Characterization of Some Registered Chickpea (Cicer arietinum L.) Varieties with Simple Sequence Repetitions (SSRs) Markers

Abstract

Chickpea (Cicer arietinum L.) is an economically important edible legume plant that is grown worldwide. In this study, genetic similarities of 10 registered chickpea varieties which are registered after 2011 were investigated by using 6 polymorphic SSR markers selected from 15 SSR markers. The total number of alleles were 29 and the average number of alleles for each locus were 4.83. The average heterozygous rate was 0.62, PIC (polymorphism information content) was between 0.41 and 0.74 and an average of 0.58. It was observed that 10 chickpea varieties were divided into two groups with the genetic similarity dendogram created using Neighbor-joining and UPGMA from the genetic similarity matrix. In terms of genetic similarity, Sezenbey and Zuhal varieties (96%) registered by the Black Sea Agricultural Research Institute (96%) and Ilgaz and Aslanbey varieties (96%) registered by the Eastern Mediterranean Agricultural Research Institute were found the closest varieties. On the other hand, Seçkin registered by the Mediterranean Agricultural Research Institute and Akça registered by Transitional Zone Agricultural Research Institute were found the farthest varieties (21%). With this study, determining of the genetic similarities some registered chickpea varieties was aimed to contribute to chickpea breeding studies and the other genetic-based studies.

Keywords

• SSRs
• Chickpea
• genetic diversity
• characterization

Bazı Tescilli Nohut (Cicer arietinum L.) Çeşitlerinin Simple Sequence Repeats (SSRs) Markörler ile Karakterizasyonu

Abstract

Nohut (Cicer arietinum L.) dünya çapında yetiştirilen ve ekonomik açıdan önemli olan yemeklik baklagil bitkisidir. Bu çalışmada, 2011 yılı sonrası tescil edilen 10 tescilli nohut çeşidi 15 SSR markörü içerisinden polimorfizm gösteren 6 SSR markörü kullanılarak genetik benzerlikleri incelenmiştir. Toplam allel sayısı 29 ve her bir lokus için ortalama allel sayısı 4.83 olarak belirlenmiştir. Ortalama heterozigotluk oranı 0.62, PIC (polymorphism information content) değeri 0.41 ile 0.74 arasında ve ortalama 0.58 olarak bulunmuştur. Genetik benzerlik matriksinden Neighbour-joining ve UPGMA kullanılarak oluşturulan genetik ilişki dendogramı ile 10 nohut çeşidinin iki ayrı gruba ayrıldığı görülmüştür. Genetik benzerlik açısından birbirine en yakın çeşitlerin Karadeniz Tarımsal Araştırma Enstitüsü tarafından tescil edilen Sezenbey ve Zuhal çeşitleri (%96) ile Doğu Akdeniz Tarımsal Araştırma Enstitüsü tarafından tescil edilen Ilgaz ve Aslanbey çeşitleri (%96) olduğu, birbirlerine en uzak çeşitlerin ise Doğu Akdeniz Tarımsal Araştırma Enstitüsü tarafından tescil edilen Seçkin ile Geçit Kuşağı Tarımsal Araştırma Merkezi tarafından tescil edilen Akça çeşitleri (%21) olduğu tespit edilmiştir. Bu çalışma ile bazı tescilli nohut çeşitlerin genetik benzerlik ilişkisi belirlenmiş, nohut ıslah çalışmaları ve nohutta gerçekleştirilecek diğer genetik tabanlı çalışmalara katkıda bulunması amaçlanmıştır.

Keywords

• Nohut
• SSRs
• genetik çeşitlilik
• karakterizasyon

References

1. Afzal M, Alghamdi SS, Migdadi HM, Khan MA, Farooq M, 2018. Morphological and Molecular Genetic Diversity Analysis of Chickpea Genotypes. International Journal of Agriculture & Biology, 20: 1062‒1070.
2. Arumuganathan K, Earle ED, 1991. Nuclear DNA Content of Some Important Plant Species. Plant Molecular Biology Reporter, 9, 208-218.
3. Atalay E, and Babaoğlu M, 2012. Determination of Genetic Relationship in Turkish Chickpea (Cicer arietinum L.) Genotypes Using SSR Molecular Markers and Capillary Electrophoresis, The Journal of Animal & Plant Sciences, 22(2):369-375.
4. Bellemou D, Millàn T, Gil J, Abdelguerf A, Laouar M, 2020. Genetic diversity and population structure of Algerian chickpea (Cicer arietinum) genotypes: use of agro-morphological traits and molecular markers linked or not linked to the gene or QTL of interest. Crop & Pasture Science, 71, 155–170.
5. Botstein D, White RL, Skolnick MH, Davies RW, 1980. Construction of Genetic Linkage Map in Man Using Restriction Fragment Length Polymorphisms. The American Journal of Human Genetics, 32(3):314–33.
6. Brockwell J, Bottomley PJ, Thies JE, 1995. Manipulation of Rhizobia Microflora for İmproving Legumep Roductivity and Soil Fertility: a Critical Assessment-Management of Biological Nitrogen Fixation for the Development of More Productive and Sustainable Agricultural Systems. Springer Netherlands, No: 1/2, s. 143–180.
7. Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH, 2005. Development of ESTs From Chickpea Roots And Their Use in Diversity Analysis of the Cicer Genus. BMC Plant Biology, 5:16.
8. Çevik S, Unyayar S, Ergül A, 2015. Genetic Relationships Between Cultivars of Cicer arietinum and Its Progenitor Grown in Turkey Determined by Using the SSR Markers. Turkish Journal of Field Crops, 20(1), 109-114.

