Parent-of-Origin Effect Predominantly Drives Seedling Vigor Heterosis in Triploid Loquat

Triploid breeding is a promising approach for developing seedless varieties, but the long juvenile phase of perennial fruit trees necessitates efficient early selection. In loquat (Eriobotrya japonica), a fruit crop with high demand for seedlessness, the relative contributions of hybridity, ploidy level, and parent-of-origin effects (POEs) to triploid seedling vigor remain elusive. To dissect these factors, we established a comprehensive experimental system comprising reciprocal diploid (2x), triploid (3x), and tetraploid (4x) hybrids from two genetically distinct cultivars. The ploidy, hybridity and genetic architecture of hybrid and parental groups were verified using flow cytometry, chromosome counting, newly developed InDel markers and genome-wide SNP analysis. Phenotypic evaluation of eight vigor-related traits revealed that plant height and soluble starch content were the most robust indicators of triploid heterosis in loquat. Notably, paternal-excess triploids [3x(p)] consistently outperformed all other groups. Quantitative analysis revealed POE as the main positive driver of triploid heterosis (+10.37% for plant height), far exceeding the negative impacts of hybridity (−12.75%) and ploidy level (−20.87%). These findings demonstrate that POE predominantly drives seedling vigor heterosis in triploid loquat. We propose a practical breeding strategy that combines prioritizing paternal-excess crosses with novel InDel markers for rapid verification of superior seedless progeny.