Transcriptome analysis during berry development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and its seedless somatic variant

Abstract

BackgroundSeedless grapes are greatly appreciated for fresh and dry fruit consumption. Parthenocarpy and stenospermocarpy have been described as the main phenomena responsible for seedlessness in Vitis vinifera. However, the key genes underpinning molecular and cellular processes that play a significant role in seed development are not well characterized. To identify important regulators and mechanisms that may be altered in the seedless phenotype, we performed a comprehensive transcriptional analysis to compare the transcriptomes of a popular seeded wine cultivar (wild-type) and its seedless somatic variant (mutant) at three key developmental stages.ResultsThe transcriptomes revealed by Illumina mRNA-Seq technology had approximately 98% of grapevine annotated transcripts and about 80% of them were commonly expressed in the two lines. Differential gene expression analysis revealed a total of 1075 differentially expressed genes (DE) in the pairwise comparison of developmental stages, which included DE genes specific to the wild-type background, DE genes specific to the mutant background and DE genes commonly shared in both backgrounds. The analysis of differential expression patterns and functional category enrichment of wild-type and mutant DE genes highlighted significant coordination and enrichment of pollen and ovule developmental pathways. The expression of some selected DE genes was further confirmed by real-time RT-PCR analysis.ConclusionsThis study represents the most comprehensive attempt to characterize the genetic bases of seed formation in grapevine. With a high throughput method, we have shown that a seeded wine grape and its seedless somatic variant are similar in several biological processes. Nevertheless, we could identify an inventory of genes with altered expression in the mutant compared to the wild-type, which may be responsible for the seedless phenotype. The genes located within known genomic regions regulating seed content may be used for the development of molecular tools to assist table grape breeding. Therefore the data reported here have provided a rich genomic resource for practical use and functional characterization of the genes that potentially underpin seedlessness in grapevine.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1030) contains supplementary material, which is available to authorized users.

Transcriptome analysis of an apple (Malus×domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation

“…Somatic mutation in plants, including woody species, could arise from genetic ( Kobayashi et al , 2004 ; Venturi et al , 2006 ; Nwafor et al , 2014 ; Otto et al , 2014 ) or epigenetic ( Kvaalen and Johnsen, 2008 ) changes. These mutants, almost identical to their parents in genetic background, are considered desirable genetic material to study the novel traits of mutation ( Nwafor et al , 2014 ; Otto et al , 2014 ).…”

“…Somatic mutation in plants, including woody species, could arise from genetic ( Kobayashi et al , 2004 ; Venturi et al , 2006 ; Nwafor et al , 2014 ; Otto et al , 2014 ) or epigenetic ( Kvaalen and Johnsen, 2008 ) changes. These mutants, almost identical to their parents in genetic background, are considered desirable genetic material to study the novel traits of mutation ( Nwafor et al , 2014 ; Otto et al , 2014 ). Somatic mutations causing fruit colour alteration have been recognized amongst several woody fruit species, including grape ( Kobayashi et al , 2004 ; Azuma et al , 2009 ), pear ( Thomas et al , 2010 ; Wang et al , 2013 ; Qian et al , 2014 ), and apple ( Ben-Yehudah et al , 2005 ; Venturi et al , 2006 ; Xu et al , 2012 ).…”

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

“…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]. Finally, a transcriptome analysis during berry development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and its seedless somatic variant [36]. Despite all the progress mentioned above, the molecular and genetic mechanisms controlling grape seed size remain unidentified.…”

Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles

“…Nowadays, an increase in table grape world production is clearly evident and, based on consumer preferences, is accompanied by a strong interest in seedless varieties for fresh consumption. Therefore, seedlessness is among the main focus of current table grape breeding programmes [11]. In seeded grapes, flower-to-fruit transition requires pollination and ovary fertilisation toward seed formation.…”