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| 1 | The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation显示文摘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. | Chu-Yu Ye Dongya Wu Lingfeng Mao Lei Jia Jie Qiu Sangting Lao Meihong Chen Bowen Jiang Wei Tang Qiong Peng Lang Pan Lifeng Wang Xiaoxiao Feng Longbiao Guo Chulong Zhang Elizabeth A.Kellogg Kenneth M.Olsen Lianyang Bai Longjiang Fan | 2020 | Molecular Plant2020，13，9： | 4 |
| 2 | Quinclorac Resistance in Echinochloa crus-galli from China显示文摘Echinochloa crus-galli is a major weed in rice fields in China,and quinclorac has been long used for its control.Over-reliance of quinclorac has resulted in quinclorac resistance in E.crus-galli.Two resistant(R)E.crus-galli populations from Hunan,China were confirmed to be at least 78-fold more resistant to quinclorac than the susceptible(S)population.No difference in foliar uptake of 14C-labelled quinclorac was detected between the R and S plants.However,a higher level of 14C translocation and a lower level of quinclorac metabolism were found in the R plants.Basal and induced expression levels ofβ-cyanoalanine synthase(β-CAS)gene andβ-CAS activity were not significantly different between the R and S plants.However,the induction expression of 1-aminocyclopropane-1-carboxylic acid oxidase(ACO1)gene by quinclorac treatment was evident in the S plants but not in the R plants.Quinclorac resistance in the two resistant E.crus-galli populations was not likely to be related to foliar uptake,translocation or metabolism of quinclorac,nor to cyanide detoxification viaβ-CAS.Thus,target-site based quinclorac signal reception and transduction and regulation of the ethylene synthesis pathway should be the focus for further research. | PENG Qiong HAN Heping YANG Xia BAI Lianyang YU Qin Stephen BPOWLES | 2019 | Rice science2019，26，5： | 4 |
| 3 | Cultivar-dependent rhizobacteria community and cadmium accumulation in rice: Effects on cadmium availability in soils and iron-plaque formation显示文摘The association between the rhizospheric microbial community and Cd accumulation in rice is poorly understood.A field trial was conducted to investigate the different rhizobacterial communities of two rice cultivars with high Cd accumulation(HA)and low Cd accumulation(LA)at four growth stages.Results showed that the Cd content in the roots of the HA cultivar was 1.23-27.53 higher than that of the LA cultivar(0.08-10.5μg/plant)at four stages.The LA cultivar had a significantly lower Cd availability in rhizosphere and a higher quantity of iron plaque(IP)on the root surface than the HA cultivar at four stages.This resulted in the reduction of Cd concentration in IPs and Cd translocation from IP-to-root.Microbial analysis indicated that the LA cultivar formed a distinct rhizobacterial community from the HA cultivar and had lessα-diversity.The rhizosphere of the LA cultivar was enriched in specific bacterial taxa(e.g.,Massilia and Bacillus)involved in Cd immobilization by phosphate precipitation and IP formation by iron oxidization.However,the rhizosphere in the HA cultivar assembled abundant sulfur-oxidizing bacteria(e.g.,Sulfuricurvum)and iron reduction bacteria(Geobacter).They promoted Cd mobilization and reduced IP formation via the metal redox process.This study reveals a potential approach in which specific rhizobacteria decrease or increase Cd accumulation in rice on contaminated soil and provides a new perspective for secure rice production. | Feng Zhang Di Peng Lu Liu Huidan Jiang Lianyang Bai | 2022 | Journal of Environmental Sciences2022，34，6： | 2 |
