SSR genetic diversity assessment of the INRAE's walnut ( Juglans spp.) germplasm collection

In France, walnut crop is the second largest fruit crop after apple, with 36,000 tons of in-shell walnuts produced in 2016, making France the 9th producer in the world with almost 20,000 ha devoted. The INRAE's walnut germplasm collection includes 253 accessions from worldwide thanks to the prospecting work of Eric Germain from 1977 to 2007, the former head of breeding program at INRAE of Bordeaux. Among them, 217 are Juglans regia accessions including 194 cultivars and 23 intraspecific hybrids, coming from the major growing areas such as North-America, Europe and Asia. The germplasm collection includes also 36 Juglans accessions of 14 related species from the two sections Rhysocaryon (J. nigra, J. hindsii, J. microcarpa, J. californica, J. major, J. mollis) and Cardiocaryon (J. sieboldiana, J. cathayensis, J. mandshurica, J. cinerea). In this study, 13 simple sequence repeat (SSR) markers, selected from the literature (10 genomic SSRs from J. nigra and 3 EST-SSRs from J. regia), were used to genotype the 253 accessions. All SSR loci were highly polymorphic with a range from 2 to 17 alleles/locus (mean: 8.92) considering all the J. regia accessions. The results indicate a high diversity among the genotypes which could be useful for the new French walnut improvement program. This analysis permitted to select 170 accessions that will be used for association genetics studies, using the 600K SNP Affymetrix((R)) array, in order to identify the genetic determinism of agronomic traits of interest such as those related to phenology, fruit and kernel quality, and susceptibility to different diseases.