Objective Black poplar ( Populus nigra L.) is a species native to Eurasia with a wide distribution area. It is an ecologically important species from riparian ecosystems, that is used as a parent of interspecific ( P. deltoides x P. nigra ) cultivated poplar hybrids. Variant detection from transcriptomics sequences of 241 P. nigra individuals, sampled in natural populations from 11 river catchments (in four European countries) is described here. These data provide new valuable resources for population structure analysis, population genomics and genome-wide association studies. Data description We generated transcriptomics data from a mixture of young differentiating xylem and cambium tissues of 480 Populus nigra trees sampled in a common garden experiment located at Orléans (France), corresponding to 241 genotypes (2 clonal replicates per genotype, at maximum) by using RNAseq technology. We launched on the resulting sequences an in-silico pipeline that allowed us to obtain 878,957 biallelic polymorphisms without missing data. More than 99% of these positions are annotated and 98.8% are located on the 19 chromosomes of the P. trichocarpa reference genome. The raw RNAseq sequences are available at the NCBI Sequence Read Archive SPR188754 and the variant dataset at the Recherche Data Gouv repository under https://doi.org/10.15454/8DQXK5 .

Lignocellulosic biomass is a renewable resource of interest for biorefinery. However, current poplar varieties have not been selected for this specific purpose. The factors affecting biomass yield and chemical properties need thus to be studied. With this objective, we have initiated a systems biology approach, integrating genomic, transcriptomic and phenotypic data in natural populations of black poplar (Populus nigra). Up to now, we have focused on a subset of 12 genotypes from 6 populations and trialled in a randomized complete block design located at INRA Orleans, France. The transcriptome of 2 biological replicates of each genotype has been explored through RNA sequencing (RNAseq) of pools of young differentiating xylem and cambium. Additionally, biomass yield was evaluated through measurements of height and diameter on 6 replicates of each genotype across several years and rotations, while biomass propertieswere assessed through chemical analyses of lignin, cellulose and hemicellulose concentrations as well as saccharification potential on 3 replicates of each genotype. The resulting data were used to build a weighted gene co-expression network and identify gene modules whose expression was correlated with biomass yield and/or quality at the genotypic level. Remarkably, the largest module (1,460 transcripts) was significantly associated with klason lignin content and displayed an enrichment in genes involved in secondary cell wall formation. Four candidate genes from this module were further selected to validate the detected quantitative trait transcripts (QTTs) on 2 new replicates of the 12 genotypes using RT-qPCR. The resulting expression levels were significantly correlated to those previously quantified by RNAseq and to the klason lignin content in the wood samples. These results demonstrate the interest of our approach, and thus open some prospects towards the identification of new candidate genes whose functions remain to be elucidated.

Poplar leaf rusts caused by Melampsora spp. are considered as being among the most crucial sanitary problems threatening poplar stands worldwide. Several major resistance factors specific to poplar rusts have been identified, each of them discovered using a single Melampsora species. Most of them are inherited from Populus species that did not co-evolved with the pathogen, hence questioning the origin and the function of such resistance. The purpose of this presentation is to compare the genetics of exapted and co-adapted resistance to M. medusae fsp. deltoidae (Mmd) and to M. larici-populina (Mlp), respectively. To achieve this, resistance QTL against Mlp was studied in two pedigrees. The first, an F2 P. trichocarpa x P. deltoides family, was previously evaluated for resistance to M medusae fsp. deltoidae, and a major gene for resistance Mmdl inherited from the P. trichocarpa grandparent was mapped. The second pedigree was a F1 P.nigra family. In the F2 pedigree, 17 QTLs were detected that are involved in the three components of quantitative resistance to the five Mlp strains inoculated in laboratory. These QTLs explain between 3.1 and 30.4% of the phenotypic variance. None ofthese QTLs have a broad range effect. No major resistance factor against Mlp was identified in this pedigree showing that Mmdl is not functional against Mlp strains tested. In the P. nigra family, 11 QTL explaining between 2% and 60 % of the phenotypic variation observed after inoculation with the two Mlp strains were detected. Most of these QTL were trait- or strain-specific except one. A major QTL inherited from the most resistant parent and located at the end of LG I explained more than 60% of uredinia size variation after inoculation with one Mlp strain and showed a moderate effect after inoculation with the other strain. The genomic mining of the QTL region revealed a cluster of 25 NB-LRR genes. Those results confirm in P.nigra the gene-for-gene model suggesting specific interactions between QTLs for quantitative resistance and Mlp strains. The results presented will be compared and discussed together with results of previous studies on Melampsora/Salicaceae pathosystems.