Journal
MOLECULAR PLANT
Volume 15, Issue 6, Pages 1045-1058Publisher
CELL PRESS
DOI: 10.1016/j.molp.2022.05.001
Keywords
Leptochloa weeds; genome polyploidization; genome evolution; genetic diversity; adaptive selection; herbicide resistance
Categories
Funding
- National Key R&D Program of China [2021YFD1700101]
- National Natural Science Foun-dation of China [32130091, 32001923]
- science And and Technology Innovation Program of Hunan Province [2020WK2014, 2020WK2023]
- Training Program for Excellent Young Innovators of Changsha [kq2106079]
- China Agriculture Research System of MOF and MARA [CARS-16-E19]
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This study reports the genome characteristics and variation of tetraploid Chinese sprangletop, which exhibits high resistance to herbicides. Population genomic analysis reveals the spread of Chinese sprangletop from southern and southwestern provinces to the middle and lower reaches of the Yangtze River.
Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from two diploid progenitors that diverged similar to 10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae and, together with transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.
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