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.
Highlights
Seedlessness in grape (Vitis vinifera) is of considerable commercial importance for both the table grape and processing industries
Identification and expression patterns of differentially expressed genes (DEGs) indicate the involvement of Transcription factor (TF) and transcription regulators (TRs) in grape seed development Approximately 90 % of the cleaned reads could be mapped to the reference V. vinifera PN40024 genome (Additional file 1: Table S1)
Most of the TF DEGs showed an up-regulated expression in the seedless progeny compared to the seeded progeny, some DEGs identified in the C2H2, MYB, LOB and MADS-box families were down-regulated (SL/S) at all three developmental stages (Additional file 4: Figure S1)
Summary
Seedlessness 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. Seed development in angiosperms is initiated by double fertilization, in which two sperm cells separately fuse with the egg and the central cell of the female gametophyte, leading to the formation of a diploid embryo and a triploid endosperm [1]. This process occurs inside the ovule that, following fertilization, develops into a seed. Genetic studies have identified many of the genes that participate in A. thaliana ovule development, such as SHOOT MERISTEMLESS. The MADS-box genes AGAMOUS (AG), SEPALLATA (SEP1, SEP2 and SEP3), SHATTERPROOF (SHP1 and SHP2) and SEEDSTICK (STK, known as AGL11) share a common function in promoting ovule and seed identity [12,13,14,15]
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