The Japanese green tea cultivar 'Seimei', released by National Agriculture and Food Research Organization (NARO), is rapidly expanding in cultivation area due to its suitability for producing both sencha and matcha. To establish 'Seimei' as a model cultivar for future green tea breeding, NARO has sequenced its whole genome. This represents a world-first achievement, as it is the first time that the complete reference genome sequence and gene annotation of a Japanese green tea cultivar has ever been revealed. This genomic resource will facilitate the identification and functional analysis of candidate genes associated with key agronomic traits, such as tea quality and resistance to pests and diseases. This information will be used to design DNA markers for marker-assisted selection, thereby accelerating the breeding of superior cultivars.
Overview
'Seimei' Matcha
While Japanese green tea is highly regarded worldwide, tea production faces several challenges, including climate change, damage from pests and diseases, and labor shortages. To address these issues, there is an urgent need to develop new cultivars that combine high quality with improved yield performance. Genomic breeding, which utilizes genome information to accelerate cultivar development, has attracted increasing attention as a promising approach for efficient tea breeding. However, due to the lack of comprehensive genomic data for Japanese green tea cultivars, its practical application has remained limited.
NARO has successfully obtained the chromosome-scale genome sequence of the Japanese green tea cultivar 'Seimei', comprising approximately 3.1 billion base pairs. 'Seimei' is a NARO-developed cultivar known for its excellent tea quality, not only as sencha, but also as matcha and powdered tea. With its outstanding characteristics, 'Seimei' is expected to serve as an ideal reference genome for future tea breeding efforts. The decoding of the complete genome sequence of 'Seimei' enables the identification of genes associated with important traits such as tea quality, yield, and resistance to pests and diseases, laying the foundation for more efficient and targeted breeding of green tea cultivars.
Furthermore, NARO conducted genome analyses of 23 tea cultivars and lines from both Japan and overseas. By comparing these genome data with the reference genome sequence of 'Seimei', nucleotide sequence variations (polymorphisms) among the cultivars were identified through comparative genome analysis. This led to the establishment of a foundational dataset of polymorphism information, which can be utilized for future genome-assisted breeding efforts. The polymorphism data obtained have been made publicly available through TASUKE+, a genome browser developed by NARO. (https://agrigenome.dna.affrc.go.jp/tasuke/Tea_Seimei/)
Utilizing this information is expected to accelerate genome-assisted breeding, which enables the efficient development of cultivars with targeted traits in a shorter time by applying genomic data such as DNA markers. This advancement will contribute significantly to improving tea characteristics, including flavor and aroma, enhancing yield potential, and strengthening resistance to pests and diseases.
Publication
Kawahara Y, Tanaka J, Takayama K, Wako T, Ogino A, Yamashita S and Taniguchi F (2024) Chromosome-scale genome assembly and characterization of top-quality Japanese green tea cultivar 'Seimei', Plant and Cell Physiology. 65, 1271-1284. https://doi.org/10.1093/pcp/pcae060
Related Information
Budget: Cabinet Office, Cross-ministerial Strategic Innovation Promotion Program (SIP) "Smart Bio-industry and Agricultural Infrastructure Technologies"; Ministry of Agriculture, Forestry and Fisheries Commissioned Project Research "Green Breeding Acceleration Project" JPJ012037
