Tolga KARAKÖY, Muhammad Azhar NADEEM, Faheem Shehzad BALOCH, Muzaffer BARUT

DNA fingerprinting and genetic diversity analysis of world quinoa germplasm using iPBS-retrotransposon marker system

Quinoa is an important staple food crop for millions of impoverished rural inhabitants of the Andean region. Quinoa is considered a good source of protein,vitamins, minerals, and antioxidants. This study aimed to investigate the genetic diversity and population structure of world quinoa germplasm originating from 8 countries through the iPBS-retrotransposon marker system. Molecular characterization was performed using the 11 most polymorphic primers. A total of 235 bands were recorded, of which 66.8% were polymorphic. Mean polymorphism information content (PIC) was 0.410. Various diversity indices including mean effective number of alleles (1.269), mean Shannon’s information index (0.160) and gene diversity (0.247) revealed the existence of sufficient amount of genetic diversity in studied germplasm. Bolivia–17 and Mexico–1 were found to be genetically distinct accessions and can be suggested as candidate parents for future breeding activities. Various diversity indices were also calculated among germplasm collection counries and the results clearly showed the existence of higher genetic diversity in Bolivian and Peruvian accessions. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) grouped quinoa germplasm according to their collection country. Analysis of molecular variance (AMOVA) revealed that most of the variations (69%) in world quinoa germplasm are due to differences within populations. Findings of this study can be used for deeper understanding of the genetic relationship and in the determination of appropriate breeding and conservation strategies for quinoa.

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Andeden EE, Baloch FS, Derya M, Kilian B, Özkan H (2013). iPBSRetrotransposons-based genetic diversity and relationship among wild annual Cicer species. Journal of Plant Biochemistry and Biotechnology 22 (4): 453-466.
Al-Naggar AMM, El-Salam RA, Badran AEE, El-Moghazi MM (2017). Molecular differentiation of five quinoa (Chenopodium quinoa Willd.) genotypes using inter-simple sequence repeat (ISSR) markers. Biotechnology Journal International 20 (1): 1-12. doi: 10.9734/BJI/2017/37053
Ana-Cruz MC, Helena ME, Yacenia MC (2017). Molecular characterization of Chenopodium quinoa Willd. using intersimple sequence repeat (ISSR) markers. African Journal of Biotechnology 16 (10): 483-489.
Ando H, Chen YC, Tang H, Shimizu M, Watanabe K et al. (2002). Food components in fractions of quinoa seed. Food Science and Technology Research 8 (1): 80-84. doi: 10.3136/fstr.8.80
Aydin MF, Baloch FS (2019). Exploring the genetic diversity and population structure of Turkish common bean germplasm by the iPBS-retrotransposons markers. Legume Research-An International Journal 42 (1): 18-24. doi: 10.18805/LR-423
Baloch FS, Alsaleh A, de Miera LES, Hatipoğlu R, Çiftçi V et al (2015). DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey. Biochemical Systematics and Ecology 61: 244- 252. doi: 10.1016/j.bse.2015.06.017
Bazile D, Jacobsen SE, Verniau A (2016). The global expansion of quinoa: trends and limits. Frontiers in Plant Science 7: 622. doi: 10.3389/fpls.2016.00622
Bhargava A, Shukla S, Ohri D (2006). Chenopodium quinoa—an Indian perspective. Industrial Crops and Products 23 (1): 73- 87. doi: 10.1016/j.indcrop.2005.04.002
Bouchet S, Pot D, Deu M, Rami JF, Billot C et al. (2012). Genetic structure, linkage disequilibrium and signature of selection in sorghum: lessons from physically anchored DArT markers. PloS One 7 (3): e33470. doi: 10.1371/journal.pone.0033470
Christensen SA, Pratt DB, Pratt C, Nelson PT, Stevens MR et al. (2007). Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers. Plant Genetic Resources 5 (2): 82-95. doi: 10.1017/S1479262107672293
Doyle JJ, Doyle JL (1990). Isolation ofplant DNA from fresh tissue. Focus 12 (13): 39-40.
Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14 (8): 2611-2620. doi: 10.1111/j.1365-294X.2005.02553.x
Finnegan DJ (1989). Eukaryotic transposable elements and genome evolution. Trends in Genetics 5: 103-107. doi: 10.1016/0168- 9525(89)90039-5
Food and Agriculture Organization of the United Nations (2013). Home- International Year of Quinoa 2013 [online]. Website http://www.fao.org/quinoa-2013/en/ [accessed 01 September 2019].
Food and Agriculture Organization of the United Nations (2017). FAOSTAT [online]. Website http://www.fao.org/faostat/ en/#data/QC/visualize [accessed 01 September 2019].
Fuentes FF, Martinez EA, Hinrichsen PV, Jellen EN, Maughan PJ (2009). Assessment of genetic diversity patterns in Chilean quinoa (Chenopodium quinoa Willd.) germplasm using multiplex fluorescent microsatellite markers. Conservation Genetics 10 (2): 369-377. doi: 10.1007/s10592-008-9604-3
Galwey NW, Leakey CLA, Price KR, Fenwick GR (1989). Chemical composition and nutritional characteristics of quinoa (Chenopodium quinoa Willd.). Food Sciences and Nutrition 42 (4): 245-261. doi: 10.1080/09543465.1989.11904148
Gramazio P, Plesa IM, Truta AM, Sestras AF, Vilanova S et al. (2018). Highly informative SSR genotyping reveals large genetic diversity and limited differentiation in European larch (Larix decidua) populations from Romania. Turkish Journal of Agriculture and Forestry 42 (3):165-75.
Guliyev N, Sharifova S, Ojaghi J, Abbasov M, Akparov Z (2018). Genetic diversity among melon (Cucumis melo L.) accessions revealed by morphological traits and ISSR markers. Turkish Journal of Agriculture and Forestry 42 (6):393-401.
Habyarimana E (2016). Genomic prediction for yield improvement and safeguarding of genetic diversity in CIMMYT spring wheat (Triticum aestivum L.). Australian Journal of Crop Science 10 (1): 127.
Heiser CB, Nelson DC (1974). On the origin of the cultivated chenopods (Chenopodium). Genetics 78 (1): 503-505.
Hirose Y, Fujita T, Ishii T, Ueno N (2010). Antioxidative properties and flavonoid composition of Chenopodium quinoa seeds cultivated in Japan. Food Chemistry 119 (4): 1300-1306. doi: 10.1016/j.foodchem.2009.09.008
Hossein-Pour A, Haliloglu K, Ozkan G, Tan M (2019). Genetic diversity and population structure of quinoa (Chenopodium quinoa Willd.) using iPBS-retrotransposons markers. Applied Ecology and Environmental Research 17 (2): 1899-1911. doi: 10.15666/aeer/1702_18991911
Jacobsen SE, Mujica A, Jensen CR (2003). The resistance of quinoa (Chenopodium quinoa Willd.) to adverse abiotic factors. Food Reviews International 19 (1-2): 99-109. doi: 10.1081/FRI120018872
James LEA (2009). Quinoa (Chenopodium quinoa Willd.): composition, chemistry, nutritional, and functional properties. Advances in Food and Nutrition Research 58: 1-31. doi: 10.1016/S1043-4526(09)58001-1
Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B et al. (2017). The genome of Chenopodium quinoa. Nature 542: 307-312. doi: 10.1038/nature21370
Kalendar R, Antonius K, Smýkal P, Schulman AH (2010). iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theoretical and Applied Genetics 121 (8): 1419-1430. doi: 10.1007/s00122-010-1398-2
Karık Ü, Nadeem MA, Habyarimana E, Ercişli S, Yildiz M et al. (2019). Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBSRetrotransposon Marker System. Agronomy 9 (10): 647. doi: 10.3390/agronomy9100647
