Morphological and Molecular Characterization of Iranian Wild Blackberry Species Using Multivariate Statistical Analysis and ISSR Markers

Document Type : Research paper

Authors

1 Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran

2 Institute of Biotechnology, Shiraz University, Shiraz, Iran

Abstract

This study was carried out to estimate the genetic diversity and relationships of 74 Iranian blackberry accessions assigned to 5 different species using inter-simple sequence repeats (ISSR) marker analysis and morphological trait characterization. Sixteen traits were analyzed, including phenological, vegetative and reproductive attributes (in 57 out of 74 accessions), and 10 ISSR primers were screened (in 74 accessions).  The yield and leaf width had the highest and lowest genetic diversity, (diversity index = 62.57 and 13.74), respectively. Flowering and ripening date were recorded as traits with the strongest correlations (r = 0.98). Ten ISSR primers were selected and produced a total of 161 amplified fragments (200 to 3500 bp), of which 113 were polymorphic. The highest, lowest and average PIC values were 0.53, 0.38 and 0.44, respectively. Principle component analysis (PCA) was based on morphological traits and showed that the first six components explained 84.9% of the variations among the traits. Meanwhile, the principal coordinate analysis (PCoA) was based on ISSR data and implied the first eight principal coordinates which explained 67.06% of the total variation. Cluster analysis was based on morphological traits and ISSR data ultimately classified all accessions into two and three major groups, respectively, so that the distribution pattern of genotypes was mainly based on species and the geographic origins.

Keywords


  1. Ahmed M, Anjum MA, Khaqa K, Hussain S. 2014. Biodiversity in morphological and physico-chemical characteristics of wild raspberry (Rubus idaeus L.) germplasm collected from temperate region of Azad Jammu & Kashmir (Pakistan). Acta Scientiarum Polonorum-Hortorum Cultus 13(4), 117-134.

    Amsellem L, Bourgeois TL, Noyer JL, Hossaert-Mckey M. 2001. Comparison of Genetic Diversity of the Weed Rubus alceifolius in its Introduced and Native Areas. Proceedings of the X International Symposium on Biological Control of Weeds 4-14 July, Montana State University, Bozeman, Montana, USA Neal R. Spencer [ed.]. 2001; pp. 253-260.

    Castillo N, Reed B, Graham J, Fernandez-Fernandez F, Bassil NV. 2010. Microsatellite markers for raspberry and blackberry. Journal of the American Society for Horticultural Science 135, 271–278.

    Clark JR, Finn CE. 2011. Blackberry breeding and genetics. Fruit, Vegetable and Cereal Science and Biotechnology 5 (1), 27-43. Global Science Books.

    Dossett M, Finn CE. 2016. Performance and phenology of wild black raspberry (Rubus occidentalis L.) germplasm in a common garden. Genetic Resources and Crop Evolution 63, 653–673. https://doi.org/10.1007/s10722-015-0274-y.

    Dossett M, Bassil NV, Lewers KS, Finn CE. 2012. Genetic diversity in wild and cultivated black raspberry (Rubus occidentalis L.) evaluated by simple sequence repeat markers. Genetic Resources and Crop Evolution 59, 1849–1865. https://doi.org/10.1007/s10722-012-9808-8.

    Finn CE, Clark JR. 2012. Blackberry. In: Badenes, M.L. and D.H. Byrne (eds.). Handbook of plant breeding: Volume 8: Fruit breeding. Springer, New York, NY. p 151–190.

    Garazhian M, Gharaghani A, Eshghi S. 2020. Genetic diversity and inter‑relationships of fruit bio‑chemicals and antioxidant activity in Iranian wild blackberry species. Scientific Reports 10, 18983. https://doi.org/10.1038/s41598-020-75849-1.

    Gharaghani A, Momeni SHA, Eshghi S. 2014. Comparing fruit quantitative and chemical properties of wild blackberry (Rubus sanctus Schreb) genotypes from north and south of Iran. Acta Horticulturae 1074, 59-66.

    Glisic I, Milosevic T, Veljkovic B, Glisic I, Milosevic N. 2009. Trellis height effect on the production characteristics of raspberry. Acta Horticulturae 825, 389–393.

    Graham J, Hackett C, Smith K, Woodhead M, Hein I, MacKenzie K, McCallum S. 2009. Mapping QTL for developmental traits in raspberry from bud break to ripe fruit. Theoretical and applied genetics 118, 1143-1155.

    Graham J, Marshall B, Squire GR. 2003. Genetic differentiation over a spatial environmental gradient in wild Rubus ideaus populations. New Phytologist 2003, 157, 667–675.

    Graham J, Woodhead M. 2011. Rubus. In: Volume 6 (Relatives of Temperate Fruits) of the book series, "Wild Crop Relatives: Genetic, Genomic and Breeding Resources (ed) C. Kole. p 179-197.

    Hammer Q, Harper DAT, Ryan PD. 2001. Paleontological statistics software: Package for education and data analysis. Palaeontologia Electron 4 (1), 1-9.

