Transcriptomic analysis
Transcriptomic analysis was performed comparing the tillers that flowered in the next season (17Hot) and tillers that remained vegetative (17Control) as described in Samarth et al . (2019). 150 bp generated paired-end reads were assembled into a single reference transcriptome using the Trinity pipeline (Haas et al., 2013). Reads from each of the samples were aligned to the reference assembly to generate a count matrix using the Bowtie2.0 (Langmead & Salzberg, 2012) followed by the differential expression analysis using the DESeq2 package in R. The significantly differentially expressed genes (adj. p-value<0.05) were annotated based on orthologous proteins identified in B. distachyon using blastp with an E-value of 10-5 and 50% protein identity. Gene ontology and pathway enrichment analysis was performed based on the PANTHER server (Mi et al., 2016). Validation of the RNA-seq results was performed using RT-qPCR with a random selection of four genes from the transcriptomic data (Appendix S2).