Table_2_Usefulness of a New Large Set of High Throughput EST-SNP Markers as a Tool for Olive Germplasm Collection Management.XLSX

Germplasm collections are basic tools for conservation, characterization, and efficient use of olive genetic resources. The identification of the olive cultivars maintained in the collections is an important ongoing task which has been performed by both, morphological and molecular markers. In the present study, based on the sequencing results of previous genomic projects, a new set of 1,043 EST-SNP markers has been identified. In order to evaluate its discrimination capacity and utility in diversity studies, this set of markers was used in a representative number of accessions from 20 different olive growing countries and maintained at the World Olive Germplasm Collection of IFAPA Centre ‘Alameda del Obispo’ (Córdoba, Spain), one of the world’s largest olive germplasm bank. Thus, the cultivated material included: cultivars belonging to previously defined core collections by means of SSR markers and agronomical traits, well known homonymy cases, possible redundancies previously identified in the collection, and recently introduced accessions. Marker stability was tested in repeated analyses of a selected number of accessions, as well as in different trees and accessions belonging to the same cultivar. In addition, 15 genotypes from a cross ‘Picual’ × ‘Arbequina’ cultivars from the IFAPA olive breeding program and a set of 89 wild genotypes were also included in the study. Our results indicate that, despite their relatively wide variability, the new set of EST-SNPs displayed lower levels of genetic diversity than SSRs in the set of olive core collections tested. However, the EST-SNP markers displayed consistent and reliable results from different plant material sources and plant propagation events. The EST-SNPs revealed a clear cut off between inter- and intra-cultivar variation in olive. Besides, they were able to reliably discriminate among different accessions, to detect possible homonymy cases as well as efficiently ascertain the presence of redundant germplasm in the collection. Additionally, these markers were highly transferable to the wild genotypes. These results, together with the low genotyping error rates and the easy and fully automated procedure used to get the genotyping data, validate the new set of EST-SNPs as possible markers of choice for olive cultivar identification.

种质资源库是保护、鉴定与高效利用橄榄遗传资源的基础工具。对种质库中保存的橄榄品种进行鉴定，是一项持续开展的重要工作，目前已通过形态标记与分子标记两种手段完成。本研究基于既往基因组项目的测序结果，开发出一套包含1043个表达序列标签-单核苷酸多态性（EST-SNP）标记的新型标记集。为评估该套标记的鉴别能力与在遗传多样性研究中的应用价值，研究团队将其应用于来自20个不同橄榄种植国、保存于西班牙科尔多瓦IFAPA中心“阿拉米达·德尔·奥比斯波”世界橄榄种质资源库（全球规模最大的橄榄种质库之一）的代表性种质样本。本次研究的栽培材料涵盖：通过简单序列重复（SSR, Simple Sequence Repeat）标记与农艺性状确定的既往核心种质集品种、已知的同物异名案例、种质库中此前鉴定出的潜在冗余样本，以及新引入的种质材料。研究人员针对部分筛选出的种质样本开展重复分析，并对同一品种的不同植株及种质样本进行检测，以验证标记的稳定性。此外，本研究还纳入了IFAPA橄榄育种项目中培育的‘皮夸尔’（Picual）ב阿尔贝吉纳’（Arbequina）杂交组合的15份基因型材料，以及89份野生橄榄基因型样本。研究结果显示：尽管该套EST-SNP标记存在一定的变异范围，但在本次测试的橄榄核心种质集样本中，其检测到的遗传多样性水平低于SSR标记。不过，无论采用不同的植物材料来源或是不同的繁殖方式，EST-SNP标记均能产出稳定可靠的检测结果。EST-SNP标记可清晰区分橄榄品种间与品种内的遗传变异。此外，该标记集可准确鉴别不同种质样本，检测潜在的同物异名情况，并高效确认种质库中冗余种质的存在。此外，该套标记对野生基因型材料具有极高的跨扩增性。结合较低的基因分型错误率与获取基因分型数据时简便且完全自动化的实验流程，上述结果证实该套新型EST-SNP标记可作为橄榄品种鉴定的优选标记。