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Updated: Aug 28, 2026

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling
Published on: May 21, 2020
Integrated Transcriptome and WGCNA Analyses Reveal Candidate Regulatory Networks Associated with Shell Hardening in
Qingyi Long1, Yang Li1, Jianjian Geng1
1Yunnan Institute of Tropical Crops, Jinghong 666100, China.
Abstract:
To characterize the transcriptomic dynamics underlying shell hardening in Macadamia integrifolia, RNA sequencing was performed on pericarp and shell tissues collected at three key developmental stages. A total of 18 libraries were generated, yielding 125.19 Gb of clean data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that husk-associated DEGs were mainly enriched in photosynthesis-related functions, whereas shell-associated DEGs were enriched in phenylpropanoid biosynthesis, secondary metabolism, and cell wall organization. Weighted gene co-expression network analysis (WGCNA) identified module M8 as being strongly associated with the middle and late stages of shell development. Genes in this module were mainly enriched in phenylpropanoid metabolism, redox-related processes, and extracellular region functions. The hub genes within M8 included those encoding a glutaredoxin family protein, a WNK-type protein kinase, a tRNA methyltransferase-related protein, an EFR3 membrane-associated protein, a pectin modification-related protein, and a WAT1-related protein. Collectively, these results reveal clear tissue-specific transcriptomic patterns during pericarp and shell development and identify candidate co-expression networks that may contribute to shell hardening.
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