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

ABSTRACT: We report the application of Illumina mRNA sequencing technology for high-throughput profiling of the transcriptome of a seeded wine cultivar (wild-type) and its seedless somatic variant (mutant), sampled at three key growth stages of grapevine: E-L 15 (single flowers in compact groups), E-L 27 (young berries enlarging) and E-L 38 (berries harvest-ripe). By obtaining over 126 to 143 million and 102 to 127 million reads of 100-bp in length for the wild-type and mutant respectively, we have for the first time provided a holistic view of the transcriptional landscape during seed development in both phenotypes. We found that comparison of differentially expressed (DE) genes, gene patterns and gene enrichment between the wild-type and mutant distinguished transcriptional events in the two lines. For example, differential expression analysis in the pairwise comparison between developmental stages identified 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 DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have lead to the identification of candidate genes for seedlessness that have altered expression in wild-type and mutant. In conclusion, we have shown here a logical approach to identify possible regulators and processes required for normal seed development that may be altered in the seedless phenotype, and highlighted the importance of somatic variants as a resources.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE58061 | GEO | 2014/12/31

SECONDARY ACCESSION(S): PRJNA248771

REPOSITORIES: GEO