Comparison of structure analyses and core collections for themanagement of walnut genetic resources

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.