Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers

The common bean (Phaseolus vulgaris L.) is an important crop throughout the world and is highly recommended for many developing countries due to its nutritional components. A retrotransposon-based DNA marker system, interprimer binding sites (iPBSs), developed from reverse transcriptase primer binding sites, was used to determine genetic diversity in common bean accessions. The genetic polymorphism and effectiveness of the marker system were evaluated. A total of 180 polymorphic bands were detected using 47 iPBS primers among 67 common bean accessions, with an average of 4 polymorphic fragments per primer. The genetic similarity between accessions was calculated using the software NTSYS-pc and ranged from 0.09 to 0.99. The average polymorphism information content value for the iPBS markers was 0.73. A model-based clustering method classified the common bean accessions into 4 populations using STRUCTURE software. The results indicated that the iPBS marker method can successfully determine the genetic diversity level in common bean accessions.

Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers

The common bean (Phaseolus vulgaris L.) is an important crop throughout the world and is highly recommended for many developing countries due to its nutritional components. A retrotransposon-based DNA marker system, interprimer binding sites (iPBSs), developed from reverse transcriptase primer binding sites, was used to determine genetic diversity in common bean accessions. The genetic polymorphism and effectiveness of the marker system were evaluated. A total of 180 polymorphic bands were detected using 47 iPBS primers among 67 common bean accessions, with an average of 4 polymorphic fragments per primer. The genetic similarity between accessions was calculated using the software NTSYS-pc and ranged from 0.09 to 0.99. The average polymorphism information content value for the iPBS markers was 0.73. A model-based clustering method classified the common bean accessions into 4 populations using STRUCTURE software. The results indicated that the iPBS marker method can successfully determine the genetic diversity level in common bean accessions.

