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Genomic analyses provide insights into the polyploidization-driven herbicide adaptation in Leptochloa weeds |
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| Authors: | Ke Chen Haona Yang Yajun Peng Ducai Liu Jingyuan Zhang Zhenghong Zhao Lamei Wu Tao Lin Lianyang Bai Lifeng Wang |
| Affiliation: | 1. State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China;2. State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China These authors contributed equally to this work.;3. State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China;4. Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China;5. Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China;6. State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China Longping Branch, College of Biology, Hunan University, Changsha, China;7. State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China |
| Abstract: | Polyploidy confers a selective advantage under stress conditions; however, whether polyploidization mediates enhanced herbicide adaptation remains largely unknown. Tetraploid Leptochloa chinensis is a notorious weed in the rice ecosystem, causing severe yield loss in rice. In China, L. chinensis has only one sister species, the diploid L. panicea, whose damage is rarely reported. To gain insights into the effects of polyploidization on herbicide adaptation, we first assembled a high-quality genome of L. panicea and identified genome structure variations with L. chinensis. Moreover, we identified herbicide-resistance genes specifically expanded in L. chinensis, which may confer a greater herbicide adaptability in L. chinensis. Analysis of gene retention and loss showed that five herbicide target-site genes and several herbicide nontarget-site resistance gene families were retained during polyploidization. Notably, we identified three pairs of polyploidization-retained genes including LcABCC8, LcCYP76C1 and LcCYP76C4 that may enhance herbicide resistance. More importantly, we found that both copies of LcCYP76C4 were under herbicide selection during the spread of L. chinensis in China. Furthermore, we identified another gene potentially involved in herbicide resistance, LcCYP709B2, which is also retained during polyploidization and under selection. This study provides insights into the genomic basis of the enhanced herbicide adaptability of Leptochloa weeds during polyploidization and provides guidance for the precise and efficient control of polyploidy weeds. |
| Keywords: | Leptochloa weeds comparative genomics genome polyploidization genome evolution herbicide resistance |