ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Bioinformatics
This article is part of the Research TopicMulti-omics and Computational Biology in Horticultural Plants: From Genotype to Phenotype, Volume IVView all 3 articles
Integrated Physiological, Multi-Omics Analyses Reveal Key Factors Underlying Seed Abortion in Dimocarpus longan
Provisionally accepted
- Guangxi Academy of Agriculture Sciences, Nanning, China
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Embryo abortion severely limits fruit set and yield stability in longan (Dimocarpus longan), yet the upstream physiological triggers and coordinated molecular program remain incompletely defined. Here, we characterized normal seed-forming (NF) and aborted seed-forming (AF) fruits at the critical abortion window by integrating phenotyping, mineral nutrient profiling, embryo-targeted RNA sequencing, and quantitative proteomics, followed by cross-omics association analyses. Orchards with high abortion incidence exhibited markedly low available boron, and aborted embryos displayed a distinctive nutrient-partitioning pattern characterized by severe embryonic boron depletion despite broad changes in other elements. Transcriptome analysis identified 3,865 differentially expressed genes (1,993 upregulated and 1,872 downregulated in AF), with enrichment in pathways related to phenylpropanoid biosynthesis, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, plant hormone signal transduction, and MAPK signaling. Quantitative proteomics revealed 1,518 differentially accumulated proteins (342 increased and 1,176 decreased in AF), highlighting a global trend toward reduced protein abundance in aborted embryos. Integrated transcriptome–proteome analysis detected 374 shared features with strong concordance between mRNA and protein fold changes (93.6% concordant; r = 0.82), reinforcing a coordinated regulatory program at the abortion stage. Across datasets, embryo abortion was associated with disrupted boron-related cell wall processes, altered carbohydrate transport and mobilization, extensive hormone/MAPK rewiring, and pronounced repression of chloroplast-associated programs including photosynthetic light reactions and pigment/tetrapyrrole metabolism, coupled with redox and energy imbalance. qRT-PCR of eight mechanism-anchored candidates supported RNA-seq trends. Together, these results support a model in which embryonic boron depletion and impaired cell wall integrity are associated with, and may contribute to, a cascade of metabolic and signaling reprogramming that culminates in embryo growth arrest and degeneration, providing actionable markers and targets to improve seed development and fruit set in longan.
Keywords: boron deficiency, Embryo abortion, Longan (Dimocarpus longan), nutrient imbalance, Proteomics, Transcriptomics
Received: 30 Dec 2025; Accepted: 27 Jan 2026.
Copyright: © 2026 Qiu, Qin, Fang, Hou, Li, You, Xu, Cai and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Xiaolin Cai
Hongli Li
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