A., Hernández‐Verdugo, S., Rocha‐Ramírez, V, González‐Rodríguez, A., & Oyama, K. (2012). Genetic diversity and structure of pepper (Capsicum annuum L.) from Northwestern Mexico analyzed by microsatellite markers. Crop Science, 52(1), 231-241. https://doi.org/10.2135/cropsci2011.06.0319
20. Rai, V. P., Kumar, R., Kumar, S., Rai, A., Kumar, S., Singh, M., Singh, S. P., Rai, A. B., & Paliwal, R. (2013). Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers. Physiology Molecular Biology of Plants 19(4): 575–586. https://doi.org/10.1007/s12298-013-0185-3
21. Rodriguez, J. M., Berke, T., Engle, L., & Nienhuis, J. (1999). Variation among and within Capsicum species revealed by RAPD markers. Theoretical and Applied Genetics, 99(1-2), 147-156. https://doi.org/10.1007/s001220051219
22. Rohlf, F. J. (1992). NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System. Applied Biostatistics. 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(5), 819-831. https://doi.org/10.1007/s00122-004-1837-z
23. Thul, S. T., Darokar, M. P., Shasany, A. K., & Khanuja, S. P. (2012). Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers. Molecular biotechnology, 51(2), 137-147. https://doi.org/10.1007/s12033-011-9446-y
24. Wahyuni, Y., Ballester, A. R., Tikunov, Y., de Vos, R. C., Pelgrom, K. T. B., Maharijaya, A., Sudarmonowati, E., Bino, R. J., & Bovy, A. G. (2013). Metabolomics and molecular marker analysis to explore pepper (Capsicum sp.) biodiversity. Metabolomics, 9(1), 130-144. https://doi.org/10.1007/s11306-012-0432-6
25. Xu, X., Liu, Z., Lin, X., Mou, S., Guan, D., & He, S. (2011). Genetic diversity and relationship analysis of pepper germplasm resources based on phenotype traits and SRAP molecular markers. Journal of Fujian Agriculture and Forestry University (Natural Science Edition), 40(1), 48-53. https://www.cabdirect.org/cabdirect/abstract/20113152835
26. Zhang, X. M., Zhang, Z. H., Gu, X. Z., Mao, S. L., Li, X. X., Chadœuf, J., Palloix, A., Wang, L. H., & Zhang, B. X. (2016). Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution. Journal of integrative agriculture, 15(9), 1991-2001. https://doi.org/10.1016/S2095-3119(16)61364-3