Evaluation of the Genetic Structure of Some Accessions Belonging to Onobrychis spp. Using Microsatellite DNA Markers

Yıl 2023, Cilt: 20 Sayı: 2, 399 - 409, 22.05.2023

Elbi Cansu Yılmaz , Behiye Banu Bilgen , Metin Tuna

https://doi.org/10.33462/jotaf.1141367

Cited By: 1

Öz

Turkey is in a very convenient position for animal husbandry in terms of both natural resources and ecological conditions. Forage crops, which has a very important place in agricultural activities, is the insurance of plant and animal production. Sainfoin is a perennial forage legume species that grown in the northern temperate regions of the world from the Mediterranean region and the Caucasus, and to Central Asia. In this study the genetic diversity of 100 genotypes representing 44 accessions from 18 different Onobrychis species (O. arenaria subsp. arenaria, O. inermis, O. petraea, O. cyri, O. iberica, O. altissima, O. vassilczenkoi, O. conferta subsp. argentea, O. alba subsp. laconica, O. biebersteinii, O. grandis, O. kachetica, O. kemulariae, O. oxyodonta, O. megataphros, O. pallasii, Onobrychis spp., and O. viciifolia) were evaluated using 8 simple sequence repeat (microsatellite) markers. Based on the results, OVK036, OVK094, OVK125, OVM033, OVK161, OVK046, OVM061, and OVK174 loci were polymorphic. The observed number of alleles per SSR locus ranged from 6 to 21 alleles (mean of 11.625). Maximum allele frequency ranged from 0.51 to 0.93 with a mean value of 0.73. The PIC value ranged from 0.124 to 0.244. The mean polymorphism information content of loci was 0.188. Genetic diversity coefficients according to the UPGMA ranged from 0.000 to 0.9375. Cluster analysis divided the 100 sainfoin genotypes into two main groups (Cluster-I and Cluster-II). All diploid genotypes (except for 1 diploid genotype) used in the study formed a separate group within Cluster-I. The results revealed that SSR markers used in this study are useful for molecular characterization and assessing genetic diversity of sainfoin accessions. The obtained SSR alleles and genetic variability in a studied certain loci provided significant information about the genetic structure of sainfoin accessions that could be used as parental lines in sainfoin breeding programs.

Anahtar Kelimeler

Breeding, Molecular Characterization, Sainfoin, SSR, UPGMA

Destekleyen Kurum

The Scientific and Technological Research Council of Turkey (TÜBİTAK)

Proje Numarası

215O526

Teşekkür

This work was supported by The Scientific and Technological Research Council of Turkey (TÜBİTAK, Project No: 215O526).

Evaluation of the Genetic Structure of Some Accessions Belonging to Onobrychis spp. Using Microsatellite DNA Markers

Öz

Türkiye hem doğal kaynaklar hem de ekolojik koşullar bakımından hayvancılığa oldukça elverişli bir konuma sahiptir. Tarımsal faaliyetler içerisinde çok önemli bir yere sahip olan yem bitkileri tarımı, bitkisel ve hayvansal üretimin sigortası konumundadır. Korunga, dünyanın kuzey ılıman bölgelerinde özellikle Akdeniz bölgesi ve Kafkaslardan Orta Asya'ya kadar yetişen çok yıllık bir baklagil yem bitkisi türüdür. Bu çalışmada 18 farklı Onobrychis türüne ait 44 aksesyonu temsil eden 100 genotipin (O. arenaria subsp. arenaria, O. inermis, O. petraea, O. cyri, O. iberica, O. altissima, O. vassilczenkoi, O. conferta subsp. argentea, O. alba subsp. laconica, O. biebersteinii, O. grandis, O. kachetica, O. kemulariae, O. oxyodonta, O. megataphros, O. pallasii, Onobrychis spp. ve O. viciifolia) genetik çeşitliliği 8 adet basit dizi tekrarları (mikrosatellit) belirteci kullanılarak incelenmiştir. Mikrosatellit analizi sonuçlarına göre, OVK036, OVK094, OVK125, OVM033, OVK161, OVK046, OVM061 ve OVK174 lokusları polimorfik olarak saptanmıştır. SSR lokusu başına gözlenen allel sayısı 6 ile 21 arasında gözlenmiştir (ortalama 11.625). Maksimum allel frekansı 0.51 ile 0.93 arasında değişmekte olup, ortalama 0.73 değerindedir. PIC değeri 0.124 ile 0.244 arasında hesaplanmış, ortalama polimorfik bilgi içeriği 0.188 olarak belirlenmiştir. UPGMA'ya göre genetik çeşitlilik katsayıları 0.000 ile 0.9375 arasında değişmiştir. Dendrogram analizine göre, 100 korunga genotipi iki ana gruba (Grup-I ve Grup-II) ayrılmıştır. Çalışmada kullanılan tüm diploid genotipler (1 diploid genotip hariç) Grup-I içerisinde ayrı bir grup oluşturmuştur. Bu çalışmada kullanılan SSR belirteçleri, korunga aksesyonlarının moleküler karakterizasyonu ve genetik çeşitliliğinin değerlendirilmesi için yararlı olduğu sonucuna varılmıştır. Spesifik lokuslardan elde edilen SSR alelleri ve genetik varyasyon, korunga ıslah programlarında ebeveyn hatları olarak kullanılabilecek korunga aksesyonlarının genetik yapısı hakkında önemli bilgiler sağlamıştır.

