First draft genome sequencing of fennel (Foeniculum vulgare Mill.): identification of simple sequence repeats and their application in marker-assisted breeding

The development of F1 hybrid varieties benefits from the synergistic effect of conventional and molecular marker-assisted breeding schemes. A sequencing run was carried out in Foeniculum vulgare (2n = 2x = 22) to develop the first genome draft and to identify microsatellites suitable for implementing multilocus SSR marker assays. A preliminary cytometric analysis allowed us to estimate the genome size (2C = 2.64–2.86 pg), equal to about 1.34 Mbp for 1C genome, and to calculate the sequencing coverage (53×). The genome draft assembly into 300,408 scaffolds and its bioinformatic analysis enabled the annotation of coding and non-coding regions across the genome, including 103,306 SSR elements. A total of 100 microsatellites were randomly chosen among those with dinucleotide and trinucleotide repeat motifs and with a repeat motif length ≥ 25 times and were preliminarily tested. Of these, 27 SSR markers, classified as suitable for genetic diversity analyses, were efficiently organized in five PCR multiplex assays and validated using a core collection of 100 fennel individuals potentially useful for the development of inbred lines and F1 hybrids. All SSR loci were found to be polymorphic, scoring an observed number of marker alleles Na = 207 and an average polymorphism information content PIC = 0.69. The SSR data were used to calculate (i) the degree of homozygosity for the individual inbred lines (0.35 < Ho < 0.96), to eventually plan additional selfing or sibling cycles, and (ii) the degree of genetic similarity for all possible pair-wise comparisons between parental inbred lines (GS = 0.55–0.77), to identify the most divergent combinations for the constitution of experimental F1 hybrids. The integration of genotypic and phenotypic data was useful for implementing guidelines for precision hybrid breeding schemes in fennel.