Rapid identification of inflorescence type markers by genotyping-by-sequencing of diploid and triploid F1 plants of Hydrangea macrophylla. Hydrangea macrophylla genomic markers

The ornamental crop Hydrangea macrophylla develops highly attractive lacecap or mophead inflorescences. The mophead trait, which is mostly favored by consumers, is recessively inherited by a major locus, following called inflorescence type locus (INF). If lacecap cultivars are crossed with mophead cultivars, then either 50% or all progenies develop lacecap inflorescences, depending on the zygosity in the lacecap parents. For most cultivars, the zygosity at the inf locus is unknown and the detection of the inflorescence type in the offspring is time-consuming, because seedlings flower the first time in the 2nd year after sowing. Here, molecular markers allow the marker-assisted selection of mophead varieties already in the non-flowering stage during the first year of cultivation. In order to develop molecular markers for the inflorescence type, we used a F1 population consisting of 422 plants that segregated into lacecap, mophead and non-flowering as well as diploid and triploid plants. Genotyping occurred by genotyping-by-sequencing. For marker identification, we created a H. macrophylla reference genome assembly and developed a computational pipeline for genome-wide bulk sequence analysis. We identified 2 markers linked to the INF locus, each of them explaining 99.7% of the inflorescence phenotype. For marker A109A110, we detected 6 sequence variants in a H. macrophylla collection consisting of 56 varieties, including diploid, triploid and tetraploid plants. Two out of these sequence variants are coupled with mophead alleles at the INF locus. In addition, we found a co-segregation between the mophead and the non-flowering trait based on our marker analyses.