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.摘要：光滑悬钩子（Rubus glaucus Benth，俗称卡斯蒂利亚黑莓（mora de castilla））是哥伦比亚极具开发潜力的特色农产品，该果实兼具树莓亚属（Idaeobatus）与悬钩子亚属（Rubus subgenera）的双重特征。尽管其对小型种植户的经济价值已得到广泛认可，但该作物的技术研发程度仍相对滞后，目前该物种的种植仍依赖种植户无性繁殖的本地品种。哥伦比亚本土的悬钩子种植从业者已意识到，需通过启动植物育种项目，培育兼具更高产量与更便于田间管理的形态学性状的新品种，以此规范种植材料的供应体系。本研究基于此前转录组RNA测序（RNA-Seq）实验中获得的简单序列重复（Simple Sequence Repeats, SSR）与单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）标记，对相关实验结果进行评估，本次研究共评估了15个具有应用前景的光滑悬钩子品种，这些品种可作为未来育种计划中的潜在亲本材料。研究通过22对SSR微卫星标记与78个SNP标记完成遗传鉴定：其中15对SSR标记可获得有效聚合酶链式反应（PCR）扩增产物，共扩增得到29个基因位点与58个等位基因；78个SNP标记中，36个可获得有效PCR扩增产物，经测序验证的SNP扩增产物序列与蔷薇科（Rosaceae）物种的同源性较高。亲本材料的筛选标准基于分子鉴定结果与便于田间管理的形态学性状制定，本研究证实了分子标记在评估植物育种可用潜在亲本遗传多样性中的应用价值，而亲本群体的构建作为植物育种流程的核心环节，在极大程度上决定了育种项目的最终成败。