Evaluation of SSR and SNP markers in Rubus glaucus Benth progenitors selection

Abstract

Rubus glaucus Benth (known as “mora de castilla”) is a Colombian agricultural product, with probably, the major potential. This fruit combines features of Idaeobatus and Rubus subgenera. Despite its recognized importance in the economy of small producers, this crop has received little technological development; as a result, sowing procedures of this specie is done by using local cultivars asexually propagated by producers. Associated Rubus producers in Colombia has noticed the necessity to formalize the offer of planting material, starting with plant breeding programs tending to the obtention of more productive varieties with morphological features that facilitates cultural activities. This study presents the results of the evaluation of SSR and SNPs markers obtained in previous experimental works from a RNA-Seq transcriptome analysis. It was evaluated 15 promissory R. glaucus cultivars, which could be potential progenitors in future breeding schemes. Genetic characterization was accomplished by testing 22 SSR microsatellite and 78 single nucleotide polymorphisms (SNPs) markers. From evaluated SSR markers, 15 yielded positive PCR amplification generating 29 loci and 58 alleles. From evaluated SNPs markers, 36 yielded positive PCR amplification. Obtained sequences from amplified products with SNPs showed high homology with species belonging to Rosaceae family. Selection criteria of progenitors were based on the results of molecular characterizations and useful morphological features in the culture management. This research demonstrates the utility of molecular markers to assess genetic diversity of potential progenitors susceptible to plant breeding processes. This process, highly known as development of parental populations, determines in a great manner the success of plant breeding processes.

Molecular characterization of a species in the genus Rubus in Boyacá, Colombia

“…The markers used for this characterization are shown in table 2. Seven of them were homologous and coded by CL and Rg, used by LÓPEZ et al (2019); MARULANDA et al (2012) and developed by the Universidad Tecnológica de Pereira. Four microsatellite markers were used from the "Rubus" series, developed by CASTILLO (2006) for the species R. idaeus and the cultivar called Marion corresponding to a Rubus hybrid.…”

“…However, this genus of plants is difficult to identify due to its frequent hybridization and apomixis. This leads to cultivars of similar morphology which makes testing for SSR markers (Simple sequence repeats) in this genus of plants of enormous interest (LÓPEZ et al, 2019). This procedure has contributed to the selection of species that present agronomic potential, provide reliable identification, and allow the genetic diversity of populations to be measured (ROA et al, 2014;MARULANDA et al, 2012).…”

“…Studies were performed to identify the genetic diversity of cultivars in different locations in Venezuela (ROA et al, 2014) and from 32 Rubus cultivars in Europe and the United States with differences in ploidy and berry color. Additionally, LÓPEZ et al (2019) recently evaluated the genetic diversity of parental plants in Colombia, which are used in the process of reproduction or development of parental populations, based on their morphology and tolerance to C. gloeosporioides.…”

Molecular markers in the genetic diversity studies of representatives of the genus <i>Rubus</i> L. and prospects of their application in breeding

“…В дальнейшем многочисленные группы исследователей создавали наборы SSR-маркеров для разных видов малин и ежевик: R. hochstetterorum (Lopes et al, 2006), R. occidentalis (Dossett et al, 2012a), R. coreanus (Lee et al, 2015), R. glaucus (López et al, 2019), а также сортов ежевики (Lewers et al, 2008). В ряде работ были разработаны мультиплексные системы (Fernández-Fernández et al, 2011;Zurn et al, 2018), разрешающую способность которых проверяли на разных моделях.…”

“…Полногеномное секвенирование позволяет одновременно генерировать огромное количество SNP-марке ров, которые применяют для создания генетических карт (Ward et al, 2013;Hackett et al, 2018), идентификации генов устойчивости к патогенам, например к Verticillium , а также для картирования хозяйственно ценных признаков (López et al, 2019). В работе J.…”