Abstract
SummaryOat 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.
Highlights
Oat ranks sixth in world cereal production (USDA, 2019), and has a high content of healthpromoting compounds in comparison to other cereals
Oat produces unique phenolic compounds known as avenanthramides (Avns), which have been reported to modulate signaling pathways associated with cancer, diabetes, inflammation, and cardiovascular diseases (Tripathi et al, 2018)
We found that the number of transcripts in an expression pattern was predicted by the number of differential expression events in the pattern (e.g., "One-step-up-at-8DAA (Top-8)", "Up-at-13DAA-down-at18DAA (Top-19)", and "Three-steps-up-at-8DAA (Top-9)" have one, two, and three differential expression events, respectively
Summary
Oat ranks sixth in world cereal production (USDA, 2019), and has a high content of healthpromoting compounds in comparison to other cereals. Oat produces unique phenolic compounds known as avenanthramides (Avns), which have been reported to modulate signaling pathways associated with cancer, diabetes, inflammation, and cardiovascular diseases (Tripathi et al, 2018). Despite worldwide production of this nutrient rich food, genomic studies in oats have lagged behind other cereal grains. A robust and comprehensively annotated oat reference genome is not yet available, and a limited number of oat transcriptome analyses have been published. The first de novo seed transcriptome assembly was generated by GutierrezGonzalez et al (2013). This version of the transcriptome included only 412 of 1440
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