RNA-Seq analysis of genes involved in pistillate flower initiation in Carya illinoinensis

Carya illinoinensis (pecan) is an economically important nut tree species that is native to North America and has been introduced to diverse environments around the world. Alternate bearing is one of the most significant constraints to reliable pecan production and is defined as high yields of lower quality nuts in one year and lower production of high quality nuts the next year and is directly related to pistillate flower initiation. Phytohormones and carbohydrate status play a pivotal role in flower initiation and are regulated by the expression of specific genetic signals within the plant, however, the timing of flower initiation in pecan is unknown. We hypothesize that a two-step process occurs with pistillate flower initiation in pecan with the first step occurring the growing season before flowers appear followed by the second step occurring right after the trees are active in the spring. To address this hypothesis RNA-Seq analyses of buds from ' Western' pecan trees were conducted during the months of June to September to obtain a complete gene expression profile and qRT-PCR was used to validate expression of specific pecan flowering genes. RNA-Seq analyses of the first eight transcriptome libraries elucidated differential gene expression in at least 50 flowering genes during the growing season. Gene expression of FT in leaves during early summer and promoter analysis elucidated both phytohormone and carbohydrate motifs. Plant growth regulator application had an impact on both the return bloom status and expression of flowering gene homologs in pecans. The RNA-Seq data has given us the first glimpse of the gene networks and timing of the genes involved in pecan floral initiation. These results along with further study will characterize the signals responsible for flower induction and elucidate the timing of these signals.