Identification of repetitive sequences and evolutionary analysis of long terminal repeat retrotransposon (LTR-RT) families in subgenomes of the cultivated strawberry genome.
Strawberry cultivation has long been valued for its significant economic impact and consumer appeal. However, the complex genetic background of octoploid strawberries, arising from the hybridization of multiple diploid ancestors, poses challenges for genetic research and crop improvement. To fully leverage its genetic diversity and address limitations like disease susceptibility, a high-quality, complete genome is essential. These challenges necessitate comprehensive research to deepen understanding and refine breeding strategies for strawberry improvement.
On November 27, 2023, researchers from the Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences published (DOI: 10.1093/hr/uhad252) a detailed genome assembly for the 'Benihoppe' strawberry in Horticulture Research. This groundbreaking study, published with Oxford University Press, achieves a phased, gap-free genome structure for each subgenome (ABCD) of the strawberry. The assembly is expected to transform genetic research on strawberries by providing a robust foundation for studying traits tied to disease resistance, flavor, and fruit ripening.
The study reveals that subgenome A, closely related to Fragaria vesca, is dominant in the octoploid cultivated strawberry, retaining the highest gene count with minimal transposable elements, low DNA methylation, and high expression levels associated with fruit ripening. In contrast, subgenomes B, C, and D show structural differences and varying methylation patterns, especially around transposable elements near genes. These differences illustrate a parallel evolution among subgenomes B, C, and D while subgenome A remains stable, evolving under strong purifying selection. Notably, genes in subgenome A are enriched in processes critical for fruit development, marking it as a primary driver of key agronomic traits. The insights gained from these findings hold promise for targeted breeding strategies to enhance fruit quality, resilience, and adaptability in strawberries by leveraging the genetic strengths of subgenome A.
Dr. Houcheng Zhou, a lead author of the study, emphasized the potential of this assembly to advance strawberry breeding. “With this fully resolved genome, we now have the tools to explore genetic contributions of each subgenome in ways that were previously unfeasible. This research opens the door to developing strawberries that are not only higher quality but also more resilient to environmental challenges and diseases,” Dr. Zhou stated.
The high-resolution genome of 'Benihoppe' provides a template for advancing strawberry breeding programs, particularly in areas of flavor, disease resistance, and yield. By exploring the genetic makeup of the dominant subgenome A, breeders can harness its traits for improving fruit quality and enhancing resilience to pathogens, potentially reducing reliance on chemical treatments. Future applications may extend to other octoploid crops, fostering improvements across horticulture.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhad252
Funding information
This study was supported by grants from the National Key Research and Development Program (2022YFD1600700, 2019YFD1000203), the Major Science and Technology Projects of Henan Province (221100110400), the Special Fund for Henan Agriculture Research System (HARS-22-09-G2), and the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2021-ZFRI).
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.
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