Türkiye’de yetiştirilen farklı fasulye (Phaseolus vulgaris L.) genotiplerinin genetik çeşitlilik analizi

Year 2023, Volume: 16 Issue: 1, 23 - 30, 15.04.2023

Berru Şahin Hündürel , İsmail Poyraz , Evren Atmaca

https://doi.org/10.46309/biodicon.2023.1187272

Abstract

Fabaceae (Baklagiller) üyesi olan Phaseolus vulgaris L. (fasulye), Türkiye ve dünyada yaygın olarak kullanıma sahip önemli bir tarım bitkisidir. Fasulye üretiminde verimliliği arttırmaya yönelik ıslah çalışmaları yapılmakta ve fasulye genotiplerinin genetik çeşitliliğine yönelik analizler, bu çalışmalar için uygun ebeveynlerin seçimine katkı sağlamaktadır. Ebeveyn seçiminde kullanılan geleneksel yöntemler, uzun zaman ve işçilik maliyetleri nedeniyle pratik değildir. DNA tabanlı markörlerin kullanıldığı moleküler yöntemler, genetik benzerlik ve farkları belirlemede oldukça başarılı olup geleneksel yöntemlere göre daha hızlı ve etkilidirler. RAPD (rastgele çoğaltılmış polimorfik DNA) markörleri, tür içi genetik çeşitliliği belirlemede yaygın olarak kullanılmaktadır. Bu çalışmada, Türkiye’de yetiştirilen otuz yedi adet fasulye (P. vulgaris) genotipi ve dış grup olarak ateş fasulyesi (Phaseolus coccineus L.) kullanılmıştır. İzole edilen bitki DNA'ları, RAPD markörleri kullanılarak PCR (polimeraz zincir reaksiyonu) yöntemiyle çoğaltılmıştır. PCR bant profilleri Phoretix 1D Pro yazılımı kullanılarak analiz edilmiştir. Fasulye genotipleri arasındaki genetik çeşitliliği gösteren dendrogram, MEGA 6.0 yazılımı ile UPGMA (aritmetik ortalamalı ağırlıksız çift grup yöntemi) kümeleme analiz yöntemi kullanılarak oluşturulmuştur. Dendrogramda P. coccineus genotipinin diğer fasulye genotiplerinden ayrı olarak dallandığı görülmüş ve RAPD-PCR yöntemiyle elde edilen genetik çeşitlilik verilerinin fasulye ıslah çalışmalarında etkin olarak kullanılabileceği anlaşılmıştır.

Keywords

Fasulye, Genetik çeşitlilik, RAPD-PCR yöntemi, Islah çalışmaları

Genetic diversity analysis of different bean (Phaseolus vulgaris L.) genotypes grown in Turkey

Abstract

Phaseolus vulgaris L. (bean), a member of Fabaceae (Legumes), is an important agricultural plant that is widely used in Turkey and the world. Breeding studies are carried out to increase productivity in bean production and the genetic diversity analyses of bean genotypes contribute to the selection of suitable parents for these studies. Traditional methods of parent selection are impractical due to long time and labour costs. Molecular methods using DNA-based markers are very successful in determining genetic similarities or differences and are faster and more effective than traditional methods. RAPD (random amplified polymorphic DNA) markers are widely used to determine intraspecies genetic diversity. In this study, thirty-seven bean (P. vulgaris) genotypes grown in Turkey and runner beans (Phaseolus coccineus L.) were used as the outgroup. Isolated plant DNAs were amplified using the PCR (polymerase chain reaction) method with RAPD markers. PCR band profiles were analysed using Phoretix 1D Pro software. A dendrogram showing genetic diversity among bean genotypes was created using UPGMA (unweighted pair group method with arithmetic mean) cluster analysis method with MEGA 6.0 software. It was seen that the P. coccineus genotype branched separately from other bean genotypes in the dendrogram, and the genetic diversity data obtained by the RAPD-PCR method could be used effectively in bean breeding studies.

