Weeds pose a significant threat to crop production,resulting in substantial yield reduction.In addition,they possess robust weedy traits that enable them to survive in extreme environments and evade human con-trol.In ...Weeds pose a significant threat to crop production,resulting in substantial yield reduction.In addition,they possess robust weedy traits that enable them to survive in extreme environments and evade human con-trol.In recent years,the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits.In this review,we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology,including the origins of weed spe-cies,weed classification,and the underlying genetic and molecular bases of important weedy traits such as crop–weed interactions,adaptability to different environments,photoperiodicflowering responses,and herbicide resistance.In addition,we discuss limitations to the application of multi-omics techniques in weed science,particularly compared with their extensive use in model plants and crops.In this regard,we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research.These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits.The resulting advances will facilitate the development of sustainable and highly effective weed management strategies,promoting greener practices in agriculture.展开更多
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 gen...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 ∼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.展开更多
Weeds cause tremendous economic and ecological damage worldwide.The number of genomes established for weed species has sharply increased during the recent decade,with some 26 weed species having been sequenced and de ...Weeds cause tremendous economic and ecological damage worldwide.The number of genomes established for weed species has sharply increased during the recent decade,with some 26 weed species having been sequenced and de novo genomes assembled.These genomes range from 270 Mb(Barbarea vulgaris)to almost 4.4 Gb(Aegilops tauschii).Importantly,chromosome-level assemblies are now available for 17 of these 26 species,and genomic investigations on weed populations have been conducted in at least 12 species.The resulting genomic data have greatly facilitated studies of weed management and biology,especially origin and evolution.Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement.In this review,we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.展开更多
The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields,especially in rice paddies.Its evolutionary history is similar to that of bread wheat,arising through polyploidization a...The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields,especially in rice paddies.Its evolutionary history is similar to that of bread wheat,arising through polyploidization after hybridization between a tetraploid and a diploid species.In this study,we generated and analyzed high-quality genome sequences of diploid(E.haploclada),tetraploid(E.oryzicola),and hexaploid(E.crus-galli)Echinochloa species.Gene family analysis showed a significant loss of disease-resistance genes such as those encoding NB-ARC domain-containing proteins during Echinochloa polyploidization,contrary to their significant expansionduring wheat polyploidization,suggesting that natural selection might favor reduced investment in resistance in this weed to maximize its growth and reproduction.In contrast to the asymmetric patterns of genome evolution observed in wheat and other crops,no significant differences in selection pressure were detected between the subgenomes in E.oryzicola and E.crus-galli.In addition,distinctive differences in subgenome transcriptome dynamics during hexaploidization were observed between E.crus-galli and bread wheat.Collectively,our study documents genomic mechanisms underlying the adaptation of a major agricultural weed during polyploidization.The genomic and transcriptomic resources of three Echinochloa species and new insights into the polyploidization-driven adaptive evolution would be useful for future breeding cereal crops.展开更多
基金supported by grants from the National Natural Science Foundation of China (no.32272564 and no.32302387)the National Key R&D Program of China (no.2023YFD1401100 and no.2021YFD1700101)+3 种基金the Science and Technology Innovation Program of Hunan Province (no.2022RC1017)Hunan Outstanding Youth Fund Project (no.2023JJ10025)the Training Program for Excellent Young Innovators of Changsha (kq2106079)the Hunan Agricultural Science and Technology Innovation Fund Project (2022CX01 and 2023CX02).
文摘Weeds pose a significant threat to crop production,resulting in substantial yield reduction.In addition,they possess robust weedy traits that enable them to survive in extreme environments and evade human con-trol.In recent years,the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits.In this review,we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology,including the origins of weed spe-cies,weed classification,and the underlying genetic and molecular bases of important weedy traits such as crop–weed interactions,adaptability to different environments,photoperiodicflowering responses,and herbicide resistance.In addition,we discuss limitations to the application of multi-omics techniques in weed science,particularly compared with their extensive use in model plants and crops.In this regard,we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research.These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits.The resulting advances will facilitate the development of sustainable and highly effective weed management strategies,promoting greener practices in agriculture.
基金supported by grants from the National Key R&D Program of China(No.2021YFD1700101)the National Natural Science Foundation of China(No.32130091 and No.32001923)+2 种基金the science And and Technology Innovation Program of Hunan Province (No.2020WK2014 and No.2020WK2023)the Training Program for Excellent Young Innovators of Changsha(kg2106079)the China Agriculture Research System of MOF and MARA(CARS-16-E19)。
文摘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 ∼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.
基金supported by National Natural Science Foundation of China(31971865)to LF.
文摘Weeds cause tremendous economic and ecological damage worldwide.The number of genomes established for weed species has sharply increased during the recent decade,with some 26 weed species having been sequenced and de novo genomes assembled.These genomes range from 270 Mb(Barbarea vulgaris)to almost 4.4 Gb(Aegilops tauschii).Importantly,chromosome-level assemblies are now available for 17 of these 26 species,and genomic investigations on weed populations have been conducted in at least 12 species.The resulting genomic data have greatly facilitated studies of weed management and biology,especially origin and evolution.Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement.In this review,we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.
基金financially supported in part by the National Natural Science Foundation of China(9143511 and 31901899)Zhejiang Natural Science Foundation(LZ17C130001)the Fundamental Research Funds for the Central Universities(2020XZZX001).
文摘The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields,especially in rice paddies.Its evolutionary history is similar to that of bread wheat,arising through polyploidization after hybridization between a tetraploid and a diploid species.In this study,we generated and analyzed high-quality genome sequences of diploid(E.haploclada),tetraploid(E.oryzicola),and hexaploid(E.crus-galli)Echinochloa species.Gene family analysis showed a significant loss of disease-resistance genes such as those encoding NB-ARC domain-containing proteins during Echinochloa polyploidization,contrary to their significant expansionduring wheat polyploidization,suggesting that natural selection might favor reduced investment in resistance in this weed to maximize its growth and reproduction.In contrast to the asymmetric patterns of genome evolution observed in wheat and other crops,no significant differences in selection pressure were detected between the subgenomes in E.oryzicola and E.crus-galli.In addition,distinctive differences in subgenome transcriptome dynamics during hexaploidization were observed between E.crus-galli and bread wheat.Collectively,our study documents genomic mechanisms underlying the adaptation of a major agricultural weed during polyploidization.The genomic and transcriptomic resources of three Echinochloa species and new insights into the polyploidization-driven adaptive evolution would be useful for future breeding cereal crops.
