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Elucidating the genetic determinants of fruit quality traits in walnut is essential to breed new cultivars meeting the producers and consumers’ needs. We conducted a genome-wide association study (GWAS) using multi-locus models in a panel of 170 accessions of Juglans regia from the INRAE walnut germplasm collection, previously genotyped using the AxiomTMJ. regia 700K SNP array. We phenotyped the panel for 25 fruit traits related to morphometrics, shape, volume, weight, ease of cracking, and nutritional composition. We found more than 60 marker-trait associations (MTAs), including a highly significant SNP associated with nut face diameter, nut volume and kernel volume on chromosome 14, and 5 additional associations were detected for walnut weight. We proposed several candidate genes involved in nut characteristics, such as a gene coding for a beta-galactosidase linked to several size-related traits and known to be involved in fruit development in other species. We also confirmed associations on chromosomes 5 and 11 with nut suture strength, recently reported by the University of California, Davis. Our results enhance knowledge of the genetic control of important agronomic traits related to fruit quality in walnut, and pave the way for the development of molecular markers for future assisted selection.

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International audience; Sweet cherry (Prunus avium L.) is a diploid species with an estimated genome size of 338 MB (Arumuganathan et al. 1991). It is mostly selfincompatible, and therefore has a heterozygous genetic background. We have sequenced the genome of the 'Regina' sweet cherry variety, which is a late blooming cultivar. Here we present whole-chromosomes assembly and phasing using a combination of long read sequencing, proximity ligation (HiC) data and GBS markers.Regina PacBio long reads were de novo assembled using FALCON UNZIP. A first assembly using optical mapping and high density genetic linkage maps with GBS data resulted in a genome of 264,8 Mb (78,4 % of estimated genome size) distributed on 8 linkage groups with a scaffold N50~6Mb (Regina V1). A new assembly (ReginaV2) combining Falcon Unzip assembly of PacBio long reads, proximity ligation (HiC) data and GBS markers has been done with Falcon Phased and the Proximo pipeline of Phase Genomics. It produced complete, fully phased, diploid chromosome scale scaffolds with a genome coverage of~90%, a N50 of~37 Mb and a complete BUSCO score of 95,6%. Structural and functional annotations of Regina V2 are in progress. Obtaining these phased chromosomes will allow very detailed studies of the allelic effects on the traits studied, in particular by making it possible to study the allelic expressions of candidate genes.

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.

International audience; In perennial fruit species, phenology and fruit quality traits are highly dependent on environmental conditions. In the context of climate change, a rise of fall and winter temperatures leads to a slowing down of the dormancy release which may result in a dramatic decrease of the production. Also, a rise of spring temperatures induces a significant advance of blooming date, increasing risks of damages by the frost. Moreover, the higher frequency of spring rainy periods has serious consequences for fruit quality, particularly on fruit cracking. The objective of our study is to identify the genetic determinism of the cherry tree response to the climate change. Several F1 sweet cherry progenies and a germplasm collection were evaluated for phenological traits and fruit quality. One of the mapping progenies, Regina × Lapins, was evaluated in five sites in order to study the genotype × environment interactions. The progenies were genotyped with the SNP RosBREED arrays and the collection using a genotyping-by-sequencing (GBS) approach. QTL detection and GWAS were performed allowing the identification of the genomic regions associated with the phenological and the fruit quality traits. The comparison of the genomic regions identified by the two analyses was achieved. For both datasets, we revealed that a genomic region at the end of Chromosome 1 controls both flowering and chilling requirements in sweet cherry, consistent with the observed strong phenotypical correlation between these traits. For the first time, marker-trait associations on several chromosomes were found for traits related to sweet cherry fruit quality.

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BackgroundUnravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™J. regia700 K SNP array, with phenological data from 2018, 2019 and legacy data. These accessions come from the INRAE walnut germplasm collection which is the result of important prospecting work performed in many countries around the world. In parallel, an F1progeny of 78 individuals segregating for phenology-related traits, was genotyped with the same array and phenotyped for the same traits, to construct linkage maps and perform Quantitative Trait Loci (QTLs) detection.ResultsUsing GWAS, we found strong associations of SNPs located at the beginning of chromosome 1 with both budbreak and female flowering dates. These findings were supported by QTLs detected in the same genomic region. Highly significant associated SNPs were also detected using GWAS for heterodichogamy and lateral bearing habit, both on chromosome 11. We developed a Kompetitive Allele Specific PCR (KASP) marker for budbreak date in walnut, and validated it using plant material from the Walnut Improvement Program of the University of California, Davis, demonstrating its effectiveness for marker-assisted selection in Persian walnut. We found several candidate genes involved in flowering events in walnut, including a gene related to heterodichogamy encoding a sugar catabolism enzyme and a cell division related gene linked to female flowering date.ConclusionsThis study enhances knowledge of the genetic architecture of important agronomic traits related to male and female flowering processes and lateral bearing in walnut. The new marker available for budbreak date, one of the most important traits for good fruiting, will facilitate the selection and development of new walnut cultivars suitable for specific climates.

The preservation of the maximum of diversity within the smallest number of accessions is one of the challenges of germplasm management. To construct core-collections, the assessment of the population structure and the relationships between the accessions represents a key step and the choice of suitable molecular markers is the starting point. Since the expansion of available SNP-based genomics tools, a debate has emerged regarding the usefulness of the widely used microsatellites (SSRs) markers. In this study, we analysed a part of the INRAE walnut germplasm collection of 150 accessions, unique in Europe for walnut biodiversity conservation, by comparing the power of both types of marker. We found that the first level of structure is equally detected using 13 SSRs or the Axiom™ J. regia 700K SNP array, and is in relation with the geographical origin of the accessions. For K=2, there was no exchange of accession between the two groups when both markers were compared. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to SSRs in Principal Coordinate Analysis (PCoA). The neighbor-joining trees constructed were also consistent between both types of marker. The main differences lied in the upper levels of structure from K=3 to K=6, more powerful using the SNPs, and in the percentage of the explained variation in PCoA for K=2, higher using SSRs. We then constructed core-collections of 50 accessions, a crucial step in genetic resources management to reduce the costs and preserve the allelic diversity. Using two different construction methods, both SSR and SNP markers were suitable and able to keep at least 88.57% of the alleles. 32/50 accessions were in common between the two markers, for both methods. We concluded that the use of either marker is dependent on the researcher’s goal.

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In temperate trees, optimal timing and quality of flowering directly depend on adequate winter dormancy progression, regulated by a combination of chilling and warm temperatures. Physiological, genetic and functional genomic studies have shown that hormones play a key role in bud dormancy establishment, maintenance and release. We combined physiological, transcriptional analyses, quantification of abscisic acid (ABA) and gibberellins (GAs), and modelling to further investigate how these signaling pathways are associated with dormancy progression in the flower buds of two sweet cherry cultivars.Our results demonstrated that GA-associated pathways have distinct functions and may be differentially related with dormancy. In addition, ABA levels rise at the onset of dormancy, associated with enhanced expression of ABA biosynthesisPavNCEDgenes, and decreased prior to dormancy release. Following the observations that ABA levels are correlated with dormancy depth, we identifiedPavUG71B6, a sweet cherryUDP-GLYCOSYLTRANSFERASEgene that up-regulates active catabolism of ABA to ABA-GE and may be associated with low ABA content in the early cultivar. Subsequently, we modelled ABA content and dormancy behavior in three cultivars based on the expression of a small set of genes regulating ABA levels. These results strongly suggest the central role of ABA pathway in the control of dormancy progression and open up new perspectives for the development of molecular-based phenological modelling.