Vineyard victory: Decoding the Thompson Seedless genome for enhanced grape breeding
image: Overview of the T2T and gap-free genome of Thompson Seedless. The Circos plot depicts gene features at 500-kb intervals across the 19 chromosomes of Thompson Seedless. From the outer to the inner ring, the plot shows the GC content, gene density, TE-LTR content, TE content, tandem repeat content, SNPs, and InDels. The WGS reads were mapped to the TSv2_T2T genome for detecting SNPs and InDels. Numbers of SNPs and InDels of Thompson Seedless were calculated per 500 kb. Circos software was used for plotting the figure.
Credit: Horticulture Research
A pivotal study has revealed a high-quality, gap-free genome assembly of the Thompson Seedless grape, a variety that plays a crucial role in fresh consumption and winemaking. This remarkable achievement provides a comprehensive genetic blueprint, shedding light on the genetic foundations of key traits such as seedlessness, disease resistance, and color in grapes. By closing significant gaps in our understanding of grape genetics, this research opens new doors for molecular breeding, with the potential to develop disease-resistant, high-quality grape cultivars.
Grapevines are at the heart of global wine and food production, yet breeding them remains a complex challenge due to their intricate genomes and vulnerability to diseases. The absence of a complete genome assembly has long hindered advancements in grape genetic modification, limiting the development of disease-resistant varieties. This knowledge gap has highlighted the critical need for a thorough exploration of the Thompson Seedless genome to unlock its breeding potential and reveal its genetic secrets.
In a major step forward for viticulture, researchers from Northwest A&F University have published an unprecedented genome assembly of the Thompson Seedless grape in the journal Horticulture Research. Released on December 13, 2023, the study (DOI: 10.1093/hr/uhad260) offers a comprehensive, telomere-to-telomere, gap-free genome assembly, ushering in a new era of grape functional genomics. This milestone not only completes the genetic map of the Thompson Seedless but also sets a new standard for grapevine research.
The research presents an exceptionally detailed genome assembly of the Thompson Seedless grape, marking a significant advancement in grapevine genomics. Using cutting-edge sequencing technologies, the team achieved a gap-free genome assembly that spans all 19 chromosomes, with a remarkable N50 contiguity of 27.1 Mb. This new assembly not only fills gaps left by previous efforts but also incorporates an additional 31.5 Mb of high-quality sequence data, allowing for the annotation of over 30,000 protein-coding genes. A key highlight of the study is the detailed analysis of nucleotide-binding leucine-rich repeat (NLR) genes, which are crucial for plant disease resistance. The researchers identified a notable reduction in two types of NLRs, which may explain the variety’s susceptibility to fungal diseases. On the other hand, an increase in a third NLR gene type was observed, suggesting an evolutionary adaptation to pathogen pressures. These discoveries offer a genetic framework for understanding disease resistance mechanisms in grapes and provide a foundation for developing cultivars with greater disease resilience.
Dr. Junyang Song, the corresponding author of the study, commented, "Our work not only addresses gaps in the previous genome assembly but also provides a comprehensive genetic roadmap for grapevine breeding. This breakthrough will facilitate the development of disease-resistant grape varieties and deepen our understanding of grape genetics."
The high-quality reference genome of the Thompson Seedless will significantly accelerate grape molecular breeding initiatives. This genetic resource provides crucial insights into key traits such as seedlessness, disease resistance, and color characteristics, which can be leveraged to improve grapevine cultivation worldwide. The research paves the way for the creation of new grape varieties with enhanced traits, promising benefits for both the agricultural industry and consumers.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhad260
Funding information
This work was supported by the National Natural Science Foundation of China (U1603234, 32002000, 32202423), the Key Research and Development Program of Shaanxi (Program No.2023-YBNY-075), and China National GeneBank (CNGB).
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.