9. Choudhary S, Sethy NK, Shokeen B, Bhatia S, 2008. Development of Chickpea EST-SSR Markers and Analysis of Allelic Variation Across Related Species. Theoretical and Applied Genetics, 118:591–608.
10. Cıngıllı H, Altınkut A, Akçin A, 2005. The Use of Microsatellite Markers in the Annual and Perennial Cicer Species Growing in Turkey, Biologia, Bratislava, 60(1):93-98.
11. De Giovanni C, Pavan S, Taranto F, Di Rienzo V, Miazzi MM, Marcotrigiano AR, Mangini G, Montemurro C, Ricciardi L, Lotti C, 2017. Genetic Variation of a Global Germplasm Collection of Chickpea (Cicer arietinum L.) Including Italian Accessions at Risk of Genetic Erosion. Physiology and Molecular Biology of Plants. 23(1):197-205.
12. FAOSTAT 2018. http://www.fao.org/faostat/en/#data/QC/visualize. Son erişim tarihi 22 Nisan 2020.
13. Friedman M, 1996. Nutritional Value of Food Proteins from Different Food Sources. Journal of Agricultural and Food Chemistry, 44:6-29.
14. Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK, 2011. Microsatellite Markers: an Overview of The Recent Progress in Plants. Euphytica, 177:309-334.
15. Ladizinsky G, Adler A, 1976. Genetic Relationships Among the Annual Species of Cicer L. Theoretical and Applied Genetics, 48: 197-203.
16. Lefort F, Lally M, Thompson D, Douglas GC, 1998. Morphological Traits, Microsatellite Fingerprinting and Genetic Relatedness of a Stand of Elite Oaks (Q. robur L.) at Tullynally Ireland. Silvae Genetica, 47:5–6
17. Liu K, Muse SV, 2005. PowerMarker: an Integrated Analysis Environment for Genetic Marker Analysis. Bioinformatics, 21:2128–2129.
18. Mandal R, Pal S, Shit N, 2017. Unlocking Genetic Diversity in Selected Chickpea Genotypes using Morphological and Molecular Markers. Current Agriculture Research Journal, Vol. 5(1), 50-57.
19. Metin A, 2012. Nohut Çeşitlerinde SSR Varyasyonu ve Genetik İlişkilerin Değerlendirilmesi, Bozok Üniversitesi Fen Bilimleri Enstitüsü, Yüksek Lisans Tezi (Basılmış).
20. Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam KN, Latif MA, 2013. A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance. International Journal of Molecular Sciences, 14: 22499-22528.
21. Nayak SN, Zhu H, Varghese N, Datta S, Choi HK, Horres R, Jüngling R, Singh J, Kavi Kishor PB, Sivaramakrihnan S, Hoisington DA, Kahl G, Winter P, Cook DR, Varshney RK, 2010. Integration of Novel SSR and Gene-Based SNP Marker Loci in The Chickpea Genetic Map and Establishment of New Anchor Points with Medicago truncatula Genome. Theoretical and Applied Genetics, 120:1415–1441.
22. Nei M, 1973. Analysis of Gene Diversity in Subdivided Populations. Proceedings of the National Academy of Sciences of the United States of America, 70:3321–3323. Rajesh PN, Sant VJ, Gupta VS, Muehlbauer FJ, Rajesh PK, 2003.Genetic Relationships Among Annual and Perennial Wild Species of Cicer using Inter Simple Sequence Repeat (ISSR) Polymorphism. Euphytica, 129, 15-23.
23. Rao AS, Usha Rani P, Deshmukh PS, Kumar PA, Panguluri SK, 2007. RAPD and ISSR Fingerprinting in Cultivated Chickpea (Cicer arietinum L.) and its Wild Progenitor Cicer reticulatum L. Genetic Resources and Crop Evolution, 54 (6): 1235- 1244.
24. Saeed A, Hovsepyan H, Darvishzadeh R, Imtiaz M, Panguluri SK, Nazaryan R, 2011. Genetic Diversity of Iranian Accessions, Improved Lines of Chickpea (Cicer arietinum L.) and Their Wild Relatives by Using Simple Sequence Repeats, Plant Molecular Biology Reporter, 100(4): 433‒440.