Anahtar Kelimeler

Islah, Moleküler karakterizasyon, Korunga, SSR, UPGMA

Proje Numarası

215O526

Kaynakça

• Aktoklu, M. (1995). The Revision of Onobrychis Miller (Fabaceae) species of Turkey. (Ph.D. Thesis) The Graduate School of Natural and Applied Science of İnönü University, Malatya.
• Anonymous (2021). Republic of Türkiye, Ministry of Agriculture and Forestry Variety Registration and Seed Certification Center. Available from: https://www.tarimorman.gov.tr/BUGEM/TTSM/Sayfalar/Detay.aspx?SayfaId=8 (Accessed date: 21 March 2022).
• Bagshaw, A. (2017). Functional mechanisms of microsatellite DNA in eukaryotic genomes. Genome Biology and Evolution, 9(9): 2428-2443.
• Bhattarai, S. (2017). Characterization of diverse germplasm of sainfoin (Onobrychis viciifolia Scop.) using agro-morphological traits and AFLP molecular markers. (Msc. Thesis) Department of Plant Science, University of Saskatchewan, Saskatoon, Canada.
• Bhattarai, S., Coulman, B. and Biligetu, B. (2016). Sainfoin (Onobrychis viciifolia Scop.): renewed interest as a forage legume for western Canada. Canadian Journal of Plant Science, 96(5): 748-756.
• Carbonero, C. H., Harvey, I. M., Brown, T. A. and Smith, L. (2011). Sainfoin (Onobrychis viciifolia): a beneficial forage legume. Plant Genetic Resources, 9: 70-85.
• Christenhusz, M. J. M. and Byng, J. W. (2016). The number of known plants species in the world and its annual increase. Phytotaxa, 261(3): 201-217.
• Delgado, I., Salvia, J. and Andres, C. (2008). The agronomic variability of a collection of sainfoin accessions. Spanish Journal of Agricultural Research, 6(3): 401-407.
• Demdoum, S., Munoz, F., Delgado, I., Valderrabano, J. and Wunsch, A. (2012). EST-SSR cross amplification and genetic similarity in Onobrychis genus. Genetic Resources and Crop Evolution, 59: 253-260.
• Doyle, J. J. and Doyle, J. I. (1990). Isolation of plant DNA from fresh tissue. Focus, 12: 13-15.
• Ertus, M. M. (2021). Genetic relationship in sainfoin (Onobrychis viciifolia) landraces cultivated East Anatolia by using RAPD and ISSR markers. Legume Research, 44: 888-893.
• Hejrankesh, N., Haghighi, A. R., Mousavizadeh, S. A. and Rashidi, V. (2014). Evaluation of genetic diversity of sainfoin (Onobrychis viciifolia Scop.) landraces using RAPD markers. Journal of Current Research in Science, 2: 739-748.
• Kempf, K., Mora-Ortiz, M., Smith, M. J., Kölliker, R. and Skot, L. (2016) Characterization of novel SSR markers in diverse sainfoin (Onobrychis viciifolia) germplazm. BMC Genetics, 17: 124.
• Langella, O. (1999). Populations 1.2.32, Population Genetic Software. Gif-sur-Yvette, France: Laboratoire Evolution, Génomes et Spéciation.
• Lewis, G., Schrire, B., Mackinder, B. and Lock, M. (2005). Legumes of the World. Kew, UK: Royal Botanical Gardens.
• Nadeem, M. A., Nawaz, M. A., Shahid, M. Q., Doğan, Y., Comertpay, G., Yıldız, M., Hatipoğlu, R., Ahmad, F., Alsaleh, A., Labhane, N., Özkan, H., Chung, G. and Baloch, F. S. (2018). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 32: 261-285.
• Nei, M. (1987). Molecular Evalutionary Genetics. Columbia University Press, New York. 512 p.
• Noroozi, J., Zare, G., Sherafati, M., Mahmoodi, M., Moser, D., Asgarpour, Z. and Schneeweiss, G. M. (2019). Patterns of endemism in Turkey, the meeting point of three global biodiversity hotspots, based on three diverse families of vascular plants. Frontiers in Ecology and Evolution, 7: 159.
• Nosrati, H., Feizi, M. A. H, Latifian, F. and Haghighi, A. R. (2016). Eco-geographical variations of ISSRs among populations of Onobrychis viciifolia (Sainfoin, Fabacae). Analele Universităţii din Oradea Fascicula Biologie, 2: 62-66.
• Nosrati, H., Feizi, M. A. H., Tarrah, S. S. and Haghighi, A. R. (2012). Population genetic variation in sainfoin (Fabaceae) revealed by RAPD markers. Analele Universităţii din Oradea Fascicula Biologie, 1: 11-16.