     Hong YP, Kim MJ, Hong, KN. 2003. Genetic diversity in natural populations of two geographic isolates of Korean black raspberry. The Journal of Horticultural Science and Biotechnology 78, 350–354.

     Hummer KE. 2010. Rubus Pharmacology: Antiquity to the Present. HortScience 45(11), 1587-1591.

    Innis AF, Forseth IN, Whigham DF, McCormick MK. 2011. Genetic diversity in the invasive Rubus phoenicolasius as compared to the native Rubus argutus using inter-simple sequence repeat (ISSR) markers.

    Biological Invasions 13, 1735–1738. https://doi.org/10.1007/s10530-011-0012-0.

    Khanuja SPS, Shasany AK, Darokar MP, Kumar S. 1999. Rapid Isolation of DNA from Dry and Fresh Samples of Plants Producing Large Amounts of Secondary Metabolites and Essential Oils. Plant Molecular Biology Reporter 17(1), 74–74.

    Khatamsaz M. 1992. Flora of Iran (Rosaceae) (eds. Assadi M, Khatamsaz M, and Maassoumi A A). Research institute of forests and rangelands publication, Tehran, Iran (in Persian). 6, 20-35.

    Khadivi-Khub A, Anjam K. 2014. Morphological characterization of Prunus scoparia using multivariate analysis. Plant Systematics and Evolution 300(6), 1361-1372.

    Lee KJ, Lee GA, Kang HK, Lee JR, Raveendar S, Shin MJ, Cho YH, Ma KH. 2016. Genetic Diversity and population structure of Rubus accessions using simple sequence repeat markers. Plant Breeding and Biotechnology 4(3), 345-351.  https://doi.org/10.9787/PBB.2016.4.3.345.   

    Lewers KS, Wang SY, Vinyard BT. 2010. Evaluation of blackberry cultivars and breeding selections for fruit quality traits and flowering and fruiting dates. Crop Science 50, 2475–2491.

    Maro LAC, Pio R, Guedes MNS, Abreu CMP, Moura PHA. 2014. Environmental and genetic variation in the post-harvest quality of raspberries in subtropical areas in Brazil. Acta Scientiarum 36(3), 323-328. https://doi.org/10.4025/actasciagron.v36i3.18050.     

    Minitab Inc. 1998. Minitab reference manual, version 16, Chikago, Minitab, Inc.

    Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A. 1996 The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2, 225–238.

    Perasovic I. 2013. Red raspberry (Rubus idaeus L.) cultivars in a Nordic climate-morphological traits and berry quality. Master Thesis 60 credits 2013. Department of Plant and Environmental Sciences, IPM.

    Rohlf FJ. 2000. NTSYS-pc Numerical taxonomy and multivariate analysis system, version 2.01. Setauket New York: Applied Biostatistics.

    Ryabova D. 2007. An evaluation of Rubus idaeus L. Genetic Resources and Crop Evolution 54, 973–980.

    1. Ryu J, Ha BK, Kim DS, Kim JB, Kim SH, Ahn JW, Jeong IY, Jo HJ, Kim EY, Kang SY. 2014. Genetic Diversity and Relationship Assessment based on AFLP Analysis in Blackberry (Rubus fructicosus L.) Mutant Lines. Plant Breeding and Biotechnology 2(4), 386-395.

    Sedighi E, Rahimmalek M. 2015. Evaluation of genetic diversity of Rubus hyrcanus using Inter Simple Sequence Repeat (ISSR) and morphological markers. Biologia 70(3), 339-348 (Section Botany) https://doi.org/10.1515/biolog-2015-0039.

    Singh D, Kumar K, Sharma VK, Singh M. 2009. Expression of genetic variability and character association in raspberry (Rubus ellipticus Smith) growing wild in North-Western Himalayas. Journal of Horticultural Science 4 (1), 28-31.

    Sonsteby A, Myrheim U, Heiberg N, Heide OM. 2009. Production of high yielding red raspberry long canes in a Northern climate. Scientia Horticulturae 121(3), 289-297.

    Sorkheh K, Shiran B, Rouhi V, Asadi E, Jahanbazi H, Moradi H, Gradziel TM, Martinez-Gomez P. 2009. Phenotypic diversity within native Iranian almond (Prunus spp.) species and their breeding potential. Genetic Resources and Crop Evolution 56(7), 947.

    UPOV. 2006. UPOV, Report on the Impact of Plant Variety Protection, p. 125.

    Weber CA, Maloney KE, Sanford JC. 2005. Performance of Eight Primocane Fruiting Red Raspberry Cultivars in New York. Small Fruits Review 4(2), 41-47, https://doi.org/10.1300/J301v04n02_05.

     

    Yazdanpour F, Khadivi A, Etemadi-Khah A. 2018. Phenotypic characterization of black raspberry to select the promising genotypes. Scientia Horticulturae 235, 95-105.

    Yilmaz KU, Zengin Y, Ercisli S, Serce S, Gunduz K, Sengul M, Asma BM. 2009. Some selected physico-chemical characteristics of wild and cultivated blackberry fruits (Rubus fruticosus L.) from Turkey. Rom Society Biology Science 14(1), 4152-4163.