25. Samyuktha SM, Kannan Bapu JR, Geethanjali S, 2018. Molecular Genetic Diversity and Population Structure Analysis in Chickpea (Cicer arietinum L.) Germplasm using SSR Markers. International Journal of Current Microbiology and Applied Sciences, 7(2): 639-651.
26. Schuelke M, 2000. An Economic Method for the Fluorescent Labelling of PCR Fragments. Nature Biotechnology, 18:233–234.
27. Seyedimoradi H, Talebi R, Kanouni H, Naji AM, Karami E, 2019. Agro-morphological description, genetic diversity and population structure of chickpea using genomic-SSR and ESR-SSR molecular markers. Journal of Plant Biochemistry and Biotechnology, 28(4):483–495.
28. Shan F, Clarke HC, Plummer JA, Yan G, Siddique KHM, 2005. Geographical Patterns of Genetic Variation in the World Collections of Wild Annual Cicer Characterized by Amplified Fragment Length Polymorphisms. Theoretical and Applied Genetics, 110(2), 381-391.
29. Singh R, Sharma P, Varshney RK, Sharma SK, Singh NK, 2008. Chickpea Improvement: Role of Wild Species and Genetic Markers. Biotechnology & Genetic Engineering Reviews, 25:267–314.
30. Sudupak MA, Akkaya MS, Kence A, 2002. Analysis of Genetic Relationships Among Perennial and Annual Cicer Species Growing in Turkey using RAPD Markers. Theoretical and Applied Genetics, 105(8):1220-1228.
31. Şehirali S, 1988. Yemeklik Tane Baklagiller. Ankara Üniversitesi Ziraat Fakültesi Yayınları No:1089, s. 314, Ankara- Türkiye.
32. Tamura K, Dudley J, Nei M, Kumar S, 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution, 24:1596–1599.
33. Tar’an B, Warkentin T, Tullu A, Vandenberg A, 2007. Genetic Relationships Among Chickpea (Cicer arietinum L.) Genotypes Based on the SSRs at the Quantitative Trait Loci for Resistance to Ascochyta Blight. European Journal of Plant Pathology, 119, 39–51.
34. Udupa SM, Sharma A, Sharma AP, Pai RA, 1993. Narrow Genetic Variability in Cicer arietinum L. as Revealed by RFLP Analysis. Journal of Plant Biochemistry and Biotechnology, 2: 83-86.
35. Valadez-Moctezuma E, Cabrera-Hidalgo A, Arreguin-Espinosa R, 2019. Genetic variability and population structure of Mexican chickpea (Cicer arietinum L.) germplasm accessions revealed by microsatellite markers. Journal of Plant Biochemistry and Biotechnology, 29(3):357–367.
36. Varshney RK, Graner A, Sorrells ME, 2005. Genic Microsatellite Markers in Plants: Features and Applications. TRENDS in Biotechnology, 23(1): 48-54.
37. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar’an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo MC, Thudi M, Gowda CL, Singh NP, Lichtenzveig J, Gali KK, et al. 2013. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology, 31:240–246.
38. Vashist U, Boora KS, Kumar M, 2019. Evaluation of Genetic Diversity Among Chickpea (Cicer arietinum) Genotypes Using PCR Based Simple Sequence Repeats Markers. The Pharma Innovation Journal, 8(2): 182-188.
39. Weiss E, Zohary D, 2011. The Neolithic Southwest Asian Founder Crops. Current Anthropology, 52:4.
40. Winter P, PfaV T, Udupa SM, Hüttel B, Sharma PC, Sahi S, ArrequinEspinoza R, Weigand F, Muehlbauer FJ, Kahl G, 1999. Characterization and Mapping of Sequence-Tagged Microsatellite Sites in the Chickpea (Cicer arietinum L.). Molecular Genetics and Genomics, 262:90–101.
41. Yorgancılar M, Atalay E, Bayrak H, Hakkı EE, Önder M, Babaoğlu M, 2008. ISSR Markörleri Kullanarak Konya Bölgesinden Toplanan Nohut (Cicer arietinum L.) Popülasyonları Arasında Genetik Çeşitliliğin Belirlenmesi. Selçuk Üniversitesi Ziraat Fakültesi Dergisi, 22 (46): 1-5.