Development of insertion and deletion markers associated with pollen fertility in pears (Pyrus spp.)

Insertion and deletion (InDel) marker is a valuable complement to another sequence-based molecular marker such as single nucleotide polymorphism and simple sequence repeat for genetic analysis in plants. InDel marker shows co-dominant inheritance and wide genomic distribution. In our previous study, a genomic region related to pollen fertility was identified on the high-density genetic linkage map. Re-sequencing data of the parents were re-analyzed by customized bioinformatic pipeline to discover in silico InDel structures in the proximity to the genomic region. Candidate polymorphic InDel variations between the parents were used to design a set of primers generating 200-400 bp of PCR amplicon. InDel markers were applied to pollenless cultivar 'Whangkeumbae' (Pyrus pyrifolia), normal cultivar 'Minibae' (P. hybrid), and their 88 F₁ individuals. Predicting pollen fertility using an InDel marker (CPID154) showed 80.7% of accuracy in F₁ individuals. The developed InDel markers in the present study will be used for marker-assisted selection of pollen fertility in Pyrus spp.