Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering

基因组学 作物 生物 进化生物学 遗传学 基因组 生物技术 基因 生态学
作者
Matthias Benoit,Katharine M. Jenike,James W. Satterlee,Srividya Ramakrishnan,Iacopo Gentile,Anat Hendelman,Michael J. Passalacqua,Hamsini Suresh,Hagai Shohat,Gina Robitaille,B. P. Fitzgerald,Michael Alonge,Xingang Wang,Raíssa Nunes dos Santos,Jia He,Shujun Ou,Hana Golan,Yumi Green,Kerry Swartwood,Gina P Sierra,Andrés Orejuela,Federico Roda,Sara Goodwin,W. Richard McCombie,Elizabeth Balyejusa Kizito,Edeline Gagnon,Sandra Knapp,Tiina Särkinen,Amy Frary,Jesse Gillis,Joyce Van Eck,Michael C. Schatz,Zachary B. Lippman
标识
DOI:10.1101/2024.09.10.612244
摘要

Pan-genomics and genome editing technologies are revolutionizing the breeding of globally cultivated crops. A transformative opportunity lies in the reciprocal exchange of genotype-to-phenotype knowledge of agricultural traits between these major crops and hundreds of locally cultivated indigenous crops, thereby enhancing the diversity and resilience of our food system. However, species-specific genetic variants and their interactions with desired natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between closely related crops or genotypes. Here, by establishing a pan-genome of the crop-rich genus Solanum and integrating functional genomics and genetics, we show that gene duplication and subsequent paralog diversification are a major obstacle to genotype-phenotype predictability. Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, hundreds of global and lineage-specific gene duplications exhibited dynamic evolutionary trajectories in paralog sequence, expression, and function, including among members of key domestication gene families. Extending our pan-genome with 10 cultivars of African eggplant and leveraging quantitative genetics and genome editing, we uncovered an intricate history of paralog emergence and evolution within this indigenous crop. The loss of an ancient redundant paralog of the classical regulator of stem cell proliferation and fruit organ number, CLAVATA3 (CLV3), was compensated by a lineage-specific tandem duplication. Subsequent pseudogenization of the derived copy followed by a cultivar-specific structural variant resulted in a single fused functional copy of CLV3 that modifies locule number alongside a newly identified gene controlling the same trait. Our findings demonstrate that paralog diversifications over short evolutionary periods are critical yet underexplored contingencies in trait evolvability and independent crop domestication histories. Unraveling these contingencies is crucial for translating genotype-to-phenotype relationships across related species.
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