Understanding genetic and phenotypic drivers of parthenocarpy in pear

Parthenocarpy, the ability to produce fruit without fertilisation, is a valuable trait for ensuring consistent yields amidst increasing climate variability and pollination challenges. However, understanding of parthenocarpy in pears (Pyrus spp.) remains limited. This study investigated a segregating breeding population (P14.XXX) from The New Zealand Institute for Plant and Food Research (PFR) in Motueka, examining reproductive mechanisms that support fruit set without effective cross-pollination across 86 trees with valid phenotypes. Initial assessments revealed a high incidence of autonomous fruit set, which was assumed to indicate parthenocarpy. Multi-season analyses later demonstrated that these cases also included self-compatibility and stenospermocarpy, confirming that autonomous fruit set can arise through multiple pathways. Subsequent seed analyses identified diverse fruit-set types within the population, revealing that parthenocarpy and self-pollination may coexist within an individual genotype and uncovering autonomous-set variants that did not fit conventional definitions. To address this complexity, a Parthenocarpy Contingency Chart was developed to refine classification and guide downstream genetic investigation. Bulked Segregant Analysis identified genomic regions potentially associated with pollination-independent fruit development, including auxin-related (IAA17) and oxidative-stress/peroxidase pathway genes. PCR assays targeting insertion/deletion polymorphisms confirmed genetic variation but did not consistently predict phenotype, emphasising the need for detailed, multi-year phenotyping prior to marker development. This work represents the first integrated evaluation of parthenocarpy within a segregating pear population, demonstrating the coexistence of multiple reproductive mechanisms within a single genetic framework. The findings provide a foundation for developing climate-resilient cultivars and support sustainable orchard systems that maintain fruit quality under pollination constraints.