Integrating Genomic Markers and Non-Invasive Phenotyping for Early Sex Identification in Horticultural Plants: A Mechanism-Guided Framework

Abstract

Early sex identification is essential for the propagation, cultivation, quality improvement, and germplasm management of dioecious horticultural plants and related functionally dioecious systems, particularly in perennial species with long juvenile phases. However, the reliability and transferability of sex-identification technologies depend strongly on the underlying sex-determining mechanism. Here, we synthesize recent advances in plant sex determination and diagnostic technologies, ranging from morphological and biochemical traits to molecular markers, high-throughput sequencing, structural-variant detection, and emerging non-invasive phenotyping. We propose that sex-identification strategies should be selected according to the biological target generated by each mechanism, including heteromorphic sex chromosomes, homomorphic sex-determining regions (SDRs), functional sex-determining genes, sex chromosome turnover, dosage-dependent systems, and environmentally labile sex expression. We further distinguish genetic, developmental, physiological, and phenotypic layers of plant sex, emphasizing that DNA markers and spectral phenotyping provide complementary information. Genomic markers and non-invasive phenotyping are expected to be consistent when genetic sex is stably expressed, but they may become inconsistent when sex expression is developmentally, hormonally, or environmentally modulated. While molecular markers remain the most reliable tools for confirmatory genotyping, Raman spectroscopy, surface-enhanced Raman scattering (SERS), hyperspectral imaging, and machine learning may serve as rapid prescreening tools in large breeding populations, although their application remains at the proof-of-concept stage. Finally, we present a mechanism-guided decision framework for integrating genomic markers and non-invasive phenotyping to support early sex screening, propagation planning, planting-material optimization, and marker-assisted improvement in dioecious horticultural plants.

Plant phenotyping relevance

植物の性表現型を対象に、非侵襲的・スペクトル表現型解析と遺伝マーカーを統合する診断技術および意思決定枠組みをレビューしており、表現型取得法が実質的な中心である。

Code and data availability

This is a critical review article with no original plant-phenotyping measurements or computational analysis. The Data Availability Statement explicitly states no new data were created or analyzed, and no author code, datasets, images, or trained models are deposited or referenced. All cited phenotyping/spectral studies

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