Transcriptomic analysis of almond (Prunus dulcis) cultivars with differential flowering time

Almond is one of the oldest and major tree nut crops consumed for its nutritious kernels. Since transcriptome analysis is crucial to identifying genes controlling important agronomic, an attempt was made for comparative transcriptomic analysis to identify the genetic differences in almond cultivars Waris and Ferralise, varying in blooming dates. Sequencing data from Illumina TruSeq libraries was processed using the FASTQC-Trimmomatic-HISAT2-Stringtie-Stringtie merge-DESeq2 pipeline. Overall alignment rates for different libraries ranged from 82.04-91.33%. DESeq2 analysis identified 3707 differentially expressed genes, out of which 1558 genes were up-regulated while the 2149 genes were down-regulated in Waris compared to Ferralise. Differential regulation of genes associated with the auxin signaling pathway, ubiquitin ligases, serine/threonine-protein phosphatases, proteasomes, translation initiation factors, phosphatidylinositol signaling and pentose phosphate pathway provides new insights into the molecular regulation of blooming in almonds. These findings will pave the way for molecularly differentiating early and late flowering almond cultivars and have implications in breeding late-blooming almond cultivars.