SNP Markers and Evaluation of Duplicate Holdings of Brassica oleracea in Two European Genebanks

Abstract

Around the world, there are more than 1500 genebanks storing plant genetic resources to be used in breeding and research. Such resources are essential for future food security, but many genebanks experience backlogs in their conservation work, often combined with limited budgets. Therefore, avoiding duplicate holdings is on the agenda. A process of coordination has started, aiming at sharing the responsibility of maintaining the unique accessions while allowing access according to the international treaty for plant genetic resources. Identifying duplicate holdings based on passport data has been one component of this. In the past, and especially in vegetables, different selections within the same varieties were common and the naming practices of cultivars/selections were flexible. Here, we examined 10 accession pairs/groups of cabbage (Brassica oleracea var. capitata) with similar names maintained in the Russian and Nordic genebanks. The accessions were analyzed for 11 morphological traits and with a SNP (Single Nucleotide Polymorphism) array developed for B. napus. Both proved to be useful tools for understanding the genetic structure among the accessions and for identifying duplicates, and a subset of 500 SNP markers are suggested for future Brassica oleracea genetic characterization. Within five out of 10 pairs/groups, we detected clear genetic differences among the accessions, and three of these were confirmed by significant differences in one or several morphological traits. In one case, a white cabbage and a red cabbage had similar accession names. The study highlights the necessity to be careful when identifying duplicate accessions based solely on the name, especially in older cross-pollinated species such as cabbage.

Plant Biodiversity and Genetic Resources Matter!

“…As crop wild relatives are mostly found in the wild and are rather difficult to be conserved ex situ, the merits of payment for ecosystem services for in situ conservation have been analyzed by Tyak et al [21] for these germplasm resources, which are increasingly coming into the focus of plant breeders, given their broad genetic diversity, harboring many (new) traits of interest to build resistance to diseases and insect pests as well as tolerance to abiotic stresses into resilient modern crop cultivars. With respect to germplasm management, an example of the use of single nucleotide polymorphisms (SNP) markers for the identification of duplicate accessions of Brassica oleracea in genebank collections has been presented [22], while another paper highlights the importance of information management to assist in germplasm and genebank management and to enhance the use of germplasm [23]. Genebank phenomics is a rather novel approach in modern genebanking, and Nguyen and Norton [24] shed light on digital phenotyping methods that enable capturing traits during annual seed regeneration events to enrich genebank phenotypic datasets, thus adding value to crop collections and increasing their usefulness for the identification of traits of interest for breeding.…”

A Critical Review of the Current Global Ex Situ Conservation System for Plant Agrobiodiversity. II. Strengths and Weaknesses of the Current System and Recommendations for Its Improvement

“…Combining phenotyping and genotyping with single sequence repeats (SSR) markers allowed the identification of duplicate accessions in lettuce ( Lactuca sativa ) and the determination of the most appropriate accessions (MAA) for inclusion into AEGIS [ 84 ]. Similarly, the combination of morphological characterization with genotyping using an SNP (single nucleotide polymorphism) array, originally developed for Brassica napus, allowed the identification of duplicate accessions in Brassica oleracea, and a subset of 500 SNP markers have been suggested for genotyping Brassica oleracea accessions [ 85 ].…”

“…During the period from 2017 to 2019, landraces were the most frequently requested materials (50%), followed by breeding materials (24%) and crop wild relatives (13%). Most samples were distributed to advanced research institutes and universities (42%), followed by National Agricultural Research Systems (NARS; 38%), Non-Governmental Organizations (NGOs) and farmers (85), the commercial sector (7%), and others (5%) [47].…”

Opening the Treasure Chest: The Current Status of Research on Brassica oleracea and B. rapa Vegetables From ex situ Germplasm Collections

“…For example, the VIR passport database is based on 28 characteristics and includes all accessions from the collections; the characterization and evaluation databases include 60–90% accessions depending of crops, while also a separate trait database is operated for characteristics of genetic and breeding interest. Hence, a proportion of material consists of unwanted duplications that need to be identified and minimized within and between collections ( Solberg et al, 2018 ; Palme et al, 2020 ). A further issue is the taxonomic misclassification of accessions.…”