| 4 | Direct Optical Resolution of Chiral Pesticides by High Performance Liquid Chromatography显示文摘Enantiomer separation is one of the most important prerequisites for the investigation of environmental enantioselective behavior for chiral pesticides.The enantiomeric separation of three chiral pesticides,indoxacarb,lambda-cyhalothrin,and simeconazole,were studied on cellulose tris-(3,5-dimethylphenyl-carbamate)-coated chiral stationary phase(CDMPC-CSP) using high-performance liquid chromatography under normal phase condition.The effects of chromatographic conditions,such as the mobile phase composition including the concentration and type of alcohol modifiers in hexane,flow rate and column temperature,on enantiomer separation were examined.The thermodynamical mechanism of enantioseparation and chiral recognition mechanism were discussed.Better separation were achieved using 20% n-propanol for indoxacarb,2% iso-butanol for lambda-cyhalothrin,and 20% iso-propanol for simeconazole as modifiers in hexane at 25℃ with the selectivity factor(a) of 1.69,1.82 and 1.70,respectively.The resolution factor(Rs) decreased as the flow rate increased from 0.4 to 1.1 ml·min-1.The retention factor(k') and selectivity factor for the enantiomers of analytes decreased as temperature increased.The lna-1/T plots for racemic chiral pesticides were linear in the range of 15-35℃ in hexane/iso-propanol and the chiral separation was controlled by enthalpy.Hydrogen bonding,π-π and dipole-dipole interactions between enantiomers and CDMPC-CSP play an important role in chiral identification,and the fitting of the asymmetric portion of solutes in a chiral cavity or channel of the CSP is also important. | LI Xiaogang LIU Yiping HU Changdi BAI Lianyang GAO Bida HUANG Kelong | 2011 | Chinese Journal of Chemical Engineering2011，19，4： | 1 |
| 5 | Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields显示文摘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. | Lifeng Wang Xuepeng Sun Yajun Peng Ke Chen Shan Wu Yanan Guo Jingyuan Zhang Haona Yang Tao Jin Lamei Wu Xiaomao Zhou Bin Liang Zhenghong Zhao Ducai Liu Zhangjun Fei Lianyang Bai | 2022 | Molecular Plant2022，15，6： | 1 |
| 6 | Weed genomics:yielding insights into the genetics of weedy traits for crop improvement显示文摘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. | Yujie Huang Dongya Wu Zhaofeng Huang Xiangyu Li Aldo Merotto Jr Lianyang Bai Longjiang Fan | 2023 | aBIOTECH2023，4，1： | 0 |
| 7 | Co-planted barnyardgrass reduces rice yield by inhibiting plant above-and belowground-growth during post-heading stages显示文摘Barnyardgrass (Echinochloa spp.) is the most common noxious weed in rice paddies as it inhibits rice growth and reduces grain yield.To date,little information is available on above-and belowgroundgrowth changes in rice due to neighboring barnyardgrass.This study aimed to investigate the changes in root traits and shoot growth of rice when it is grown with different kinds of barnyardgrass.Japonica rice plants (var.Nanjing 9108) were co-cultured with two varieties of Echinochloa crusgalli (L.) Beauv.(EP,var.mitis (pursh) Petern;EH,var.zelayensis (H.B.K.) Hitchc),and E.colonum (L.) Link (EL) in the field in 2017 and 2018.Four treatments included control (i.e.,weed free rice plants) and co-cultures with each of three barnyardgrasses (EP,EH,and EL).The results revealed that EP,EH,and EL treatments significantly reduced rice grain yields by 30.6%–36.2%,42.5%–46.5%,and 10.6%–14.3%,respectively.Shoot growth including shoot dry weight,leaf photosynthetic rate,zeatin (Z) and zeatin riboside (ZR) in grains,and activities of key enzymes involved in sucrose-to-starch conversion in grains and root traits,such as length density,root dry weight,total absorbing surface area,active absorption surface area,oxidation activity,and Z+ZR contents in roots were dramatically reduced during post-heading stages of rice when grown with the three kinds of barnyardgrass.Moreover,above-mentioned rice shoot growth indices were strongly and positively correlated with root traits.These results suggested the decrease in rice shoot growth and root traits during post-heading stages contributes to the reduction in the rice yield when it grows with barnyardgrass neighbors. | Zichang Zhang Jingjing Cao Tao Gu Xia Yang Qiong Peng Lianyang Bai Yongfeng Li | 2021 | The Crop Journal2021，9，5： | 0 |
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