Structural genomics and transcriptional characterization of the Dormancy-Associated MADS-box genes during bud dormancy progression in apple

Abstract

The molecular control of bud dormancy establishment and release is still not well understood, although some genes have already been demonstrated to play important roles in this process. The dormancy-associated MADS-box (DAM) genes were first identified in the peach EVERGROWING locus and are considered the main regulators of bud dormancy control. In this work, the apple (Malus × domestica Borkh.), a perennial plant adapted to temperate climates that displays cycles of growth and bud dormancy, was screened for the presence of DAM genes. The candidate genes retrieved were characterized in comparison to DAM genes from other species. Four of them (MdDAM1-4) are structurally very similar to the reported DAM genes. When apple genomic segments containing these candidates were compared to the peach EVERGROWING locus, a highly conserved noncoding region was detected inside their largest intron. Similar sequences were also identified inside introns of apricot and pear DAM genes. Organ expression patterns revealed that MdDAM1-4 are mainly expressed in dormant buds and seeds, with low transcript accumulation in vegetative structures. In addition, the MdDAM genes showed seasonally oscillating patterns of steady-state messenger RNA (mRNA) levels and were downregulated by artificial chilling. Motif analyses in the promoter and in the intronic conserved region of the MdDAM genes disclosed some clues to the regulation of the expression patterns observed. Possible roles for the conserved intronic sequence in dormancy regulation are discussed.

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.…”

“…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).…”

“…In Rosaceae, DAM genes form a subclade separate from true Arabidopsis SVP -like and potato StMADS11 -like subclades (Velasco et al, 2010; Wells et al, 2015; Niu et al, 2016; Porto et al, 2016). In peach, the SVP gene family is expanded to six DAM genes, tandemly arranged on peach chromosome 1 (Jimenez et al, 2009; Illa et al, 2011), one true SVP ortholog PpeMADS57 and the less similar PpeMADS58 , located on chromosomes 6 and 8, respectively (Wells et al, 2015).…”

“…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).…”