10.5061/DRYAD.FN2Z34TR5
Gottschalk, Chris
0000-0003-4584-0014
Michigan State University
van Nocker, Steve
0000-0002-5810-1694
Michigan State University
Genetic mechanisms associated with floral initiation and the repressive
effect of fruit on flowering in apple (Malus x domestica Borkh)
Dryad
dataset
2020
biennial bearing
Malus x domestica
Developmental Transcriptome
transition to flowering
TERMINAL FLOWER 1
2020-12-02T00:00:00Z
2020-12-02T00:00:00Z
en
1293689004 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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
>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.
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.
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 (e.g. StringTie, Cufflinks, etc) or annotation
reader (e.g. gffread). S2 File. FASTA sequences of de novo transcrits
assembled from unmapped reads. This file can be read and accessed using
any FASTA software (e.g. BLAST). S3 File. Annotation file of sequences
of de novo transcrits assembled from unmapped reads. Annotation file is
formated as a .gtf file and can be used with any transcriptome assembler
(e.g. StringTie, Cufflinks, etc) or annotation reader (e.g. 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.