{"id":"802a0806-ce68-4110-92e0-846001fde5ee","sourceKey":"114","paperList":[{"id":"a4eb616d-06a4-44dd-a66f-f8d580fd97ce","title":"Solanum pan-genetics reveals paralogues as contingencies in crop engineering","authors":["Benoit, Matthias","Jenike, Katharine M.","Satterlee, James W.","Ramakrishnan, Srividya","Gentile, Iacopo","Hendelman, Anat","Passalacqua, Michael J.","Suresh, Hamsini","Shohat, Hagai","Robitaille, Gina M.","Fitzgerald, Blaine","Alonge, Michael","Wang, Xingang","Santos, Ryan","He, Jia","Ou, Shujun","Golan, Hezi","Green, Yumi","Swartwood, Kerry","Karavolias, Nicholas G.","Sierra, Gina P.","Orejuela, Andres","Roda, Federico","Goodwin, Sara","McCombie, W. Richard","Kizito, Elizabeth B.","Gagnon, Edeline","Knapp, Sandra","Särkinen, Tiina E.","Frary, Amy","Gillis, Jesse","Van Eck, Joyce","Schatz, Michael C.","Lippman, Zachary B."],"journal":"Nature","publishDate":"2025-03-05","doi":"10.1038/s41586-025-08619-6","summary":"

Pan-genomics and genome-editing technologies are revolutionizing breeding of global crops1,2. A transformative opportunity lies in exchanging genotype-to-phenotype knowledge between major crops (that is, those cultivated globally) and indigenous crops\u00a0(that is, those locally cultivated within a circumscribed area)3,4,5 to enhance our food system. However, species-specific genetic variants and their interactions with desirable natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between related crops6,7. Here, by establishing a pan-genome of the crop-rich genus Solanum8 and integrating functional genomics and pan-genetics, we show that gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability. Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, thousands of gene duplications, particularly within key domestication gene families, exhibited dynamic trajectories in sequence, expression and function. By augmenting our pan-genome with African eggplant cultivars9 and applying quantitative genetics and genome editing, we dissected an intricate history of paralogue evolution affecting fruit size. The loss of a redundant paralogue of the classical fruit size regulator CLAVATA3 (CLV3)10,11 was compensated by a lineage-specific tandem duplication. Subsequent pseudogenization of the derived copy, followed by a large cultivar-specific deletion, created a single fused CLV3 allele that modulates fruit organ number alongside an enzymatic gene controlling the same trait. Our findings demonstrate that paralogue diversifications over short timescales are underexplored contingencies in trait evolvability. Exposing and navigating these contingencies is crucial for translating genotype-to-phenotype relationships across species.