Kimura M (1965). A stochastic model concerning the maintenance of genetic variability in quantitative characters. Proceedings of the National Academy of Sciences of the United States of America 54 (3): 731. doi: 10.1073/pnas.54.3.731
Maughan PJ, Smith SM, Rojas-Beltran JA, Elzinga D, Raney JA et al. (2012). Single nucleotide polymorphism identification, characterization, and linkage mapping in quinoa. The Plant Genome 5 (3): 114-125. doi: 10.3835/plantgenome2012.06.0011
Mir RR, Kumar J, Balyan HS, Gupta PK (2012). A study of genetic diversity among Indian bread wheat (Triticum aestivum L.) cultivars released during last 100 years. Genetic Resources and Crop Evolution 59 (5): 717-726. doi: 10.1007/s10722-011- 9713-6
Nemli S, Kianoosh T, Tanyolac MB (2015). Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers. Turkish Journal of Agriculture and Forestry 39 (6): 940-948. doi: 10.3906/tar-1505-59
Newell MA, Cook D, Hofmann H, Jannink JL (2013). An algorithm for deciding the number of clusters and validation using simulated data with application to exploring crop population structure. The Annals of Applied Statistics 7 (4): 1898-1916. doi: 10.1214/13-AOAS671
Repo-Carrasco R, Espinoza C, Jacobsen SE (2003). Nutritional value and use of the Andean cropsquinoa (Chenopodium quinoa) and kañiwa (Chenopodium pallidicaule). Food Reviews International 19 (1-2): 179-189. doi: 10.1081/FRI-120018884
Risi JC (1984). The Chenopodium grains of the Andes: Inca crops for modern agriculture. Adv. Applied Biology 10: 145-216.
Rojas W, Pinto M, Alanoca C, Gómez Pando L, León-Lobos P et al. (2015). Quinoa genetic resources and ex situ conservation. In: State of the art report on quinoa around the world in 2013. Bazile Didier, Bertero Hector Daniel, Nieto Carlos (editors). Rome, Italy : FAO, pp. 56-82.
Romero M, Sanchez AMM, Pineda E, Ccamapaza Y, Zavalla N (2019). Genetic identity based on simple sequence repeat (SSR) markers for quinoa (Chenopodium quinoa Willd.). Ciencia e InvestigaciónAgraria 46 (2): 166-178. doi: 10.7764/rcia. v46i2.2144
Saad-Allah KM, Youssef MS (2018). Phytochemical and genetic characterization of five quinoa (Chenopodium quinoa Willd.) genotypes introduced to Egypt. Physiology and Molecular Biology of Plants 24 (4): 617-629. doi: 10.1007/s12298-018- 0541-4
Salazar J, de Lourdes Torres M, Gutierrez B, Torres AF (2019). Molecular characterization of Ecuadorian quinoa (Chenopodium quinoa Willd.) diversity: implications for conservation and breeding. Euphytica 215 (3): 60. doi: 10.1007/ s10681-019-2371-z
Smouse RPP andPeakall R (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28 (19): 2537-2539. doi: 10.1111/j.1471-8286.2005.01155.x
Team RC (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria, ISBN 3-900051-07-0. Available at: http://www.Rproject.org/.
Yeh FC, Yang R, Boyle TJ, Ye Z, Xiyan JM (2000). PopGene32, Microsoft Windows-based freeware for population genetic analysis, version 1.32. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, Alberta, Canada.
Yildiz M, Kocak M, Nadeem MA, Cavagnaro P, Barboza K et al. (2019). Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposon-based markers. Turkish Journal of Agriculture and Forestry 43. doi: 10.3906/tar-1902-10
Zhang T, Gu M, Liu Y, Lv Y, Zhou L et al. (2017). Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing. BMC Genomics 18 (1): 685. doi: 10.1186/s12864-017-4093-8