Comparative phylogenetic analysis and transcriptional profiling of MADS-box gene family identified DAM and FLC-like genes in apple (Malusx domestica)

Abstract

The MADS-box transcription factors play essential roles in various processes of plant growth and development. In the present study, phylogenetic analysis of 142 apple MADS-box proteins with that of other dicotyledonous species identified six putative Dormancy-Associated MADS-box (DAM) and four putative Flowering Locus C-like (FLC-like) proteins. In order to study the expression of apple MADS-box genes, RNA-seq analysis of 3 apical and 5 spur bud stages during dormancy, 6 flower stages and 7 fruit development stages was performed. The dramatic reduction in expression of two MdDAMs, MdMADS063 and MdMADS125 and two MdFLC-like genes, MdMADS135 and MdMADS136 during dormancy release suggests their role as flowering-repressors in apple. Apple orthologs of Arabidopsis genes, FLOWERING LOCUS T, FRIGIDA, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 and LEAFY exhibit similar expression patterns as reported in Arabidopsis, suggesting functional conservation in floral signal integration and meristem determination pathways. Gene ontology enrichment analysis of predicted targets of DAM revealed their involvement in regulation of reproductive processes and meristematic activities, indicating functional conservation of SVP orthologs (DAM) in apple. This study provides valuable insights into the functions of MADS-box proteins during apple phenology, which may help in devising strategies to improve important traits in apple.

SVP-like MADS Box Genes Control Dormancy and Budbreak in Apple

“…Further interrogation of ‘Royal Gala’ transcripts identified partial sequences that were highly similar to previously reported MdDAMa / MdDAM1, MdDAMc / MdDAM2 and MdSVPb / MdDAM3 / MdJb sequences (Mimida et al, 2015; Nakano et al, 2015; Wisniewski et al, 2015; Porto et al, 2016). Amplification of full-length sequences from ‘Royal Gala’ tissues confirmed that the ‘Royal Gala’ sequences were identical or almost identical to previous reports.…”

“…Amplification of full-length sequences from ‘Royal Gala’ tissues confirmed that the ‘Royal Gala’ sequences were identical or almost identical to previous reports. However, we could not identify a ‘Royal Gala’ MdDAMd / MdDAM3 , already suggested to be either a pseudogene or a result of misannotation (Mimida et al, 2015; Porto et al, 2016), nor MdDAM4 (KT582789) (Porto et al, 2016). To prevent confusion, the nomenclature proposed by Mimida et al (2015) was chosen (Supplementary Table S2) to reflect the relationship to DAM and true SVP homologs.…”

“…However, we could not identify a ‘Royal Gala’ MdDAMd / MdDAM3 , already suggested to be either a pseudogene or a result of misannotation (Mimida et al, 2015; Porto et al, 2016), nor MdDAM4 (KT582789) (Porto et al, 2016). To prevent confusion, the nomenclature proposed by Mimida et al (2015) was chosen (Supplementary Table S2) to reflect the relationship to DAM and true SVP homologs. Phylogenetic study of predicted full-length protein sequences confirmed the placement of ‘Royal Gala’ MdDAM and MdSVP proteins in the DAM and SVP subclades ( Figure 1 ).…”

“…Several studies attempted to identify and characterize apple DAM genes after the apple genome sequence release (Velasco et al, 2010). The presence of DAM and SVP orthologs was confirmed (Mimida et al, 2015; Wisniewski et al, 2015; Kumar G. et al, 2016; Porto et al, 2016), with some discrepancies in nomenclature used in reports and the possible presence of misannotated genes or pseudogenes (Mimida et al, 2015; Porto et al, 2016). Despite the nomenclature discrepancies, apple DAM genes appear to be arranged in tandem on chromosomes 8 and 16, in regions syntenic to the peach chromosome 1, where six peach DAM genes are located (Illa et al, 2011; Mimida et al, 2015; Porto et al, 2016).…”

“…Two SVP orthologs are located on apple chromosomes 4 and 11, respectively. Ectopic expression of the SVP ortholog MdJOINTLESSa ( MdJa ) restored the JOINTLESS -deficient tomato mutant (Nakano et al, 2015), demonstrating similar molecular activity between SVP -like genes, while differential seasonal expression of apple DAM and SVP genes at different stages of apical bud development suggested roles in bud dormancy (da Silveira Falavigna et al, 2013; Mimida et al, 2015; Porto et al, 2016). Seasonality and differential expression patterns were also demonstrated in bark tissue of apple (Wisniewski et al, 2015).…”