","translateSummary":"泛基因组与基因组编辑技术正在彻底改变全球作物的育种方式1,2。通过在全球主粮作物（即广泛种植的品种）与地方特色作物（即特定区域种植的品种）3,4,5之间建立基因型-表型关联的知识迁移，将为粮食系统升级带来革命性机遇。然而，即便在亲缘作物之间6,7，物种特异性遗传变异及其与自然或人工诱变间的互作效应，仍会阻碍表型预测的准确性。本研究通过构建茄科作物泛基因组8，结合功能基因组学与泛遗传学分析，揭示基因复制及其后续的旁系同源基因分化是影响基因型-表型可预测性的主要障碍。尽管22个物种（含13种地方作物）的染色体级参考基因组显示基因宏观共线性高度保守，但数千个基因复制事件（尤其关键驯化基因家族）在序列、表达及功能上呈现动态演化轨迹。通过整合非洲茄子栽培种9的泛基因组数据，运用数量遗传学与基因组编辑技术，我们解析了影响果实大小的复杂旁系同源基因演化史：经典果实大小调控因子CLAVATA3（CLV3）10,11冗余旁系同源基因的缺失，被谱系特异性串联复制所补偿；随后衍生拷贝的假基因化及栽培种特异性大片段缺失，最终形成既能调控果实器官数目、又与同性状酶控基因协同作用的融合CLV3等位基因。本研究发现，短期内发生的旁系同源基因分化是性状演化中被低估的偶发因素，揭示并驾驭这些变异对跨物种基因型-表型关联的转化应用具有关键意义。","subjects":["植物学"],"link":"https://www.nature.com/articles/s41586-025-08619-6","type":"期刊","checkname":"Nature"}],"source":{"sourceId":"PlantRSS","sourceName":"iPlants","sourceType":"WEIXIN"},"cover":"https://cdn.linkresearcher.com/51b19010-f747-456f-a090-6c6537fecc55","journals":["Nature"],"tags":["茄属","泛基因组","功能基因组学","基因编辑","作物驯化"],"relevant":[{"type":"THESIS","timestamp":0},{"type":"THESIS","timestamp":0},{"type":"THESIS","timestamp":0}],"sourceType":"WEIXIN","userType":0,"template":false,"columns":["Nature 导读"],"link":"https://www.nature.com/articles/s41586-025-08619-6","title":"植物学大牛Lippman组又一大作！茄属泛基因组揭示重复基因在作物育种中的作用和命运","content":"
2025年3月5日，Nature杂志在线发表了来自美国冷泉港实验室Zachary B. Lippman实验室题为“Solanum pan-genetics reveals paralogues as contingencies in crop engineering”的研究论文，该研究通过构建茄属（Solanum）泛基因组，结合功能基因组学与基因编辑技术，系统解析旁系同源基因的进化规律，以揭示作物驯化中表型可预测性的关键制约因素。

全球农业严重依赖少数高产商品作物（如玉米、水稻、小麦等），其狭窄的遗传基础导致农业系统脆弱性加剧。相比之下，数百种本土作物（如非洲茄、穇子、豇豆等）虽在区域饮食和生态适应中至关重要，却因研究不足和育种滞后未能充分发挥潜力。近年来，基因组测序与编辑技术的进步为改良本土作物提供了机遇，但基因型到表型的预测仍受限于“背景依赖”——即遗传变异的表型效应因物种或品种的遗传背景差异而不可预测。研究表明，基因重复产生的旁系同源基因（paralogs）可通过冗余、亚功能化或新功能化影响表型，但其在短期演化中的动态轨迹及其对作物驯化的作用尚不清晰。


该研究团队对22种茄属物种（含13种本土作物）进行染色体水平基因组组装，构建了覆盖野生种、地方品种及驯化作物的泛基因组。分析显示：基因重复的复杂动态：70%的基因存在旁系同源关系，其中全基因组复制（WGD）事件驱动核心基因的保守性，而近期小规模重复（如串联重复）则主导物种特异性基因的扩张（图2）。功能分化模式差异：WGD来源的旁系同源基因多参与剂量敏感过程（如DNA复制），而串联重复基因则富集于防御和代谢通路（图2d）。


图2 重复基因多样性与Orthogroups保守性的泛基因组学分析


此后，该研究通过多组织转录组分析，发现旁系同源基因对在演化中普遍受剂量约束（总表达量保守），但其表达模式呈现连续分化：包括剂量平衡、旁系同源优势、组织特化及完全分化（图3）。此外，该研究还表明古老WGD基因通过顺式调控保守性维持功能冗余，而近期串联重复基因则通过剂量调整实现补偿（如CLV3基因的动态重复与假基因化）。


图3 多组织基因表达分析揭示了茄属植物广泛的旁系同源基因多样化


综上所说，本研究通过整合泛基因组学、功能遗传学与基因组编辑，首次系统揭示了旁系同源基因的短期演化动态及其对表型可预测性的制约机制，主要贡献包括：提出“补偿性演化”模型，阐明基因重复后剂量调整与功能补偿的连续轨迹，挑战了传统“新功能化/亚功能化”的二分框架。构建的高质量茄属泛基因组为近缘物种间遗传知识转化提供了蓝图，尤其是非洲茄中CLV3结构变异的发现，为精准设计驯化性状提供了新靶点。


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