Abstract
The preservation of maximum diversity within the smallest number ofaccessions is one of the challenges of germplasm management, and the assessment ofthe population structure, the relationships between the accessions, and theconstruction of core collections are the key steps. The choice of suitable molecularmarkers is often the starting point. In this study, we analyzed a part of the INRAEwalnut germplasm collection, which is highly diverse and unique in Europe,consisting of 150 accessions from American, European, and Asian continents. Based ongenotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that thefirst level of structure is detected equally. We also highlighted empirically thatapproximately 100 SNPs are needed to obtain similar clustering to 13 SSRs inPrincipal Coordinate Analysis (PCoA). We constructed eight core collectionsfollowing two strategies (percentage of total allelic diversity or number ofaccessions) and two construction methods based on different algorithms (“maximumlength subtree” and “entry-to-nearest-entry” methods). We showed that corecollections based on few SSR markers are able to capture at least 99.5% of the SNPallelic diversity, irrespective of the construction method used. Then, corecollections based on each marker type are highly similar, using both constructionmethods. All these steps are crucial to identify the suitable tools and methods toimprove plant genetic resources management.
Highlights
In the context of climate change and human population growth, plant genetic resources (PGR) are of the utmost importance
Using Simple Sequence Repeats (SSRs) markers, the higher drop of ΔK is for K = 2, followed by a rise for K = 6, and very similar results were obtained using Single-Nucleotide Polymorphisms (SNPs) markers, since the higher drop of the cross-entropy criterion is for K = 2, with a curve slope starting for K = 6 (Fig. 2)
To compare the results using SSR and SNP markers, we focused on the first level of structure for K = 2 (S2 Table)
Summary
In the context of climate change and human population growth, plant genetic resources (PGR) are of the utmost importance They constitute the foundations of agricultural sustainability and global food safety (Ulukan 2011; Ogwu et al 2014), but they are facing conservation issues. In the Persian walnut (Juglans regia L.), a species which is widely disseminated and grown in many temperate regions, more than 20 publications mention the use of SSRs (Bernard et al 2018a).
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