Red rice Is an Interfertlle, weedy form of cultivated rice （Oryza sativa L.） that competes aggressively with the crop In the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In No...Red rice Is an Interfertlle, weedy form of cultivated rice （Oryza sativa L.） that competes aggressively with the crop In the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America and the weed has been proposed to have evolved through multiple mechanisms, Including ＂de-domestication＂ of US crop cultlvars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from ＂crop mimics＂, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have Indicated that many weed strains are closely related to Asian taxa （Including indica and aus rice varieties, which have never been cultivated In the US, and the Asian crop progenitor O. ruflpogon）, whereas others show genetic similarity to the tropical Japonica varieties cultivated In the southern US. Herein, we review what Is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomlcs of this aggressive weed.展开更多
Since many aerodynamic optimization problems in the area of aeronautics contain highly nonlinear objectives and multiple local optima, it is still a challenge for most of the traditional optimization methods to find t...Since many aerodynamic optimization problems in the area of aeronautics contain highly nonlinear objectives and multiple local optima, it is still a challenge for most of the traditional optimization methods to find the global optima. In this paper, a new hybrid optimization framework based on Differential Evolution and Invasive Weed Optimization（IWO_DE/Ring） is developed, which combines global and local search to improve the performance, where a Multiple-Output Gaussian Process（MOGP） is used as the surrogate model. We first use several test functions to verify the performance of the IWO_DE/Ring method, and then apply the optimization framework to a supercritical airfoil design problem. The convergence and the robustness of the proposed framework are compared against some other optimization methods. The IWO_DE/Ringbased approach provides much quicker and steadier convergence than the traditional methods.The results show that the stability of the dynamic optimization process is an important indication of the confidence in the obtained optimum, and the proposed optimization framework based on IWO_DE/Ring is a reliable and promising alternative for complex aeronautical optimization problems.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
基金Supported by the National Science Foundation Plant Genome Research Program （DBI-0638820）. Publication of this paper is supported by the National Natural Science Foundation of China （30624808）.Acknowledgements The authors thank David R. Gealy of the Dale Bumpers National Rice Research Center for his insightful comments on US red rice natural history and genetic diversity.
文摘Red rice Is an Interfertlle, weedy form of cultivated rice （Oryza sativa L.） that competes aggressively with the crop In the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America and the weed has been proposed to have evolved through multiple mechanisms, Including ＂de-domestication＂ of US crop cultlvars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from ＂crop mimics＂, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have Indicated that many weed strains are closely related to Asian taxa （Including indica and aus rice varieties, which have never been cultivated In the US, and the Asian crop progenitor O. ruflpogon）, whereas others show genetic similarity to the tropical Japonica varieties cultivated In the southern US. Herein, we review what Is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomlcs of this aggressive weed.
基金supported by the Aeronautical Science Foundation of China (Nos.20151452021 and 20152752033)the National Natural Science Foundation of China (No.61300159)+1 种基金the Natural Science Foundation of Jiangsu Province of China (No.BK20130808)China Postdoctoral Science Foundation (No.2015M571751)
文摘Since many aerodynamic optimization problems in the area of aeronautics contain highly nonlinear objectives and multiple local optima, it is still a challenge for most of the traditional optimization methods to find the global optima. In this paper, a new hybrid optimization framework based on Differential Evolution and Invasive Weed Optimization（IWO_DE/Ring） is developed, which combines global and local search to improve the performance, where a Multiple-Output Gaussian Process（MOGP） is used as the surrogate model. We first use several test functions to verify the performance of the IWO_DE/Ring method, and then apply the optimization framework to a supercritical airfoil design problem. The convergence and the robustness of the proposed framework are compared against some other optimization methods. The IWO_DE/Ringbased approach provides much quicker and steadier convergence than the traditional methods.The results show that the stability of the dynamic optimization process is an important indication of the confidence in the obtained optimum, and the proposed optimization framework based on IWO_DE/Ring is a reliable and promising alternative for complex aeronautical optimization problems.
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.
