美国冷泉港实验室Zachary B. Lippman团队的一项最新研究认为茄的泛遗传学揭示了作物工程中的偶然性。2025年3月5日出版的《自然》发表了这项成果。

通过建立富含作物基因Solanum的泛基因组，并整合功能基因组学和泛遗传学，课题组研究人员发现基因重复和随后的平行多样化是基因型到表型可预测性的主要障碍。尽管包括13种本土作物在内的22个物种的染色体尺度参考文献中存在广泛的基因宏观同质性，但基因复制的需求，特别是在关键驯化基因家族中，在序列、表达和功能上表现出动态轨迹。

通过用非洲茄子品种扩增它们的泛基因组，并应用定量遗传学和基因组编辑技术，课题组研究人员剖析了影响果实大小的副系谱进化的复杂历史。经典的果实大小调节因子CLAVATA3 (CLV3)的冗余序列的丢失被一个谱系特异性串联重复所补偿。随后，衍生副本的假原化，随后是一个大的品种特异性缺失，产生了一个单一的主题CLV3等位基因，该等位基因调节果实器官数量，同时控制相同性状的酶基因。他们的发现表明，在短时间尺度上的平行多样化在性状进化中的偶然性尚未得到充分的探索。揭示和驾驭这些偶然性对于翻译跨物种的基因型-表型关系至关重要。

据介绍，泛基因组学和基因组编辑技术正在彻底改变全球作物的育种。一个变革的机会在于主要作物（即全球种植的作物）和本土作物（即在限定区域内当地种植的作物）之间交换基因型到表型的知识，以加强其粮食系统。然而，物种特异性遗传变异及其与理想的自然或工程突变的相互作用对实现可预测的表型效应构成障碍，即使在相关作物之间也是如此。

附：英文原文

Title: Solanum pan-genetics reveals paralogues as contingencies in crop engineering

Author: 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, Srkinen, Tiina E., Frary, Amy, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael C., Lippman, Zachary B.

Issue&Volume: 2025-03-05

Abstract: 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 (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.

DOI: 10.1038/s41586-025-08619-6

Source: https://www.nature.com/articles/s41586-025-08619-6