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

Abstract

BackgroundSeedlessness in grape (Vitis vinifera) is of considerable commercial importance for both the table grape and processing industries. Studies to date of grape seed development have been made certain progress, but many key genes have yet to be identified and characterized.ResultsIn this study we analyzed the seed transcriptomes of progeny derived from the V. vinifera seeded maternal parent ‘Red Globe’ and the seedless paternal parent ‘Centennial seedless’ to identify genes associated with seedlessness. A total of 6,607 differentially expressed genes (DEGs) were identified and examined from multiple perspectives, including expression patterns, Gene Ontology (GO) annotations, pathway enrichment, inferred hormone influence and epigenetic regulation. The expression data of hormone-related genes and hormone level measurement reveals the differences during seed development between seedless and seeded progeny. Based on both our results and previous studies of A. thaliana seed development, we generated network maps of grape seed-related DEGs, with particular reference to hormone balance, seed coat and endosperm development, and seed identity complexes.ConclusionIn summary, the major differences identified during seed development of seedless and seeded progeny were associated with hormone and epigenetic regulation, the development of the seed coat and endosperm, and the formation of seed identity complexes. Overall the data provides insights into the possible molecular mechanism controlling grape seed size, which is of great importance for both basic research and future translation applications in the grape industry.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3193-1) contains supplementary material, which is available to authorized users.

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

“…These studies indicate that the influence of monooxygenases on plant growth and development is via regulating GA and auxin content. In the seedless vs. seeded progeny populations used for transcriptional profiling, the content of both GA and auxin was significantly higher in seedless progeny compared to seeded ones during ovule development [17]. Moreover, overexpression of Arabidopsis CYP78A9,whichencodescytochrome P450,resulted large and seedlessfruit [35].…”

“…A total of 114 F1 individuals were obtained from a cross between the seeded maternal parent 'Red Globe' (V. vinifera) and the seedless paternal parent 'Centennial seedless' (V. vinifera) in 2009, which is the same population used in a ovule transcriptome analysis [17].All seedling plants were developed and maintained at the Zhengzhou Fruit Institute, Zhengzhou, China (113°42'N 34°43'E), and seed phenotypes were evaluated for three years.A total of 65 progeny with stable seed phenotype were obtained, including 31 seedless and 34 seeded. Of these, 19 seeded and 19 seedless individuals were randomly selected as experimental materials for genome sequencing.…”

“…All plants were identified and maintained in the grape germplasm resource orchard of Northwest Agriculture & Forestry University, Yangling, China (34°20′N 108°24′E).During ovule collection, ovule weight was measured along with development. Three landmark ovule developmental stages were defined based on seedless grape ovule weight change (initial stage, stage with the highest weight, and stage with the lowest weight) as done previously [17]. Samples were immediately frozen in liquid nitrogen and stored at −80 °C for subsequent gene The resulting raw Illumina reads were processed to remove duplicated read pairs (defined as those having identical bases in the first 100 bp of both left and right reads).…”

“…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]. A transcriptome analysis of ovule development in grape hybrids was used to develop a network map of possible mechanisms influencing seed size [17].…”

“…Variantswere identified by genome sequencing and analyzed with respect to previously published ovule transcriptome data [17] in order to identify variants and genes potentially affecting seed size.…”