A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]

Abstract

BackgroundMADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using next-generation sequencing. We then focused on the dormancy-related SVP/AGL24 and FLC subfamilies, comparing their numbers and phylogenetic relationships with those of other sequenced woody perennial genomes.ResultsWe identified 79 MADS-box genes distributed across all eight peach chromosomes and frequently located in clusters of two or more genes. They encode proteins with a mean length of 248 ± 72 amino acids and include representatives from most of the thirteen Type II (MIKC) subfamilies, as well as members of the Type I Mα, Mβ, and Mγ subfamilies. Most Type I genes were present in species-specific monophyletic lineages, and their expression in the peach sporophyte was low or absent. Most Type II genes had Arabidopsis orthologs and were expressed at much higher levels throughout vegetative and fruit tissues. During short-day-induced growth cessation, seven Type II genes from the SVP/AGL24, AGL17, and SEP subfamilies showed significant changes in expression. Phylogenetic analyses indicated that multiple, independent expansions have taken place within the SVP/AGL24 and FLC lineages in woody perennial species.ConclusionsMost Type I genes appear to have arisen through tandem duplications after the divergence of the Arabidopsis and peach lineages, whereas Type II genes appear to have increased following whole genome duplication events. An exception to the latter rule occurs in the FLC and SVP/AGL24 Type II subfamilies, in which species-specific tandem duplicates have been retained in a number of perennial species. These subfamilies comprise part of a genetic toolkit that regulates endodormancy transitions, but phylogenetic and expression data suggest that individual orthologs may not function identically across all species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0436-2) contains supplementary material, which is available to authorized users.

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

“…The remaining DAM -like and SVP -like coding sequences were amplified using oligonucleotide primers designed from ‘Royal Gala’ partial sequences and previously reported apple DAM / SVP / JOINTLESS genes (Supplementary Table S1). The predicted full length amino acid sequences were aligned with the full length of amino acid sequences of Arabidopsis SVP (AT2G22450) and AGL24 (AT4G24540), potato StMADS11 (AF008652), apple MdDAM1 (KT582786), MdDAM2 (KT582787), MdDAM4 (KT582789), MdJb (LC004730), apricot PmDAM6 (AB437345), leafy spurge EeDAM2 (EU339320), three pear DAM ( PpyDAM1 , PpyDAM2 and PpyDAM3 ) and one pear SVP ( PpySVP) (Niu et al, 2016), six peach DAM ( PpeDAM1, PpeDAM2, PpeDAM3, PpeDAM4, PpeDAM5 and PpeDAM6) (Bielenberg et al, 2006) and one peach SVP ( PpeMADS57 ) (Wells et al, 2015), trifoliate orange PtSVP (FJ373211), kiwifruit SVP gene s ( AcSVP1 , AcSVP2, AcSVP3 and AcSVP4 ) (Wu et al, 2012). The alignments were performed using Clustal W (opening = 10, extension = 0.2).…”

“…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).…”

“…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). A similar expansion of six tandemly arranged DAM genes was found on Japanese apricot chromosome 2, but two SVP orthologs are located on chromosomes 1 and 6 (Sasaki et al, 2011; Xu et al, 2014).…”

Photoperiod‐ and temperature‐mediated control of phenology in trees – a molecular perspective

“…Changes in H3K27me3 at certain loci, such as DAM genes in peach, have been observed during bud dormancy release (Leida et al ., ). Interestingly, the DAM genes are expressed in terminal buds of pear and apricot (Yamane et al ., , ; Li et al ., ; Wells et al ., ). However, their physiological roles in bud dormancy regulation are far from clear, and it is essential to determine whether the blocking of trimethylation of H3K27 at candidate loci perturbs dormancy before drawing definitive conclusions with regard to the roles of H3K27me3 or DAM genes in this process.…”

Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry ( Prunus avium L.)

“…Many MADS-box genes have arisen via duplication events and have since acquired new functions [59]. Among the acquired functions is regulation of endodormancy release [60] which makes the MADS-box genes particularly useful in comparing the selected cultivars as the genotypes exhibit a late fruit maturation phenotype. Because this is a sequence based method, single nucleotide polymorphisms, which may not be visible using the gel-based approach, can be easily detected.…”