Characterization of the poplar pan-genome by genome-wide identification of structural variation

Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2?Mb and 62.9?Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits. We produced a haploid rose line from R. chinensis "Old Blush" and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae

Développement d'un outil pour la sélection assistée par marqueurs chez le ray-grass anglais

Forage varieties are synthetic varieties obtained by the intercross of a small number of elite genotypes selected in recurrent selection programs. This breeding method has been successful to improve forage species but its efficiency could be increased by the use of molecular markers. The goal of this study was to develop a tool for an easy genotyping of thousands of individuals with an hundred markers evenly spread across the genome in perennial ryegrass. The strategy was to design primer pairs in conserved regions on both sides of an intron for amplification and sequencing in genotypes of interest (polycross parents). Sequences were used to develop SNP markers. We developed 363 primer pairs evenly distributed across the genome with good amplification in perennial ryegrass. Moreover, these primer pairs showed an excellent transferability to other forage grass species (between 73 and 97% in fescues and 77% in cocksfoot). Polymorphism study on seven perennial ryegrass genotypes revealed one SNP every 42 bases on average. Only 38% of the SNPs were heterozygous in more than one genotype. This required to develop specific SNP markers in order to study segregating progenies within each of the seven genotypes.Les variétés fourragères sont des variétés synthétiques obtenues par intercroisement en panmixie d’un certain nombre de constituants sélectionnés selon des schémas de sélection récurrente. Cette stratégie d’amélioration a permis un progrès génétique indéniable, mais son efficacité pourrait être accrue grâce à l’utilisation de marqueurs moléculaires. L’objectif de cette étude était de développer un outil permettant de génotyper facilement plusieurs milliers d’individus avec une centaine de marqueurs répartis sur l’ensemble du génome chez le ray-grass anglais. La stratégie a été de développer des couples d’amorces dans des régions conservées encadrant un intron pour amplification et séquençage dans les génotypes d’intérêt (parents de polycross). Les séquences ont ensuite été utilisées pour développer des marqueurs SNP. Au total, nous avons développé 363 couples d’amorces bien répartis sur le génome et présentant une amplification correcte chez le ray-grass anglais. De plus, ces amorces ont montré une excellente transférabilité à d’autres espèces de graminées fourragères (de 73 à 97 % pour les fétuques et 77 % pour le dactyle). L’étude du polymorphisme sur sept génotypes de ray-grass anglais a révélé en moyenne un SNP toutes les 42 bases. Seulement 38 % des SNP étaient hétérozygotes chez plus d’un génotype, ceci a conduit à développer des marqueurs SNP spécifiques à chacun des sept génotypes pour l’étude de la ségrégation de leurs descendances respectives

New Resources for genetic studies in Populus Nigra: genome-wide SNP discovery and development of a 12K Infinium array

Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5–7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra