Microsatellite markers as a tool for active germplasm management and bridging the gap between national and local collections of apple

Abstract

Simple sequence repeat (SSR) microsatellite markers have been extensively used to identify duplication and analyse genetic diversity in germplasm collections of apple. Here, we present findings from the use of a standard set of SSR loci in the managed repropagation of a significant international germplasm collection: the UK National Fruit Collection (NFC). A subset of eight SSR loci was deemed sufficient to distinguish all apart from the clonal relatives across a sample of 1995 accessions, with a single exception being one pair of full siblings. In total, 99% of accessions were able to be confirmed present and correct after the replacement of trees initially identified to be incorrectly propagated. In parallel to the curation of the collection itself, through an initiative led by the UK local apple enthusiast community, 3373 SSR profiles for apples held in local collections were compared to the NFC holdings. Overall, in both sets of material, diversity remained high with average gene diversity values of 0.800 and 0.812 in the NFC holdings and local collections, respectively. Accessions in local collections were not found to differ in their overall coverage of genetic diversity to that of the NFC collection (FST = 0.0035) although significant numbers of locally valued, and genetically distinguishable individuals were identified, some of which may represent ‘lost’ cultivars.

What's in a name? The importance of identity in heirloom apple tree preservation

“…The success of genotyping for identification (Method S1b) is dependent upon having reference DNA fingerprints available for large collections of verified-identity cultivars, such as the reference specimens available in genebanks (including the USDA National Plant Germplasm System Apple Collection in Geneva, NY), heirloom orchards, and breeding collections (Gutierrez et al, 2020). Small sets of microsatellite markers were used to characterize apple cultivar collections (Gross et al, 2012;Guilford et al, 1997), which provided genotypic datasets that then served as reference panels for identifying unknown cultivars (Venison et al, 2022;Volk et al, 2021aVolk et al, , 2021b, cultivar synonyms, and mislabeled accessions (e.g., Evans et al, 2011;Gross et al, 2012). These genotypic datasets were useful but limited because of difficulties such as comparing datasets among laboratories (Evans et al, 2011;Gross et al, 2012;Venison et al, 2022).…”

“…Small sets of microsatellite markers were used to characterize apple cultivar collections (Gross et al, 2012;Guilford et al, 1997), which provided genotypic datasets that then served as reference panels for identifying unknown cultivars (Venison et al, 2022;Volk et al, 2021aVolk et al, , 2021b, cultivar synonyms, and mislabeled accessions (e.g., Evans et al, 2011;Gross et al, 2012). These genotypic datasets were useful but limited because of difficulties such as comparing datasets among laboratories (Evans et al, 2011;Gross et al, 2012;Venison et al, 2022). Despite limitations, these efforts resulted in establishing the cultivar identities of hundreds of heirloom trees in the North American landscape (Routson et al, 2009;Volk et al, 2021aVolk et al, , 2021bVolk & Henk, 2016).…”

SSR Markers-Based DNA Fingerprinting for Varietal Identification in Mango Cultivars

“…Germplasm evaluation and genetic diversity in mango using SSR markers gain significant advancement for evaluation of hybrids or cultivars, determination of genetic variations and conservation of germplasm [7]. SSR markers have widely used for identification of the domestication and movement of germplasm [19]. Genetic diversity evaluation in candidate cultivar using SSR molecular technology is based on SSR-PCR amplifications.…”

Simple Sequence Repeats-Based DNA Fingerprinting and Varietal Identification of Mango Cultivars

“…Germplasm evaluation and genetic diversity in mango using SSR markers gain significant advancement for evaluation of hybrids or cultivars, determination of genetic variations and conservation of germplasm [7,34]. SSR markers have widely used for identification of the domestication and movement of germplasm [35]. Genetic diversity evaluation in candidate cultivar using SSR molecular technology is based on SSR-PCR amplifications.…”