DOI: 10.5061/dryad.fn2z34tr5
title: Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh)

description: Many apple cultivars are subject to biennial fluctuations in flowering and
 fruiting. It is believed that this phenomenon is caused by a repressive
 effect of developing fruit on the initiation of flowers in the apex of
 proximal bourse shoots. However, the genetic pathways of floral initiation
 are incompletely described in apple, and the biological nature of floral
 repession by fruit is currently unknown. In this study, we characterize
 the transcriptional landscape of bourse shoot apices in the biennial
 cultivar, 'Honeycrisp', during the period of floral initiation,
 in trees bearing a high fruit load and in trees without fruit. Trees with
 high fruit load produced almost exclusively vegetative growth in the
 subsequent year, whereas the trees without fruit produced flowers on the
 majority of the potential flowering nodes. Using RNA-based sequence data,
 we documented gene expression at high resolution, identifying
 &gt;11,000 transcripts that had not been previously annotated, and
 characterized expression profiles associated with vegetative growth and
 flowering. We also conducted a census of genes related to known flowering
 genes, organized the phylogenetic and syntenic relationships of these
 genes, and compared expression among homologs. Several genes closely
 related to AP1, FT, FUL,
 LFY, and SPLS were more strongly expressed in
 apices from non-bearing, floral-determined trees, consistent with their
 presumed floral-promotive roles. In contast, a homolog
 of TFL1 exhibited strong and persistent up-regulation
 only in apices from bearing, vegetative-determined trees, suggesting a
 roles in floral repression. Additionally, we identified
 four GIBBERELLIC ACID (GA) 2 OXIDASE genes that were
 expressed to relatively high levels in apices from bearing trees. These
 results define the flowering-related transcriptional landscape in apple,
 and strongly support previous studies implicating both gibberellins
 and TFL1 as key components in repression of flowering by
 fruit. 
description: S1 File was constructed using the StringTie transcriptome
 assembler following RNAseq read alignment using HISAT2. 
 S2 File was constructed by the Trinity transcriptome assembler
 using reads that failed to map to the GDDH13 reference genome using
 HISAT2. S3 File was constructed by running the FASTA
 output from the Trinity transcriptome assembler through the python program
 Trinity_gene_splice_modeler.py provided by the Trinity suite.
 S4 File was generated using the Cuffdiff program within the
 Cufflinks suite. S5 File was generated using the
 Cuffdiff program within the Cufflinks suite. All .png
 files image files are peptide phylogenies of Arabidopsis genes and their
 apple homologs genereated using ETE3. 
description: S1 File. Annotation file of assembled Honeycrisp transcript
 models from StringTie. Annotation file is formated as a .gtf file and can
 be used with any transcriptome assembler
 (<em>e.g. </em>StringTie, Cufflinks, etc) or annotation reader
 (<em>e.g.</em> gffread). S2 File. FASTA
 sequences of <em>de novo </em>transcrits assembled from
 unmapped reads. This file can be read and accessed using any FASTA
 software (<em>e.g.</em> BLAST). S3 File.
 Annotation file of sequences of <em>de novo </em>transcrits
 assembled from unmapped reads. Annotation file is formated as a .gtf file
 and can be used with any transcriptome assembler
 (<em>e.g. </em>StringTie, Cufflinks, etc) or annotation reader
 (<em>e.g.</em> gffread). S4 File.
 Differentially expressed genes. File is saved as a .diff output from
 Cufflinks which is a text deliminated file and can be read using cufflinks
 or any text editor.  S5 File. Differentially expressed
 genes. File is saved as a .diff output from Cufflinks which is a text
 deliminated file and can be read using cufflinks or any text
 editor.  All .png files can be viewed using any image
 viewer.