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Genetic diversity of the Andean blackberry (Rubus glaucus Benth.) in Ecuador assessed by AFLP markers

Published online by Cambridge University Press:  23 September 2020

Patricia Garrido ,
Eduardo Morillo Open the ORCID record for Eduardo Morillo [Opens in a new window]  and
Wilson Vásquez-Castillo
Patricia Garrido
Affiliation:
Instituto Nacional de Investigaciones Agropecuarias (INIAP), Estación Experimental Santa Catalina, Mejía, Ecuador Universidad UTE, Centro de Investigación de Alimentos, CIAL, Quito, Ecuador
Eduardo Morillo*
Affiliation:
Instituto Nacional de Investigaciones Agropecuarias (INIAP), Estación Experimental Santa Catalina, Mejía, Ecuador
Wilson Vásquez-Castillo
Affiliation:
Instituto Nacional de Investigaciones Agropecuarias (INIAP), Estación Experimental Santa Catalina, Mejía, Ecuador Universidad de las Américas (UDLA), Ingeniería Agroindustrial y Alimentos, Quito, Ecuador
*
*Corresponding author. E-mail: [email protected]
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Abstract

Andean blackberry (Rubus glaucus Benth.) is an emerging fruit crop with significant commercial potential. Despite its growing popularity, basic research about its genetic resources and breeding remains insufficient. The aim of this study was to assess the genetic diversity of Andean blackberry cultivars and related berries species from the main production areas in Ecuador. We analysed a total of 106 samples and performed DNA screening with different molecular markers: random-amplified polymorphic DNAs (RAPDs), inter-simple sequence repeats (ISSRs) and a set of representative samples with amplified fragment length polymorphisms (AFLPs). The tested RAPD primers did not reveal any differentiation among accessions identified as R. glaucus, however one ISSR primer was useful to find polymorphisms allowing the selection of 29 accessions for the analysis with AFLP markers. AFLP-M13 technology was used for screen genetic variations among these accessions and eight wild Rubus accessions. We scored 203 bands using five primer combinations; out of these 152 were informative in R. glaucus. AFLP markers clearly distinguish R. glaucus from the screened wild Rubus species, also an unexpected genetic structure was revealed among R. glaucus cultivars. This genetic differentiation and detection of admixed genotypes suggest a possible introgression of wild Rubus species in R. glaucus. Our findings are relevant for blackberry genetic breeding and use of these genetic resources.

Keywords

Andean blackberryDNA fingerprintingRubus diversity
Type
Research Article
Information
Plant Genetic Resources , Volume 18 , Issue 4 , August 2020 , pp. 243 - 250
Copyright
Copyright © The Author(s), 2020. Published by Cambridge University Press on behalf of NIAB

