Yu Jingyin, Chen Qionglin, Yuan Lu, Feng Shouli, Huang Miaomiao, Zheng Peng, Chen Guang, Tao Xiaoyuan, Edwards David, Chen Zhong-Hua, Xu Shengchun
Xianghu Laboratory, Hangzhou, China.
Institute of Digital Agriculture, Zhejiang Academy of Agricultural Science, Hangzhou, China.
Plant Biotechnol J. 2025 Jun 15. doi: 10.1111/pbi.70199.
The tomato (Solanum lycopersicum L.), a principal fruit crop, exhibits significant genetic diversity shaped by domestication and breeding. Analysis of the gene-based super-pangenome, a catalogue of all genes across diverse genome-sequenced tomatoes, has not yet been fully explored. Here, we present a comprehensive analysis of the gene-based super-pangenome across 61 genetically diverse tomato varieties, revealing 59 066 orthologous groups, thereby providing a detailed genetic framework for understanding the evolution of tomatoes. Our phylogenetic analysis recalibrates the position of S. galapagense, challenging existing paradigms of tomato evolution. Identification of genes linked to key agronomic traits such as fruit size, ripening and stress tolerance, along with their presence/absence variation among accessions, offers a rich source of genetic markers for breeding programs. The study also highlights the impact of whole-genome triplication (WGT) and tandem gene duplication (TD) events on gene family expansion, particularly in distant wild relatives. The analysis of the LRR-RLK gene family, important for plant development and defence, reveals substantial sequence diversity and conservation. Rapidly evolving genes and those under positive selection, such as HAI3, CYP711A1/MAX1, WRKY9 and CNGC15, are implicated in stress tolerance and defence mechanisms. The identification of these genes, along with specific pathogenesis-related genes in distant wild relatives, suggests potential strategies to improve fruit shelf life, fruit set and stress tolerance in elite tomato cultivar breeding. Additionally, we have developed the tomatoPangenome platform, integrating genomic and pangenomic data, gene families and tools, to support sustainable production of high-quality, climate-resilient tomatoes and advance selective breeding for future food security.
番茄（Solanum lycopersicum L.）是一种主要的水果作物，展现出由驯化和育种塑造的显著遗传多样性。基于基因的超级泛基因组分析，即对各种基因组测序番茄中所有基因的编目，尚未得到充分探索。在此，我们对61个遗传多样的番茄品种进行了基于基因的超级泛基因组的全面分析，揭示了59066个直系同源组，从而为理解番茄的进化提供了详细的遗传框架。我们的系统发育分析重新校准了加拉帕戈斯番茄（S. galapagense）的位置，挑战了现有的番茄进化范式。鉴定与果实大小、成熟和胁迫耐受性等关键农艺性状相关的基因，以及它们在不同种质间的存在/缺失变异，为育种计划提供了丰富的遗传标记来源。该研究还强调了全基因组三倍化（WGT）和串联基因重复（TD）事件对基因家族扩张的影响，特别是在亲缘关系较远的野生近缘种中。对植物发育和防御重要的LRR-RLK基因家族的分析揭示了大量的序列多样性和保守性。快速进化的基因以及那些受到正选择的基因，如HAI3、CYP711A1/MAX1、WRKY9和CNGC15，与胁迫耐受性和防御机制有关。这些基因的鉴定，以及亲缘关系较远的野生近缘种中特定的病程相关基因，为在优良番茄品种育种中提高果实货架期、坐果率和胁迫耐受性提供了潜在策略。此外，我们开发了番茄泛基因组平台，整合了基因组和泛基因组数据、基因家族和工具，以支持高质量、适应气候变化的番茄的可持续生产，并推进未来粮食安全的选择性育种。
