Duplication assessments in<i>Brassica</i>vegetable accessions

Solberg, Svein Øivind; Artemyeva, A. M.; Yndgaard, Flemming; Dorre, Malin; Niss, Jerker; Burleigh, Stephen

doi:10.1017/s1479262117000156

Cited by 3 publications

(2 citation statements)

References 19 publications

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“…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.…”

Section: Current Status Of B Oleracea and B Rapa Vegetable Collectionsmentioning

confidence: 99%

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

2021

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Germplasm collections reflect the genetic variability in crops and their wild relatives. Hence, those genetic resources are tremendously valuable for breeders and researchers, especially in light of climatic change and stagnant crop production rates. In order to achieve improvements in crop production and end-use quality, favorable traits and donor alleles present in germplasm collections need to be identified and utilized. This review covers recent reports on the utilization of germplasm material to isolate genotypes of Brassica oleracea and B. rapa vegetables, focusing on high nutrient use efficiency, accumulation of biologically active metabolites, pest resistance, and favorable phenotypic appearance. We discuss the current state of Brassica vegetable collections in genebanks and summarize studies directed to the molecular characterization of those collections.

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Section: Current Status Of B Oleracea and B Rapa Vegetable Collectionsmentioning

confidence: 99%

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

2021

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“…In total, 980 cabbage accessions are maintained at VIR and 189 at NGB. An initial study [46] characterized six groups for morphological traits, and some differences within the groups could be detected. In this study, another 10 groups (Table 1) were examined to see if there were differences among accessions within a group.…”

Section: Plant Material Cultivation and Morphological Characterizationmentioning

confidence: 99%

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

Palmé¹,

Hagenblad

Solberg

et al. 2020

Plants

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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.

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G-DIRT: a web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data

Sahu

Singh

Mittal

et al. 2022

Briefings in Bioinformatics

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Maintaining duplicate germplasms in genebanks hampers effective conservation and utilization of genebank resources. The redundant germplasm adds to the cost of germplasm conservation by requiring a large proportion of the genebank financial resources towards conservation rather than enriching the diversity. Besides, genome-wide-association analysis using an association panel with over-represented germplasms can be biased resulting in spurious marker-trait associations. The conventional methods of germplasm duplicate removal using passport information suffer from incomplete or missing passport information and data handling errors at various stages of germplasm enrichment. This limitation is less likely in the case of genotypic data. Therefore, we developed a web-based tool, Germplasm Duplicate Identification and Removal Tool (G-DIRT), which allows germplasm duplicate identification based on identity-by-state analysis using single-nucleotide polymorphism genotyping information along with pre-processing of genotypic data. A homozygous genotypic difference threshold of 0.1% for germplasm duplicates has been determined using tetraploid wheat genotypic data with 94.97% of accuracy. Based on the genotypic difference, the tool also builds a dendrogram that can visually depict the relationship between genotypes. To overcome the constraint of high-dimensional genotypic data, an offline version of G-DIRT in the interface of R has also been developed. The G-DIRT is expected to help genebank curators, breeders and other researchers across the world in identifying germplasm duplicates from the global genebank collections by only using the easily sharable genotypic data instead of physically exchanging the seeds or propagating materials. The web server will complement the existing methods of germplasm duplicate identification based on passport or phenotypic information being freely accessible at http://webtools.nbpgr.ernet.in/gdirt/.

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Duplication assessments inBrassicavegetable accessions

Cited by 3 publications

References 19 publications

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

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

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

G-DIRT: a web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data

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