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References

Alice, LA (2002) Evolutionary relationships in Rubus (Rosaceae) based on molecular data. Acta Horticulturae 585: 79–83.10.17660/ActaHortic.2002.585.9CrossRefGoogle Scholar
Alwang, J, Barrera, V, Andrango, G, Dominguez, J, Martinez, A, Escudero, L and Montufar, C (2019) Value-chains in the Andes: upgrading for Ecuador's blackberry producers. Journal of Agricultural Economics 70: 705–730.10.1111/1477-9552.12329CrossRefGoogle Scholar
Amsellem, L, Noyer, JL and Hossaert-McKey, M (2001) Evidence for a switch in the reproductive biology of Rubus alceifolius (Rosaceae) towards apomixis, between its native range and its area of introduction. American Journal of Botany 88: 2243–2251.10.2307/3558386CrossRefGoogle ScholarPubMed
Antonius, K and Nybom, H (1995) Discrimination between sexual recombination and apomixes automixis in a Rubus plant breeding programme. Hereditas 123: 205–213.10.1111/j.1601-5223.1995.00205.xCrossRefGoogle Scholar
Ballington, J, Luteyn, J, Thompson, M, Romoleroux, K and Castillo, R (1993) Rubus and vacciniaceous germplasm resources in the Andes of Ecuador. Plant Genetic Resources Newsletter 93: 9–15.Google Scholar
Carrillo-Perdomo, E, Aller, A, Cruz-Quintana, S, Giampieri, F and Alvarez-Suarez, J (2015) Andean berries from Ecuador: a review on botany, agronomy, chemistry and health potential. Journal of Berry Research 5: 49–69.10.3233/JBR-140093CrossRefGoogle Scholar
Earl, DA (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361.10.1007/s12686-011-9548-7CrossRefGoogle Scholar
Excoffier, L, Smouse, PE and Quattro, JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479–491.Google ScholarPubMed
Graham, J, Squire, G, Marshall, B and Harrison, R (1997) Spatially dependent genetic diversity within and between colonies of wild raspberry Rubus idaeus detected using RAPD markers. Molecular Ecology 6: 1001–1008.10.1046/j.1365-294X.1997.00272.xCrossRefGoogle Scholar
Graham, J, Marshall, B and Squire, GR (2003) Genetic differentiation over a spatial environmental gradient in wild Rubus ideaus populations. New Phytologist 157: 667–675.10.1046/j.1469-8137.2003.00693.xCrossRefGoogle Scholar
Hojsgaard, D and Hörandl, E (2019) The rise of apomixis in natural plant populations. Frontiers in Plant Science 10: 358.10.3389/fpls.2019.00358CrossRefGoogle ScholarPubMed
Jennings, DL, Daubeny, HA and Moore, JN (1991) Blackberries and raspberries (Rubus). Genetic Resources of Temperate Fruit and Nut Crops 290: 331–392.Google Scholar
Kollmann, J, Steinger, T and Roy, BA (2000) Evidence of sexuality in European Rubus (Rosaceae) species based on AFLP and allozyme analysis. American Journal of Botany 87: 1592–1598.10.2307/2656735CrossRefGoogle ScholarPubMed
Lee, KJ, Lee, GA, Kang, HK, Lee, JR, Raveendar, S, Shin, MJ, Cho, YH and Ma, KH (2016) Genetic diversity and population structure of Rubus accessions using simple sequence repeat markers. Plant Breeding and Biotechnology 4: 345–351.10.9787/PBB.2016.4.3.345CrossRefGoogle Scholar
Lindqvist-Kreuze, H, Koponen, H and Valkonen, JP (2003) Genetic diversity of Arctic bramble (Rubus arcticus L. subsp. arcticus) as measured by amplified fragment length polymorphism. Canadian Journal of Botany 81: 805–813.10.1139/b03-072CrossRefGoogle Scholar
Marulanda, M, Aguilar, S and Lopez, A (2007) Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers. Crop Breeding and Applied Technology 7: 242.10.12702/1984-7033.v07n03a03CrossRefGoogle Scholar
Marulanda, M, Lopez, A and Uribe, M (2012) Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers. Genetics and Molecular Research 11: 322–331.10.4238/2012.February.10.3CrossRefGoogle ScholarPubMed
Mejía, P (2011) Caracterización morfo agronómica de genotipos de mora (Rubus glaucus Benth) en la granja experimental Tumbaco, Tesis Ing. IASA, Quito Ecuador.Google Scholar
Morillo, A, Morillo, Y, Zamorano, A, Vásquez, H and Muñoz, J (2005) Caracterización molecular con microsatélites aleatorios RAM de la Colección de mora Rubus spp. de la UNC, Sede Palmira. Acta Agronomica 54: 15–24.Google Scholar
Peakall, R and Smouse, PE (2006) GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Molecular Ecology Resources 6: 288–295.Google Scholar
Perrier, X and Jacquemoud-Collet, JP (2006) DARwin software. Available at http://darwin.cirad.fr/darwin.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google ScholarPubMed
Šarhanová, P, Sharbel, TF, Sochor, M, Vašut, RJ, Dančák, M and Trávníček, B (2017) Hybridization drives evolution of apomicts in Rubus subgenus Rubus: evidence from microsatellite markers. Annals of botany 120: 317–328.10.1093/aob/mcx033CrossRefGoogle ScholarPubMed
VanBuren, R, Bryant, D, Bushakra, JM, Vining, KJ, Edger, PP, Rowley, ER, Priest, HD, Michael, TP, Lyons, E and Filichkin, SA (2016) The genome of black raspberry (Rubus occidentalis). The Plant Journal 87: 535–547.10.1111/tpj.13215CrossRefGoogle Scholar
Viteri, P, Martínez, M, Jácome, R, Ayala, G, Villares, M, Viera, W, Sotomayor, A, Posso, M and Hinojosa, M (2016). Métodos de propagación y establecimiento del cultivo de mora. In. Galarza, D, Garcés, S, Velásquez, J, Sánchez, V and Zambrano, J Eds. El cultivo de la mora en Ecuador. Quito-Ecuador: INIAP 1: 61–76.Google Scholar
Vos, P, Hogers, R, Bleeker, M, Reijans, M, Lee, T, Hornes, M, Friters, A, Pot, J, Paleman, J and Kuiper, M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407–4414.10.1093/nar/23.21.4407CrossRefGoogle ScholarPubMed
Wang, Y, Wang, XR, Chen, Q, Zhang, L, Tang, HR, Luo, Y and Liu, ZJ (2015) Phylogenetic insight into subgenera Idaeobatus and Malachobatus (Rubus, Rosaceae) inferring from ISH analysis. Molecular Cytogenetics 8: 11.10.1186/s13039-015-0114-yCrossRefGoogle ScholarPubMed
Ward, JA, Bhangoo, J, Fernández-Fernández, F, Moore, P, Swanson, JD, Viola, R, Velasco, R, Bassil, N, Weber, C and Sargent, D (2013) Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 14: 2.10.1186/1471-2164-14-2CrossRefGoogle ScholarPubMed
Weber, C (2003) Genetic diversity in black raspberry detected by RAPD markers. HortScience 38: 269–272.10.21273/HORTSCI.38.2.269CrossRefGoogle Scholar
Williams, JG, Kubelik, AR, Livak, K, Rafalski, J and Tingey, S (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18: 6531–6535.10.1093/nar/18.22.6531CrossRefGoogle ScholarPubMed
Zietkiewicz, E, Rafalski, A and Labuda, D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20: 176–183.10.1006/geno.1994.1151CrossRefGoogle ScholarPubMed