Comparison of structure analyses and core collections for the management of walnut genetic resources
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ORIGINAL ARTICLE
Comparison of structure analyses and core collections for the management of walnut genetic resources Anthony Bernard 1,2 & Teresa Barreneche 1 & Armel Donkpegan 1 & Fabrice Lheureux 2 & Elisabeth Dirlewanger 1 Received: 27 July 2020 / Revised: 2 September 2020 / Accepted: 3 September 2020 # The Author(s) 2020
Abstract The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods based on different algorithms (“maximum length subtree” and “entry-to-nearest-entry” methods). We showed that core collections based on few SSR markers are able to capture at least 99.5% of the SNP allelic diversity, irrespective of the construction method used. Then, core collections based on each marker type are highly similar, using both construction methods. All these steps are crucial to identify the suitable tools and methods to improve plant genetic resources management. Keywords Germplasm management . SNP . SSR . Core collection . Walnut
Introduction 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. Regarding ex situ management of PGR, this mainly involves seeds and some collections are at risk, due in part to the fact that they are generally underfunded and that evaluation and characterization are often Communicated by M. Troggio Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11295-020-01469-5) contains supplementary material, which is available to authorized users. * Elisabeth Dirlewanger [email protected] 1
University Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
2
CTIFL, Centre Opérationnel de Lanxade, 24130 Prigonrieux, France
imprecise or inadequate (Fu 2017). In that respect, careful PGR management is crucial from storage to use (Maxted et al. 1997). For clonally propagated perennial species, such as fruit and nut tree species, PGR are generally conserve
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