• Ozalp, M. and Temel, O. (2016). Effects of elevation and some soil properties on the yield and quality of sainfoin (Onobrychis sativa Scop.) forage crop grown in Savsat district, Artvin. Anadolu Journal of Agricultural Sciences, 31: 106-116.
• Ozbek, H. (2011). Sainfoin (Onobrychis viciifolia Scop.): An important bee plant. Uludag Bee Journal, 11: 51-62.
• Ozkan, S. and Bilgen, B. B. (2019). Genetic characterization of sainfoin (Onobrychis viciifolia) varieties and populations using microsatellite markers. Journal of Tekirdag Agricultural Faculty, 16: 51-60.
• Page, R. D. (1996). Tree View: An application to display phylogenetics trees on personal computers. Computer Applications in the Biosciences, 12: 357-358.
• Peakall, R. and Smouse, P. E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic sofware for teaching and research-an update. Bioinformatics, 28: 2537-2539.
• Rasouli, M., Jaferi, A. A., Tabaei-Aghdaei, S. R., Shanjani, P. S. and Darvish, F. (2013). Assesment of genetic variability of 36 populations of sainfoin (Onobrychis sativa) based on RAPD markers. International Journal of Biosciences, 3: 15-26.
• Roldan-Ruiz, I., Dendauw, J., Van Bockstaele, E., Depicker, A. and De Loose, M. (2000). AFLP markers reveal high polymorphic rates in rygrasses (Lolium spp.). Molecular Breeding, 6: 125-134. Schuelke, M. (2000). An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18: 233-234.
• Sevim, E. T., Ozdil, F., Unal E. O. and Arat S. (2017). Characterization of cloned cattle obtained by nuclear transfer and their offspring with mtDNA and microsatellite markers. Journal of Tekirdag Agricultural Faculty, 14: 150-157.
• Shen, S., Chai, X., Zhou, Q., Luo, D., Wang, Y. and Liu, Z. (2019). Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia). PeerJ-The Journal of Life and Environmental Sciences, 7:1-19.
• Sekercioglu, C. H., Anderson, S., Akcay, E., Bilgin, R., Can, O. E., Semiz, G., Tavşanoğlu, C., Yokeş, M. B., Soyumert, A., İpekdal, K., Sağlam, İ. K., Yücel, M. and Dalfes, H. N. (2011). Turkey’s globally important biodiversity in crisis. Biological Conservation, 144: 2752-2769.
• Sutcu, T. (2020). Genetic characterization of some sainfoin lines by microsatellite (SSR) markers. (MSc Thesis) The Graduate School of Natural and Applied Science of Tekirdağ Namık Kemal University, Tekirdağ.
• Sutcu, T., Bilgen, B. B. and Tuna, M. (2022). Analysis of genetic diversity among Onobrychis accessions with high agronomic performance by simple sequence repeat (SSR) markers. Molecular Biology Reports, 49: 5659-5668.
• Toluei, Z., Ranjbar, M., Wink, M. and Atri, M. (2012). Molecular phylogeny and ecogeography of Onobrychis viciifolia Scop. (Fabaceae) based on nrDNA ITS sequences and genomic ISSR fingerprinting. Feddes Repertorium, 123: 193-207.
• TUBIVES (2022). Turkish Plants Data Service. Available from: http://194.27.225.161/yasin/tubives/index.php (Accessed date: 30 March 2022)
• Vieira, M. L., Santini, L., Diniz, A. L. and Munhoz, C. (2016). Microsatellite markers: what they mean and why they are so useful. Genetics and Molecular Biology, 39(3): 312-328.
• Yildiz, B., Ciplak, B. and Aktoklu, E. (1999). Fruit morphology of sections of the genus Onobrychis Miller (Fabaceae) and its phylogenetic implications. Israel Journal of Plant Sciences, 47: 269-282.
• Zarrabian, M. and Majidi, M. M. (2015). Genetic diversity and relationships within and among Onobrychis species using molecular markers. Turkish Journal of Botany, 39: 681-692.
• Zarrabian, M., Majidi, M. M. and Ehtemam, M. H. (2013). Genetic diversity in a worldwide collection of sainfoin using morphological, anatomical, and molecular markers. Crop Science, 53: 2483-2496.