Grapevines are central to global wine and food production, yet breeding them presents complexities due to intricate genomes and disease vulnerabilities. The lack of a complete genome assembly has long impeded progress in grape genetic modification, limiting the development of disease-resistant varieties. This gap underscores the necessity for a thorough exploration of the Thompson Seedless genome to unlock its breeding potential.
In a significant advancement for viticulture, researchers from Northwest A&F University published a groundbreaking genome assembly of the Thompson Seedless grape in the journal Horticulture Research on December 13, 2023. The study offers a comprehensive, telomere-to-telomere, gap-free genome assembly, marking a new era for grape functional genomics. This achievement not only completes the genetic map of the Thompson Seedless but also establishes a new benchmark for grapevine research.
The research presents an exceptionally detailed genome assembly of the Thompson Seedless grape, utilizing cutting-edge sequencing technologies to achieve a gap-free assembly across all 19 chromosomes, with an N50 contiguity of 27.1 Mb. This new assembly fills gaps from previous efforts and adds 31.5 Mb of high-quality sequence data, allowing the annotation of over 30,000 protein-coding genes. A notable aspect of the study is the analysis of nucleotide-binding leucine-rich repeat (NLR) genes, essential for plant disease resistance. Researchers observed a significant reduction in two types of NLRs, potentially explaining the variety's susceptibility to fungal diseases, while an increase in a third type of NLR gene suggests an evolutionary response to pathogen pressures. These findings provide a genetic framework for understanding disease resistance mechanisms in grapes and lay the groundwork for developing cultivars with enhanced disease resilience.
Dr. Junyang Song, the corresponding author of the study, stated, "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 is expected to significantly accelerate molecular breeding initiatives in grapes. This genetic resource offers vital insights into key traits such as seedlessness, disease resistance, and color characteristics, which can be utilized to enhance grapevine cultivation globally. The research opens avenues for creating new grape varieties with improved traits, promising advantages for the agricultural sector and consumers alike.
This work received support from 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, ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal publishes original research articles, reviews, perspectives, and correspondence related to major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the domestication of crops.