Wang Yan, Zhou Jiahao, Yang Mingqi, Yao Youhua, Cui Yongmei, Li Xin, Ding Baojun, Yao Xiaohua, Wu Kunlun
Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China.
Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China.
PeerJ. 2025 Aug 8;13:e19856. doi: 10.7717/peerj.19856. eCollection 2025.
This study investigated the molecular mechanisms underlying grain size variation between two distinct naked barley varieties using comprehensive phenotypic and transcriptomic (RNA-Seq) analyses.
In this study, we employed a comparative transcriptomics approach to analyze two naked barley varieties: the large-grained Shenglibai and the small-grained Lalu Qingke. Our investigation focused on three critical developmental periods of grain growth (early, mid, and late grain-filling periods). By integrating longitudinal three-dimensional phenotypic data with temporal expression profiles and applying weighted gene co-expression network analysis (WGCNA), we successfully identified gene modules that co-vary with morphological expansion.
Phenotypic assessments revealed that grains underwent rapid expansion during the filling period, with significant differences in grain width (GW) and thickness (GT) across all three developmental periods. In contrast, grain length (GL) remained relatively consistent by the end of the filling period. Transcriptome sequencing identified a peak in differentially expressed genes (DEGs) during the mid-filling period, indicating that the regulation of grain size development is most active in the early and mid-filling phases. WGCNA identified a blue module strongly correlated with grain size, which was significantly enriched in key metabolic pathways, including starch and sucrose metabolism. Further analysis identified seven hub genes, among which exhibited pronounced upregulation in large-grain varieties during the mid-to-late filling periods, closely aligning with the observed phenotypic traits. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation confirmed the period-specific and variety-specific expression patterns of these genes, further supporting the potential of these genes as targets for improving grain size in breeding.
本研究通过全面的表型和转录组学（RNA测序）分析，探究了两个不同裸大麦品种间粒重差异的分子机制。
在本研究中，我们采用比较转录组学方法分析了两个裸大麦品种：大粒的申格里白和小粒的拉鲁青稞。我们的研究聚焦于籽粒生长的三个关键发育时期（灌浆早期、中期和晚期）。通过将纵向三维表型数据与时间表达谱相结合，并应用加权基因共表达网络分析（WGCNA），我们成功鉴定出了与形态扩展共变的基因模块。
表型评估显示，籽粒在灌浆期迅速膨大，在所有三个发育时期的粒宽（GW）和厚度（GT）存在显著差异。相比之下，灌浆期末粒长（GL）保持相对一致。转录组测序发现在灌浆中期差异表达基因（DEGs）出现峰值，表明籽粒大小发育的调控在灌浆早期和中期最为活跃。WGCNA鉴定出一个与籽粒大小强烈相关的蓝色模块，该模块在包括淀粉和蔗糖代谢在内的关键代谢途径中显著富集。进一步分析鉴定出7个枢纽基因，其中 在灌浆中后期大粒品种中表现出明显上调，与观察到的表型性状密切相关。实时定量逆转录聚合酶链反应（qRT-PCR）验证证实了这些基因的时期特异性和品种特异性表达模式，进一步支持了这些基因作为育种中改善籽粒大小靶点的潜力。
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