Mitochondrial candidate gene, orf206, for cytoplasmic male sterility in Pear (Pyrus pyrifolia)

Cytoplasmic male sterility (CMS) caused by mitochondrial genome alterations in flowering plants plays a crucial role in hybrid breeding systems. In pear (Pyrus spp.), pollenless phenotypes have been consistently observed in progeny. However, the genetic basis and inheritance mechanisms of male sterility in pears remain poorly understood. To investigate the inheritance mode, we performed segregation analysis in four F₁ populations derived from crosses using a cultivar carrying CMS-type cytoplasm as the maternal parent. The observed male sterility segregation ratios confirmed a maternal inheritance pattern consistent with the CMS model and suggested differential effects of nuclear fertility restorer genes from various pollen parents. We analyzed whole-genome sequencing data from four pear accessions, identifying an 860 bp mitochondrial DNA sequence associated with male-sterile individuals. This sequence was located near cox3 and apt8, commonly co-located with CMS loci in other plant species. Within this region, we identified orf206, a chimeric open reading frame composed of 113 bp from nad3 in Pyrus betulifolia and 403 bp from atp9-1 of Malus × domestica. The predicted protein encoded by orf206 contained three transmembrane domains, which are typical features of CMS-associated proteins. Our results demonstrate that male sterility in pears is maternally inherited and support orf206 as a strong candidate gene for CMS induction. Furthermore, we developed an InDel marker (CBpMtid03 and CBpMtid07) targeting the CMS-specific mitochondrial sequence enabling the efficient identification of CMS individuals in breeding programs. These findings provide insights into the molecular mechanisms underlying pollen sterility in pears and facilitate marker-assisted selection in pear breeding.

The online version contains supplementary material available at 10.1007/s11032-025-01591-z.