Multi-omics map reveals how pear seeds awaken
image: Differential accumulation analyses of metabolic compounds associated with seed germination.
Credit: Seed Biology
A research team has uncovered a multilayered regulatory network that controls pear seed germination by integrating metabolomic, transcriptomic, and microRNA analyses. The results show that removing the seed coat triggers coordinated changes in plant hormones, metabolites, protein-coding genes, and noncoding RNAs. Declining levels of abscisic acid (ABA) emerged as a central signal for releasing dormancy, while a newly identified long noncoding RNA–microRNA–messenger RNA pathway may regulate metabolic activity during germination. These findings provide a systems-level framework for understanding seed dormancy in perennial fruit trees and could support faster pear breeding, improved germination management, and the development of targeted treatments for overcoming seed dormancy.
Pear is an economically important perennial fruit crop, but its long reproductive cycle slows the development of new varieties. Seed dormancy is one contributor to this delay, and removing the seed coat can accelerate pear embryo germination. Previous studies have shown that germination involves shifts in hormones such as ABA, gibberellins, auxin, and jasmonates. Metabolomic and transcriptomic methods have also identified numerous compounds and genes associated with seed development. However, the key metabolites controlling pear seed germination remain unclear, and little is known about how microRNAs and long noncoding RNAs coordinate gene expression with metabolic changes. A more integrated investigation was therefore needed to reveal how these molecular layers interact during the transition from dormancy to germination.
A study (DOI: 10.48130/seedbio-0026-0002) published in Seed Biology on 28 February 2026 by Shao-Ling Zhang's team, Nanjing Agricultural University, reports that germination is governed by coordinated hormone remodeling, gene–metabolite associations, and a regulatory axis involving LNC_019909, miR395a, and Pbr039312.1.
The researchers collected 144 seeds from ripe ‘Cuiguan’ pear (Pyrus pyrifolia) fruit and divided them into coated and uncoated groups, each with three biological replicates. Seeds were incubated under controlled temperature, light, and humidity, and embryos were sampled at 0, 24, and 36 hours. Uncoated seeds began germinating after 36 hours. The team quantified hormones and other metabolites using ultra-performance liquid chromatography coupled with tandem mass spectrometry. They then performed transcriptome and small-RNA sequencing to profile protein-coding genes, long noncoding RNAs, and microRNAs. Correlation analysis was used to connect differentially accumulated compounds with differentially expressed genes, while computational target prediction and a dual-luciferase assay tested proposed RNA interactions. Across the datasets, the researchers identified 632 compounds, 30,468 genes, 293 microRNAs, and 34,303 long noncoding RNAs. A total of 114 compounds responded to germination, including indole-3-acetic acid, dihydrojasmonic acid, jasmonic acid–isoleucine, ABA, and salicylic acid. ABA, auxin, and two jasmonate-related compounds declined in germinated seeds, whereas salicylic acid increased. The team constructed a correlation-based database connecting 6,047 genes with 109 germination-associated compounds. Of these, 29 compounds and 2,670 genes also responded to ABA, confirming the hormone’s extensive influence on dormancy-related metabolism and gene expression. The network highlighted pathways involving methionine, purines, α-linolenic acid, and riboflavin. Five microRNAs were differentially expressed during germination, and three—novel_124, miR395a, and miR397—were linked to 12 genes in the gene–metabolite database. Most notably, experiments showed that miR395a directly suppressed Pbr039312.1, while LNC_019909 weakened this repression by acting as a molecular sponge for miR395a. This provides functional evidence for a long noncoding RNA–microRNA–messenger RNA regulatory axis connecting RNA control with metabolic activity.
Overall, the study presents a molecular map of pear seed germination and demonstrates that dormancy release depends on interactions extending beyond individual hormones or genes. ABA remains a dominant regulatory signal, but the results also reveal contributions from other hormones, metabolic pathways, and noncoding RNAs. By identifying candidate metabolites, genes, and RNA interactions for further functional testing, the work establishes a foundation for improving seed germination and shortening breeding cycles in pear and potentially other perennial fruit crops. Future research under field and nursery conditions will be needed to translate these molecular targets into practical seed treatments or breeding strategies.
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References
DOI
Original Source URL
https://doi.org/10.48130/seedbio-0026-0002
Funding information
This work was supported by the Jiangsu Seed Industry Revitalization Project (JBGS[2021]022), the Key Research and Development Program (Modern Agriculture) of Jiangsu Province (BE2022381), the Fundamental Research Funds for the Central Universities (YDZX2025036), and the Bioinformatics Center of Nanjing Agricultural University.
About Seed Biology
Seed Biology (e-ISSN 2834-5495) is published by Maximum Academic Press in partnership with Yazhou Bay Seed Laboratory. Seed Biology is an open access, online-only journal focusing on research related to all aspects of the biology of seeds, including but not limited to: evolution of seeds; developmental processes including sporogenesis and gametogenesis, pollination and fertilization; apomixis and artificial seed technologies; regulation and manipulation of seed yield; nutrition and health-related quality of the endosperm, cotyledons, and the seed coat; seed dormancy and germination; seed interactions with the biotic and abiotic environment; and roles of seeds in fruit development. Seed biology publishes a wide range of research approaches, such as omics, genetics, biotechnology, genome editing, cellular and molecular biology, physiology, and environmental biology. Seed Biology publishes high-quality original research, reviews, perspectives, and opinions in open access mode, promoting fast submission, review, and dissemination freely to the global research community.