Analysis of genetic diversity and structure in a worldwide walnut (Juglans regia L.) germplasm using SSR markers

Abstract

Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known and is grown worldwide in temperate areas. France is the 7th leading producer as of 2016 with 39 kt. Deciphering walnut genetic diversity and structure is important for efficient management and use of genetic resources. In this work, 253 worldwide accessions from the INRA walnut germplasm collection, containing English walnut and several related species, were genotyped using 13 SSR (Single Sequence Repeat) markers selected from the literature to assess diversity and structure. Genetic diversity parameters showed a deficiency of heterozygotes and, for several SSRs, allele-specificities among the accessions tested. Principal Coordinate Analysis (PCoA) showed the 253 accessions clustered in largely in agreement with the existing botanical classification of the genus. Among the 217 J. regia accessions, two main clusters, accessions from Eastern Europe and Asia, and accessions from Western Europe and America, were identified using STRUCTURE software. This was confirmed by Principal Coordinate Analysis and supported by Neighbor-Joining tree construction using DARwin software. Moreover, a substructure was found within the two clusters, mainly according to geographical origin. A core collection containing 50 accessions was selected using the maximum length sub-tree method and prior knowledge about their phenotype. The present study constitutes a preliminary population genetics overview of INRA walnut genetic resources collection using SSR markers. The resulting estimations of genetic diversity and structure are useful for germplasm management and for future walnut breeding programs.

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

“…In particular, chromosomes 7, 5, 1, 4, and 2 presented about 70% of the divergent sites ( Figure 2; Supplemental Figure S12 ). As suggested by the mean reduction of diversity coefficient (ROD) value (0.41), in most of the genomic regions highly differentiated, the UCD-WIP founders from the USA and Europe showed lower nucleotide diversity (π = 2.5 x 10 -4 ) than the Asian genotypes (π = 5.0 x 10 -4 ), consistent with (Bernard et al 2018a) ( Figure 2; Supplemental Figure S12 ). The proximity of our eastern genotypes to the supposed walnut center of domestication in Central Asia can explain the high level of diversity observed in this subgroup.…”

“…Many studies on genetic diversity in walnut have outlined a genetic differentiation between Eastern and Western genotypes (Ebrahimi et al 2016; Marrano et al 2018). Moreover, walnuts from Eastern Europe, Central Asia, and China exhibit higher genetic diversity and a higher number of rare alleles than the genotypes from Western countries (Bernard et al 2018a).…”

Management of a Walnut Germplasm Collection: Which of SSR or SNP Markers Are Most Suitable to Preserve Biodiversity?

“…In the case of a SNP array, all the loci available are assayed, for a 96-well DNA plate.In addition, only 59.8% of the available SNPs on the array were usable for the analyses after quality control.A second choice criterion could be the nature of the plant material managed, particularly if the researcher works only on one crop, or also with its wild species. In our case, the SSRs used were also highly transferable into wild species of the genus Juglans spp [24]…”

“…The panel choice was made thanks to a previous work based on genetic diversity results using SSRs, and phenotypic variability [24]. The genomic DNAs of the panel were extracted from young leaves as described in this previous work.…”

“…The panel was genotyped using 13 neutral SSR markers as described previously [24] and 609,658 SNPs from the Axiom™ J. regia 700K SNP array uniformly distributed over the 16 J. regia chromosomes [9]. The quality control steps were performed using "PLINK 1.9" software [25].…”