Keywords

Bean, Genetic diversity, RAPD-PCR method, Breeding studies

References

• [1] Madakbaş S.Y. & Ergin, M. (2011). Morphological and phenological characterization of Turkish bean (Phaseolus vulgaris L.) genotypes and their present variation states. African Journal of Agricultural Research, 6(28), 6155-6166.114. https://doi.org/10.5897/AJAR11.1361
• [2] Górna, B., Szpakowska, M., JNowak, J., & Hołubowicz, R. (2016). Selected breeding characters and seed protein content of adzuki bean (Phaseolus angularis W.H. White) grown in central Europe. Acta Agroph., 23(4), 569-582.
• [3] Dupliak O., Barban O., & Pysarets M. (2021). Inheritance of the performance and its constituents by common bean (Phaseolus vulgaris l.) hybrids and lines. Селекціяі насінництво, 15-21.
• [4] Gepts P. (2001). The Encyclopedia of Life-Supporting Systems. In Tolba M.K. (eds.), Origins of plant agriculture and major crop plants in our fragile world (1st ed., pp. 629–637). Oxford, UK: EOLSS Publishers.
• [5] Kaçar, O., Çakmak, F., Çöplü, N., & Azkan, N. (2004). Bursa koşullarında bazı kuru fasulye çeşitlerinde (Phaseolus vulgaris L.) bakteri aşılama ve değişik azot dozlarının verim ve verim unsurları üzerine etkisinin belirlenmesi. Uludağ Üniversitesi Ziraat Fakültesi Dergisi, 18 (1), 207-218.
• [6] Marotti, I., Bonetti, A., Minelli, M., Catizone, P., & Dinelli G. (2006). Characterization of some Italian common bean (Phaseolus vulgaris L.) landraces by RAPD, semi-random and ISSR molecular markers. Genetic Resources and Crop Evolution, 54 (1), 175-188.
• [7] Ekincialp, A., & Şensoy, S. (2018). Phenotypic and molecular determination of anthracnose disease resistance in Lake Van Basin’s bean genotypes (Phaseolus vulgaris L.). Legume Research, 41(1), 135-142.
• [8] Rossi, M., Bitocchi, E., Bellucci, E., Nanni, L., Rau, D., Attene, G., & Papa, R. (2009). Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol. Appl., 2, 504–522.
• [9] Bitocchi, E., Nanni, L., Belluci, E., Rossi, M., Giardini, A., Zeuli, P.S., Logozzo, G., Stougaard, J., McClean, P., & Attene, G.; et al. (2012). Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proc. Natl. Acad. Sci USA, 109, 788–796.
• [10] Ortwin-Sauer, C. (1966). The Early Spanish Man; University of California Press: Berkeley/Los Angeles, CA, USA. Kluwer Academic Publishers, 51–298.
• [11] Karataş, A., Büyükdinç, D.T., İpek, A., Yağcıoğlu, M., Sönmez, K.& Ellialtıoğlu, Ş.Ş. (2017). Türkiye’de Fasulyede Yapılan Morfolojik ve Moleküler Karakterizasyon Çalışmaları. Turkish Journal of Scientific Reviews, 10 (1): 16-27.
• [12] Poyraz, İ. , Şahin, B. & Atmaca, E. (2017). Detection of ten resistance genes against P. syringae pv. phaseolicola and X. axonopodis pv. phaseoli in twelve local bean varieties using scar markers. Journal of the Institute of Science and Technology, 7 (2), 241-248.
• [13] Veloso, J.S., Silva, W., Pinheiro, L.R., Dos Santos, J.B., Fonseca Jr, N.S., & Euzebio., M.P. et al. (2015). Genetic divergence of common bean cultivars is revealed by sequence data. Genet. Mol. Res., 14 (3), 11281-11291.
• [14] Galvan, M.Z., Menendez-Sevillano, M.C., De Ron, A.M., Santalla, M., & Balatti, P.A. (2006). Genetic diversity among wild common beans from Northwestern Argentina based on morphoagronomic and RAPD data. Genetic Resources and Crop Evolution, 53, 891-900.
• [15] Singh, A., Dikshit, H.K., Mishra, G.P., Aski, M., Kumar, S., & Sarker, A. (2022). Breeding for abiotic stress tolerance in lentil in genomic era. In: Kole, C. (eds). Genomic Designing for Abiotic Stress Resistant Pulse Crops. Springer Cham. https://doi.org/10.1007/978-3-030-91039-6_5
• [16] Wu, Y.P., Chang, Y.C., Kuo, H.I., Lin, B.N., Wang, S.M., & Tseng, Y.C. (2022). The development of two high-yield and high-quality functional rice cultivars using marker-assisted selection and conventional breeding methods. Int. J. Mol. Sci., 23, 4678. https://doi.org/10.3390/ijms23094678
• [17] Bilgin, O., & Korkut, K.Z. (2005). Bazı ekmeklik buğday çeşit ve hatlarının tane verimi ve bazı fenolojik özelliklerinin belirlenmesi. Tekirdağ Ziraat Fakültesi Dergisi, 2(1), 5765.
