Sandrine Balzergue

Apple (Malus domestica Borkh.) is an important fruit crop cultivated worldwide in temperate regions. Due to their frequent high content in repetitive DNA sequences and large size, plant genomes have long been considered challenging to assemble. A first reference genome of a “Golden Delicious” doubled-haploid apple tree, GDDH13, was previously produced in 2017. The chromosomes of GDDH13 present however a high percentage of N stretches, around 12%, and above 8% of the assembly was not anchored on chromosomes. Here, we provide a chromosome-level assembly of another “Golden Delicious” doubled-haploid apple tree, GDDH18. Interestingly, this tree presents phenotypic differences with GDDH13, notably associated with fruit size. In this assembly, 99.4% of the sequences were assembled into 17 contigs corresponding to the 17 expected chromosomes of apple, and all but 1 of these 17 contigs present telomeric repeats at both their extremities. A high complete benchmarking universal single-copy ortholog (BUSCO) score and a high LTR assembly index of 99.5% and above 22, respectively, attest to the high quality of the assembly and to the completeness of both the gene and the repetitive space. A de novo annotation of the assembly was produced, allowing the prediction of 51,892 protein-coding genes, of which 93% are functionally annotated. A total of 6,239 additional genes were functionally annotated in comparison with the GDDH13 assembly. This high-quality assembly of GDDH18 along with a de novo annotation will help to better understand the phenotypic differences between the trees GDDH13 and GDDH18 and will serve as an enhanced reference genome for advancing the study of apple genomics.

Alternaria leaf blight, caused by the fungus Alternaria dauci, is the most damaging foliar disease of carrot. Some carrot genotypes exhibit partial resistance to this pathogen and resistance Quantitative Trait Loci (rQTL) have been identified. Co-localization of metabolic QTL and rQTL identified camphene, α-pinene, α-bisabolene, β-cubebene, caryophyllene, germacrene D and α-humulene as terpenes potentially involved in carrot resistance against ALB. By combining genomic and transcriptomic analyses, we identified, under the co-localization regions, terpene-related genes which are differentially expressed between a resistant and a susceptible carrot genotype. These genes include five terpene synthases and twenty transcription factors. In addition, significant mycelial growth inhibition was observed in the presence of α-humulene and caryophyllene.

Apple skin color is an important trait for organoleptic quality. In fact, it has a major influence on consumer choice. Skin color is, thus, one of the most important criteria taken into account by breeders. For apples, most novel varieties are so-called “mutants” or “sports” that have been identified in clonal populations. Indeed, many “sports” exist that show distinct phenotypic differences compared to the varieties from which they originated. These differences affect a limited number of traits of economic importance, including skin color. Until recently, the detailed genetic or epigenetic changes resulting in heritable phenotypic changes in sports was largely unknown. Recent technological advances and the availability of several high-quality apple genomes now provide the bases to understand the exact nature of the underlying molecular changes that are responsible for the observed phenotypic changes observed in sports. The present review investigates the molecular nature of sports affected in apple skin color giving arguments in favor of the genetic or epigenetic explanatory models.