Data from: Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation

Project Title:  View help for Project Title Data from: Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation

Summary:  View help for Summary Background: There has been increased consumption of blueberries in recent years fueled in part because of their many recognized health benefits. Blueberry fruit is very high in anthocyanins, which have been linked to improved night vision, prevention of macular degeneration, anti-cancer activity, and reduced risk of heart disease. Very few genomic resources have been available for blueberry, however. Further development of genomic resources like expressed sequence tags (ESTs), molecular markers, and genetic linkage maps could lead to more rapid genetic improvement. Marker-assisted selection could be used to combine traits for climatic adaptation with fruit and nutritional quality traits.

Results: Efforts to sequence the transcriptome of the commercial highbush blueberry (Vaccinium corymbosum) cultivar Bluecrop and use the sequences to identify genes associated with cold acclimation and fruit development and develop SSR markers for mapping studies are presented here. Transcriptome sequences were generated from blueberry fruit at different stages of development, flower buds at different stages of cold acclimation, and leaves by next-generation Roche 454 sequencing. Over 600,000 reads were assembled into approximately 15,000 contigs and 124,000 singletons. The assembled sequences were annotated and functionally mapped to Gene Ontology (GO) terms. Frequency of the most abundant sequences in each of the libraries was compared across all libraries to identify genes that are potentially differentially expressed during cold acclimation and fruit development. Real-time PCR was performed to confirm their differential expression patterns. Overall, 14 out of 17 of the genes examined had differential expression patterns similar to what was predicted from their reads alone. The assembled sequences were also mined for SSRs. From these sequences, 15,886 blueberry EST-SSR loci were identified. Primers were designed from 7,705 of the SSR-containing sequences with adequate flanking sequence. One hundred primer pairs were tested for amplification and polymorphism among parents of two blueberry populations currently being used for genetic linkage map construction. The tetraploid mapping population was based on a cross between the highbush cultivars Draper and Jewel (V. darrowii is also in the background of ‘Jewel’). The diploid mapping population was based on a cross between an F1 hybrid of V. darrowii and diploid V. corymbosum and another diploid V. corymbosum. The overall amplification rate of the SSR primers was 68% and the polymorphism rate was 43%.

Conclusions: These results indicate that this large collection of 454 ESTs will be a valuable resource for identifying genes that are potentially differentially expressed and play important roles in flower bud development, cold acclimation, chilling unit accumulation, and fruit development in blueberry and related species. In addition, the ESTs have already proved useful for the development of SSR and EST-PCR markers, and are currently being used for construction of genetic linkage maps in blueberry.


Resources in this dataset:

Resource Title: 12870_2011_1018_MOESM1_ESM. File Name: 12870_2011_1018_MOESM1_ESM.XLSXResource Description: Additional file 1: Most highly abundant sequences from each of the libraries along with their number of reads/frequency of reads and predicted expression patterns across the bud time points and the fruit development stages. Approximately 30 most highly abundant sequences from each of the libraries along with their number of reads/ frequency of reads and predicted expression patterns across the bud time points (0, 397, 789, and 1333 chill hours) and fruit development stages (green, white, pink, and blue/ripe). Data supplement retrieved from https://static-content.springer.com/esm/art:10.1186/1471-2229-12-46/MediaObjects/12870_2011_1018_MOESM1_ESM.XLSX

Resource Title: 12870_2011_1018_MOESM1_ESM.

File Name: 12870_2011_1018_MOESM1_ESM.XLSX

Resource Description: Additional file 1: Most highly abundant sequences from each of the libraries along with their number of reads/frequency of reads and predicted expression patterns across the bud time points and the fruit development stages. Approximately 30 most highly abundant sequences from each of the libraries along with their number of reads/ frequency of reads and predicted expression patterns across the bud time points (0, 397, 789, and 1333 chill hours) and fruit development stages (green, white, pink, and blue/ripe).

Data supplement retrieved from https://static-content.springer.com/esm/art:10.1186/1471-2229-12-46/MediaObjects/12870_2011_1018_MOESM1_ESM.XLSX

Resource Title: Supplement S3 . File Name: 11032_2013_3_MOESM3_ESM.docxResource Description: Supplement S3 Alignment of FAD3A protein sequence of PI 85671 and Williams 82, and Weblogo image showing the conservation of the amino acid region surrounding the residue N110 Data supplement retrieved from https://static-content.springer.com/esm/art:10.1186/1471-2229-12-46/MediaObjects/12870_2011_1018_MOESM2_ESM.DOCX

Resource Title: Supplement S3 .

File Name: 11032_2013_3_MOESM3_ESM.docx

Resource Description: Supplement S3 Alignment of FAD3A protein sequence of PI 85671 and Williams 82, and Weblogo image showing the conservation of the amino acid region surrounding the residue N110

Data supplement retrieved from https://static-content.springer.com/esm/art:10.1186/1471-2229-12-46/MediaObjects/12870_2011_1018_MOESM2_ESM.DOCX

Original Distribution URL:  View help for Original Distribution URL https://agdatacommons.nal.usda.gov/articles/dataset/Data_from_Generation_and_analysis_of_blueberry_transcriptome_sequences_from_leaves_developing_fruit_and_flower_buds_from_cold_acclimation_through_deacclimation/24662790

Subject Terms:  View help for Subject Terms blueberries; anthocyanins; night vision; macular degeneration; antineoplastic activity; risk reduction; heart diseases; genomics; expressed sequence tags; genetic markers; chromosome mapping; genetic improvement; marker-assisted selection; nutritive value; transcriptome; Vaccinium corymbosum; cultivars; genes; acclimation; fruiting; microsatellite repeats; developmental stages; buds; leaves; gene ontology; gene expression regulation; quantitative polymerase chain reaction; polymerase chain reaction; loci; hybridization probes; parents; tetraploidy; diploidy; hybrids; cold treatment; vision

Collection Notes:  View help for Collection Notes DOI: 10.15482/USDA.ADC/1529215 Citation: Rowland, Lisa J.; Alkharouf, Nadim W.; Darwish, Omar; Ogden, Elizabeth L.; Polashock, James J.; Bassil, Nahla V.; Main, Dorrie S. (2018). Data from: Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. Springer. https://doi.org/10.15482/USDA.ADC/1529215 (Downloaded 2026-06-26)