Seed science is essential for modern agriculture, directly influencing crop yields and global food security. However, challenges such as interdisciplinary complexity and high costs with limited returns hinder progress, leading to a shortage of experts and insufficient technological support. While large language models (LLMs) have shown promise across various fields, their application in seed science remains limited due to the scarcity of digital resources, complex gene-trait relationships, and the lack of standardized benchmarks. To address this gap, we introduce SeedBench—the first multi-task benchmark specifically designed for seed science. Developed in collaboration with domain experts, SeedBench focuses on seed breeding and simulates key aspects of modern breeding processes. We conduct a comprehensive evaluation of 26 leading LLMs, encompassing proprietary, open-source, and domain-specific fine-tuned models. Our findings not only highlight the substantial gaps between the power of LLMs and the real-world seed science problems, but also make a foundational step for research on LLMs for seed design.

Large language models (LLMs) commonly struggle with specialized or emerging topics which are rarely seen in the training corpus. Graph-based retrieval-augmented generation (GraphRAG) addresses this by structuring domain knowledge as a graph for dynamic retrieval. However, existing pipelines involve complex engineering workflows, making it difficult to isolate the impact of individual components. It is also challenging to evaluate the retrieval effectiveness due to the overlap between the pretraining and evaluation datasets. In this work, we introduce ROGRAG, a Robustly Optimized GraphRAG framework. Specifically, we propose a multi-stage retrieval mechanism that integrates dual-level with logic form retrieval methods to improve retrieval robustness without increasing computational cost. To further refine the system, we incorporate various result verification methods and adopt an incremental database construction approach. Through extensive ablation experiments, we rigorously assess the effectiveness of each component. Our implementation includes comparative experiments on SeedBench, where Qwen2.5-7B-Instruct initially underperformed. ROGRAG significantly improves the score from 60.0% to 75.0% and outperforms mainstream methods. Experiments on domain-specific datasets reveal that dual-level retrieval enhances fuzzy matching, while logic form retrieval improves structured reasoning, highlighting the importance of multi-stage retrieval. ROGRAG is released as an open-source resource https://github.com/tpoisonooo/ROGRAG and supports installation with pip.