Oat ranks sixth in world cereal production and has a higher content of health-promoting compounds compared with other cereals. However, there is neither a robust oat reference genome nor transcriptome. Using deeply sequenced full-length mRNA libraries of oat cultivar Ogle-C, a de novo high-quality and comprehensive oat seed transcriptome was assembled. With this reference transcriptome and QuantSeq 3' mRNA sequencing, gene expression was quantified during seed development from 22 diverse lines across six time points. Transcript expression showed higher correlations between adjacent time points. Based on differentially expressed genes, we identified 22 major temporal co-expression (TCoE) patterns of gene expression and revealed enriched gene ontology biological processes. Within each TCoE set, highly correlated transcripts, putatively commonly affected by genetic background, were clustered and termed genetic co-expression (GCoE) sets. Seventeen of the 22 TCoE sets had GCoE sets with median heritabilities higher than 0.50, and these heritability estimates were much higher than that estimated from permutation analysis, with no divergence observed in cluster sizes between permutation and non-permutation analyses. Linear regression between 634 metabolites from mature seeds and the PC1 score of each of the GCoE sets showed significantly lower p-values than permutation analysis. Temporal expression patterns of oat avenanthramides and lipid biosynthetic genes were concordant with previous studies of avenanthramide biosynthetic enzyme activity and lipid accumulation. This study expands our understanding of physiological processes that occur during oat seed maturation and provides plant breeders the means to change oat seed composition through targeted manipulation of key pathways.

中文翻译：

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可遗传的时间基因表达模式与发育中的六倍体燕麦种子的代谢组种子含量相关。

燕麦在世界谷物产量中排名第六，与其他谷物相比，其促进健康的化合物含量更高。然而，既没有可靠的燕麦参考基因组，也没有转录组。使用深度测序的燕麦品种 Ogle-C 的全长 mRNA 文库，从头组装了高质量且全面的燕麦种子转录组。利用该参考转录组和 QuantSeq 3' mRNA 测序，对 6 个时间点的 22 个不同品系的种子发育过程中的基因表达进行了定量。转录本表达显示相邻时间点之间具有更高的相关性。基于差异表达基因，我们鉴定了22种主要的基因表达时间共表达（TCoE）模式，并揭示了丰富的基因本体生物学过程。在每个 TCoE 集中，高度相关的转录本通常受遗传背景影响，被聚集在一起并称为遗传共表达 (GCoE) 集。22 个 TCoE 集中有 17 个的 GCoE 集的遗传力中值高于 0.50，并且这些遗传力估计值远高于排列分析估计的值，排列分析和非排列分析之间的簇大小没有观察到差异。成熟种子的 634 种代谢物与每个 GCoE 组的 PC1 评分之间的线性回归显示 p 值显着低于排列分析。燕麦燕麦生物碱和脂质生物合成基因的时间表达模式与之前对燕麦生物碱生物合成酶活性和脂质积累的研究一致。这项研究扩展了我们对燕麦种子成熟过程中发生的生理过程的理解，并为植物育种者提供了通过有针对性地操纵关键途径来改变燕麦种子成分的方法。