INDELs linked to mophead-lacecap phenotype controlling gene TEMARY in Hydrangea macrophylla

H. macrophylla has two types of flower inflorescence, mophead and lacecap. Recessive mophead phenotype is shown when possessing only loss of function alleles on TEMARY gene on chromosome 4. In H. macrophylla genetic resources, three types of loss of function alleles were observed. DNA markers for discriminating loss of function alleles from functional alleles are important for breeding new cultivars with the mophead phenotype. In this study, INDEL polymorphisms linked to three loss of functional alleles were searched to develop DNA markers which can determine mophead/lacecap easily. Long read sequence obtained by single molecule real time sequencing technology of three lacecap cultivars and three mophead cultivars were mapped on 0060F scaffold of the Hma_r1.2 genome. As a result, two INDELs were linked to lacecap/mophead alleles of TEMARY gene. Then, a DNA marker based on the INDEL was developed. For functional allele detection, presence of copied region in different loci was suggested in some cultivars, and it led to misjudge of phenotype. This DNA marker could be applied to DNA marker assisted selection when there are no copied sequences in both parent genomes.