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  • Andeden EE, Baloch FS, Derya M, Kilian B, Ozkan H (2013). iPBS- Retrotransposons-based genetic diversity and relationship among wild annual Cicer species. J Plant Biochem Biot 22: 453–466.
  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993). Optimizing parental selection for genetic linkage maps. Genome 36: 181–186.
  • Arumuganthan K, Earle E (1991). Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208–218.
  • Baranek M, Meszaros M, Sochorova J, Cechova J, Raddova J (2012). Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovicka. Sci Hortic-Amsterdam 143: 1–6.
  • Bleykasten-Grosshans C, Neuveglise C (2011). Transposable elements in yeasts. Cr Biol 334: 679–686.
  • Brandt J, Schrauth S, Veith AM, Froschauer A, Haneke T, Schultheis C, Gessler M, Leimeister C, Volff JN (2005). Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. Gene 345: 101–111.
  • Breto MP, Ruiz C, Pina JA, Asins MJ (2001). The diversification of Citrus clementina hort. ex tan., a vegetatively propagated crop species. Mol Phylogenet Evol 21: 285–293.
  • Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003). Beans (Phaseolus spp.) – model food legumes. Plant Soil 252: 55–128.
  • Casacuberta JM, Santiago N (2003). Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. Gene 311: 1–11.
  • Castro I, D’Onofrio C, Martin JP, Ortiz JM, De Lorenzis G, Ferreira V, Pinto-Carnide O (2012). Effectiveness of AFLPs and retrotransposon-based markers for the identification of Portuguese grapevine cultivars and clones. Mol Biotechnol 52: 26–39.
  • Chen FY, Liu JH (2014). Germplasm genetic diversity of Myrica rubra in Zhejiang Province studied using inter-primer binding site and start codon-targeted polymorphism markers. Sci Hortic-Amsterdam 170: 169–175.
  • Earl D, vonHoldt B (2011). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361.
  • Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611–2620.
  • FAO (2010). Food and Agriculture Organization of the United Nations.
  • Ferreira JL, Carneiro JED, Teixeira AL, de Lanes FF, Cecon PR, Borem A (2007). Gene flow in common bean (Phaseolus vulgaris L.). Euphytica 153: 165–170.
  • Gailite A, Rungis D (2012). An initial investigation of the taxonomic status of Saussurea esthonica Baer ex Rupr. utilising DNA markers and sequencing. Plant Syst Evol 298: 913–919.
  • Gepts P, Francisco JL, Everaldo de Barros A, Blair MW, Brondani R, Broughton W, Galasso I, Hernández G et al. (2008). Chapter 5: Genomics of Phaseolus beans, a major source of dietary protein and micronutrients in the tropics. In: Genomics of Tropical Crop Plants. Philadelphia, PA, USA: Springer, pp. 112–144.
  • Guo C, Guo R, Xu X, Gao M, Li X, Song J, Zheng Y, Wang X (2014a). Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family. J Exp Bot 65: 1513–1528.
  • Guo DL, Guo MX, Hou XG, Zhang GH (2014b). Molecular diversity analysis of grape varieties based on iPBS markers. Biochem Syst Ecol 52: 27–32.
  • Guo DL, Hou XG, Zhang X (2014c). A simple and efficient method to isolate LTR sequences of plant retrotransposon. Biomed Res Int DOI 10.1155/2014/658473.
  • Guo XQ, Elston RC (1999). Linkage information content of polymorphic genetic markers. Hum Hered 49: 112–118.
  • Hamrick J, Loveless M (1989). The genetic structure of tropical tree populations: associations with reproductive biology. Evol Ecol Plant 33: 129–146.
  • Josias CF, Carneiro GES, Aragão FJL (2010). Gene flow from transgenic common beans expressing the bar gene. GM Crops 1: 94–98.
  • Kalendar R, Antonius K, Smykal P, Schulman AH (2010). iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 121: 1419–1430.
  • Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, Schulman AH (2011). Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106: 520–530.
  • Kumar A, Bennetzen JL (1999). Plant retrotransposons. Annu Rev Genet 33: 479–532.
  • Labra M, Imazio S, Grassi F, Rossoni M, Sala F (2004). Vine- 1 retrotransposon-based sequence-specific amplified polymorphism for Vitis vinifera L. genotyping. Plant Breeding 123: 180–185.
  • Mehmood A, Jaskani MJ, Ahmad S, Ahma, R (2013). Evaluation of genetic diversity in open pollinated guava by iPBS primers. Pak J Agr Sci 50: 591–597.
  • Monden Y, Yamaguchi K, Tahara M (2014). Application of iPBS in high-throughput sequencing for the development of retrotransposon-based molecular markers. Current Plant Biology 1: 40–44.
  • Nemli S, Kaya HB, Tanyolac B (2014a). Genetic assessment of common bean (Phaseolus vulgaris L.) accessions by peroxidase gene-based markers. J Sci Food Agr 94: 1672–1680.
  • Nemli S, Kaygisiz Asciogul T, Kaya H, Kahraman A, Esiyok D, Tanyolac B (2014b). Association mapping for five agronomic traits in the common bean (Phaseolus vulgaris L.) J Sci Food Agric 94: 3141–3151.
  • Pritchard J, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945– 959.
  • Rohlf F (1988). NTSYS-PC Numerical Taxonomy and Multivariate Analysis System. New York, NY, USA: Exeter Publishing.
  • Saghai-Maroof M, Soliman K, Jorgensen R, Allard R (1984). Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81: 8014–8018.
  • Sanz AM, Gonzalez SG, Syed NH, Suso MJ, Saldana CC, Flavell AJ (2007). Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers. Mol Genet Genomics 278: 433–441.
  • Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C et al. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46: 707–713.
  • Sensi E, Vignani R, Scali M, Masi E, Cresti M (2003). DNA fingerprinting and genetic relatedness among cultivated varieties of Olea europaea L. estimated by AFLP analysis. Scientia Horticulturae 97: 379–388.
  • Sharma V, Nandineni MR (2014). Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems. Mol Phylogenet Evol 73: 10–17.
  • Shen YY, Ding XJ, Wang F, Cai BH, Gao ZH, Zhang Z (2011). Analysis of genetic diversity in Japanese apricot (Prunus mume Sieb. et Zucc.) based on REMAP and IRAP molecular markers. Sci Hortic-Amsterdam 132: 50–58.
  • Smykal P, Bacova-Kerteszova N, Kalendar R, Corander J, Schulman AH, Pavelek M (2011). Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theor Appl Genet 122: 1385– 1397.
  • Xu ZJ, Ramakrishna W (2008). Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history. Gene 412: 50–58.
  • Zecca G, Abbott JR, Sun WB, Spada A, Sala F, Grassi F (2012). The timing and the mode of evolution of wild grapes (Vitis). Mol Phylogenet Evol 62: 736–747.
  • Žiarovská J, Ražná K, Senková S, Štefşnová V, Bežo M (2012). Variability of Linum usitatissimum L. based on molecular markers. ARPN Journal of Agricultural and Biological Science 7: 50–58.
Turkish Journal of Agriculture and Forestry-Cover
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  • Yayın Aralığı: Yılda 6 Sayı
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