China Unveils First Self-Developed Tomato Breeding Gene Chip

Tomatoes originated in South America and were introduced to China via the Silk Road during the Ming Dynasty, initially grown only as ornamentals. Large-scale cultivation for food began after the founding of the People's Republic of China. Today, tomatoes are a major crop in China's protected horticulture. Industry data show that China has ranked first in global tomato production since surpassing the United States in the mid-1990s. Currently, China's tomato planting area remains around 16 million mu, with total output of about 61 million tonnes and an output value of approximately RMB 180 billion. Under normal harvest conditions, the average return per mu for tomatoes is six times that of potatoes, eight times that of cabbage, and 18 times that of corn.

Because tomatoes are not native to China and systematic breeding started relatively late, the country has long relied on external tools for precise germplasm identification and targeted improvement. High breeding costs and a shortage of domestically produced tools have constrained the development of the tomato seed industry. For example, the French truss tomato variety 'Saopolo' sells for RMB 18 to 20 per seed, with 2,000 to 3,000 seeds needed per mu. Many breeding enterprises, especially small and medium-sized units, face high testing costs, poor adaptability of imported chips, and restrictions on some data and technologies, making it difficult to fully exploit the genetic value of excellent local tomato germplasm.

Recently, China released its first high-precision solid-phase gene chip for tomato breeding with fully independent intellectual property rights, named 'Jingfan Chip 1.0'. The chip covers rich genetic backgrounds, including currant tomato, cherry tomato, and cultivated varieties, and contains nearly 5,000 core loci evenly distributed across tomato chromosomes, covering important agronomic traits such as yield, quality, pest and disease resistance, and stress tolerance. Tests show a detection rate of 99.12% and repeatability of 99.85%. Developed based on China's own tomato germplasm populations, the chip is better suited to local breeding materials, significantly improving the efficiency of precise germplasm identification and breeding selection, enabling rapid screening of superior genotypes, and accelerating the development of high-quality tomato varieties.

Solid-phase gene chips can be used in molecular marker-assisted breeding to help breeders quickly screen germplasm materials, shorten breeding cycles, and improve R&D efficiency. They are also useful for seed quality control, quickly verifying seed authenticity and purity, distinguishing varieties, and providing quality assurance for seedlings. Additionally, they support variety registration and rights protection, offering fast and accurate evidence for government supervision, effectively protecting variety rights and combating counterfeit seeds. Compared with liquid-phase gene chips, which require about two weeks for sequencing and analysis, solid-phase chips deliver results in just three days from experiment to output, greatly shortening the breeding window. Moreover, the testing cost of 'Jingfan Chip 1.0' is significantly lower than that of existing liquid-phase chips and similar imported solid-phase chips, reducing the burden on breeders.