Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines

Abstract

MADS-box transcription factors are involved in many aspects of plant growth and development, such as floral organ determination, fruit ripening, and embryonic development. Yet not much is known about grape (Vitis vinifera) MADS-box genes in a relatively comprehensive genomic and functional way during ovule development. Accordingly, we identified 54 grape MADS-box genes, aiming to enhance our understanding of grape MADS-box genes from both evolutionary and functional perspectives. Synteny analysis indicated that both segmental and tandem duplication events contributed to the expansion of the grape MADS-box family. Furthermore, synteny analysis between the grape and Arabidopsis genomes suggested that several grape MADS-box genes arose before divergence of the two species. Phylogenetic analysis and comparisons of exon-intron structures provided further insight into the evolutionary relationships between the genes, as well as their putative functions. Based on phylogenetic tree analysis, grape MADS-box genes were divided into type I and type II subgroups. Tissue-specific expression analysis suggested roles in both vegetative and reproductive tissue development. Expression analysis of the MADS-box genes following gibberellic acid (GA3) treatment revealed their response to GA3 treatment and that seedlessness caused by GA3 treatment underwent a different mechanism from that of normal ovule abortion. Expression profiling of MADS-box genes from six cultivars suggests their function in ovule development and may represent potential ovule identity genes involved in parthenocarpy. The results presented provide a few candidate genes involved in ovule development for future study, which may be useful in seedlessness-related molecular breeding programs.

Transcriptome analyses of seed development in grape hybrids reveals a possible mechanism influencing seed size

“…All the selected DEGs included genes involved in flower and seed identity like VvMADS39 , VvMADS45 , VvSTM and AP2 , genes related to seed coat development like VvNAC26 , VvNAC86 , SCD1 and SCD2 ,genes related to endosperm development and epigenetic regulation like VvPHE1 , VvDME and VvDDM1 , and genes associated with hormone balance like GRAS , GH3-1 and GH3-9 . Besides, the expression patterns of two MADS-box genes VvMADS45 (GSVIVT01009393001) and VvMADS39 (GSVIVT01008139001) were found to be consistent with those presented in a previously published study [34]. Moreover, based on the above mentioned results, 15 out of the 30 DEGs were further selected and subjected to qRT-PCR validation using samples ‘V-Seeded’ (seed mixtures from another 4 seeded progeny) and ‘V-Seedless’ (seed mixtures from another 4 seedless progeny) (Fig.…”

“…Moreover, NAM ( NO APICAL MERISTEM ), CUC1 ( CUP-SHAPED COTYLEDON ) and CUC2 , all NAC genes, have been reported to be involved in regulating secondary cell wall biosynthesis [39, 40]. Many reports have indicated that MADS-box genes play critical roles in ovule, seed and flower development [34, 41, 42] and the expression of VvMADS28 , VvMADS39 and VvMADS45 in this current study was consistent with previous analysis of seeds from multiple seeded and seedless grape cultivars [34]. Additionally, TFs such a GRAS and HB are involved in GA and ABA signal transduction, and TRs such as AUX/IAA are important in auxin regulation [43].…”

“…Previous studies [34, 58] have reported that seed weight of seedless grapes usually begin to decrease at 27 ~ 33 days after full bloom (DAF), and so seeds from 9 seedless and 9 seeded grape progeny were collected at 24, 27, 30, 33, 36, 39 and 42 DAF (Additional file 11: Figure S5). Fruits of all progeny individuals were slashed with scalpel, and then seeds were immediately picked out without damage using tweezers and put into centrifuge tubes which were already soaked in liquid nitrogen.…”

“…Moreover, VvAGL11 , a MADS-box seed identity gene, has been proposed as playing a role in stenospermocarpy, and has been suggested as a candidate for use in marker-assisted selection [33]. In addition, five MADS-box genes ( VvMADS28 , VvMADS39 , VvMADS44 , VvMADS45 and VvMADS46 ) were reported to show different expression patterns during seed development between seeded and seedless grape cultivars, indicating a potential role in seed development [34]. It was proposed that parthenocarpy in the seedless somatic grapevine variant, Corinto bianco, may be caused by the absence of a mature macrogametophyte, probably due an arrest in meiosis coupled with fertilization-independent fruit growth [35].…”

QTL-seq Analysis of Seed Size Trait in Grape Provides New Molecular Insight on Seedlessness

“…Moreover, the grape berry-specific basic helix-loop-helix transcription factor VvCEB1 was reported to affect cell size [14]. In addition, some MADS-box genes, which show strong homology to an Arabidopsis ovule identity gene, were found to be differentially expressed during ovule development in multiple seeded and seedless grape cultivars, indicating a potential role in ovule development [15]. Moreover, nowdays omics analysis has cast light on mechanism related to grape seedlessness, evidence showed that parthenocarpy in the grapevine seedless somatic variant Corintobianco was caused by the absence of a mature macrogametophyte which was probably due to meiosis arrest [16].…”