The rosy future of fruits: a genomic leap with ROFT database
image: Comparative eFP browser showing the expression patterns of WIP3 in fruit tissues of all four Rosaceae species. The peach WIP3 gene (gene ID Prupe.6G127700) is entered here as a search example. There are two apple orthologs, and their expressions are both displayed. The scale bars are RNA-seq read levels expressed as log2(TPM + 1). The keys to the fruit tissue types are shown in the box, and specific fruit developmental stages as Days Post Anthesis (DPA) are shown beneath each stage.
Credit: Horticulture Research
A new study presents a significant leap in our understanding of Rosaceae fruits, unveiling a comparative genomic resource that could transform fruit breeding. The research provides insights into the gene expression patterns across different developmental stages of apples, peaches, strawberries, and raspberries, offering a robust platform for future crop improvement and variety development. This breakthrough is set to revolutionize the agricultural sector by enabling scientists to harness the genetic potential of these economically important fruits.
The Rosaceae family includes some of the world’s most essential fruit crops, yet early-stage fruit development remains underexplored. These developmental phases—ranging from fruit set to cell division and expansion—are critical for determining fruit quality. However, studying these complex processes has been challenging, prompting a need for more detailed investigations. These challenges highlight the need for deeper research into early fruit development.
The University of Maryland’s Department of Cell Biology and Molecular Genetics led a study, published (DOI: 10.1093/hr/uhad240) on November 14, 2023, in Horticulture Research, unveiling the Rosaceae Fruit Transcriptome Database (ROFT). This powerful RNA-seq database enables comparative analysis of gene expression in apples, peaches, strawberries, and raspberries. By using consistent data collection methods, ROFT offers reliable cross-species insights into early fruit development, accessible via the ROFT website.
ROFT addresses the shortcomings of existing databases by providing a unified framework to compare gene expression across different Rosaceae species. Researchers collected RNA-seq data from key fruit tissues during early development, including the hypanthium, ovary wall, and ovules. This platform enables users to explore tissue-specific and stage-specific genes, visualize expression patterns, and study co-expressed genes across species. The database’s focus on fruit type diversity, such as drupe (peach), pome (apple), achenetum (strawberry), and drupetum (raspberry), allows for broader research into evolutionary biology and agricultural applications.
“ROFT is a significant step forward for fruit development research,” said Dr. Zhongchi Liu, lead researcher on the project. “By enabling cross-species analysis, we can now better understand the genetic factors that drive fruit quality and growth. This tool will help target genes that influence traits like size, flavor, and yield.”
ROFT holds immense potential for accelerating the development of new fruit varieties with enhanced characteristics. Its comprehensive gene expression data offers a critical resource for molecular breeding programs, paving the way for future innovations in fruit production. These advances could lead to a richer variety of high-quality fruits available to consumers worldwide.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhad240
Funding information
This work has been supported by a grant from the National Science Foundation (NSF) (IOS-1444987) to ZL and SMM. ML was supported in part by a National Science Foundation award (DGE-1632976).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.