• [18] Madakbaş, S.Y., Hız M.C., Gültekin, Y. & Sayar, M.T. (2016). Genetic characterization of green bean (Phaseolus vulgaris L.) accessions from Turkey with SCAR and SSR markers. Biochem. Genet., 54: 495-505.
• [19] Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A., & Tingey, S.V. (1990). DNA polimorphisms amplified by arbitrary primers are useful as genetic markers. Nucl. Acids Res., 18, 6531-6535.
• [20] Poyraz, İ. E. , Sözen, E. , Ataşlar, E. & Poyraz, İ. (2012). Determination of genetic relationships among Velezia L. Caryophyllaceae) species using RAPD markers. Turkish Journal of Biology, 36 (3), 293-302.
• [21] Sözen, E. & Yücel, E. (2015). Determination of genetic relationships between some endemic Salvia species using RAPD markers. Biyolojik Çeşitlilik ve Koruma, 8 (3), 248-253.
• [22] Hasanah, Y., Mawarni, L., Hanum, H., & Lestami, A. (2022). Genetic diversity of shallots (Allium ascalonicum L.) from several locations in North Sumatra, Indonesia based on RAPD markers. Biodiversitas Journal of Biological Diversity. https://doi.org/10.13057/biodiv%2Fd230518
• [23] Chen, J., Zhao, J.T., Erickson, D.L., Xia, N.H., & Kress, W.J. (2015). Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China. Molecular Ecology Resources, 15, 337–348.
• [24] Amiteye, S. (2021). Basic concepts and methodologies of DNA marker systems in plant molecular breeding, Heliyon, 7 (10), https://doi.org/10.1016/j.heliyon.2021.e08093
• [25] Al-Khayri, J.M., Mahdy, E.M.B., Taha, H.S.A., Eldomiaty, A.S., Abd-Elfattah, M.A.; Abdel Latef, A.A.H., Rezk, A.A., Shehata, W.F., Almaghasla, M.I., Shalaby, T.A., et al. (2022). Genetic and morphological diversity assessment of five kalanchoe genotypes by SCoT, ISSR and RAPD-PCR markers. Plants, 11, 1722. https://doi.org/10.3390/plants11131722
• [26] Doyle, J.J., & Doyle, J.L. (1987). A rapid DNA isolation procedure from small quantities of fresh leaf tissue. Phytochem. Bull., 19, 11-15.
• [27] Pandurangan, S., Workman, C., Nilsen, K., & Kumar, S. (2022). Introduction to marker-assisted selection in wheat breeding. In Accelerated Breeding of Cereal Crops (pp. 77-117). New York, NY: Humana.
• [28] Rani, M., Jinda, S.K., Vikal, Y., & Meena, O.P. (2021). Genetic male sterility breeding in heat tolerant bell pepper: Introgression of ms10 gene from hot pepper through marker-assisted backcrossing. Scientia Horticulturae, 285, 110172. https://doi.org/10.1016/j.scienta.2021.110172.
• [29] Gupta, M., Chyi, Y.S., Romero-Severson, J., & Owen, J.L. (1994). Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor. Appl. Genetics, 89, 998-1006.
• [30] Papan, P., Chueakhunthod, W., Jinagool, W., Tharapreuksapong, A., Masari, A., Kaewkasi, C., Ngampongsai, S., Girdthai, T., & Tantasawat, P. (2021). Improvement of Cercospora leaf spot and powdery mildew resistance of mungbean variety KING through marker-assisted selection. The Journal of Agricultural Science, 159 (9-10), 676-687. https://doi:10.1017/S0021859621000976
• [31] Nasution, F., Theanhom, A.A., Sukartini, Bhuyar, P., & Chumpookam, J. (2021). Genetic diversity evaluation in wild Muntingia calabura L. based on Random Amplified Polymorphic DNA (RAPD) markers. Gene Reports, 25, 10133, http://doi.org/10.1016/j.genrep.2021.101335
• [32] Soufy, H., Laila, A.M., & Iman, M.K.A. (2021). Application of RAPD-PCR for DNA-fingerprinting of Egyptian Tilapia. New Visions in Science and Technology, 1, 58-63, https://doi.org/10.9734/bpi/nvst/v1/10607D
• [33] Videla, M.E., Iglesias, J., & Bruno, C. (2021). Relative performance of cluster algorithms and validation indices in maize genome-wide structure patterns. Euphytica, 217, 195, https://doi.org/10.1007/s10681-021-02926-5
• [34] Geçit Kuşağı Tarımsal Araştırma Enstitüsü 2017 Yılı Gelişme Raporu. (2018). Eskişehir, Türkiye: Tarım ve Orman Bakanlığı Tarımsal Araştırmalar ve Politikalar Genel Müdürlüğü.
• [35] Tarım ve Orman Bakanlığı Bitkisel Üretim Genel Müdürlüğü Yemeklik Tane Baklagiller Tescil raporu. (2017). https://www.tarimorman.gov.tr/BUGEM/TTSM/Belgeler/Yay%C4%B1nlar/2017%20Faliyet/Yemeklik%20Tane%20Bklagiller%202017%20Tescil%20Raporu.pdf