Genomic insights into the evolution of Echinochloa species as weed and orphan crop
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Published:2022-02-03
Issue:1
Volume:13
Page:
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ISSN:2041-1723
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Container-title:Nature Communications
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language:en
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Short-container-title:Nat Commun
Author:
Wu DongyaORCID, Shen Enhui, Jiang Bowen, Feng Yu, Tang Wei, Lao Sangting, Jia Lei, Lin Han-Yang, Xie Lingjuan, Weng Xifang, Dong Chenfeng, Qian Qinghong, Lin Feng, Xu HaimingORCID, Lu Huabing, Cutti LuanORCID, Chen Huajun, Deng Shuiguang, Guo LongbiaoORCID, Chuah Tse-Seng, Song Beng-Kah, Scarabel Laura, Qiu JieORCID, Zhu Qian-Hao, Yu QinORCID, Timko Michael P., Yamaguchi Hirofumi, Merotto Aldo, Qiu Yingxiong, Olsen Kenneth M.ORCID, Fan Longjiang, Ye Chu-YuORCID
Abstract
AbstractAs one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary
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