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| 1 | Bi-directional Selection in Upland Rice Leads to Its Adaptive Differentiation from Lowland Rice in Drought Resistance and Productivity显示文摘Drought resistance is required in rice breeding to address the challenge of frequent droughts . However, the evolutionary mechanism of rice drought resistance is not fully understood. We investigated the genetic differentiation between upland and lowland rice domesticated in agro-ecosystems with contrasting water-soil conditions using genome-wide SNPs. We estimated morphological differences among upland and lowland rice in drought resistance and productivity through common garden experiments. Upland rice had better drought resistance but poorer productivity. The negative correlations between traits of drought resistance and productivity are attributed to the underlying genetic trade-offs through tight linkages (e.g., DCA1 and OsCesA7) or pleiotropic effects (e.g., LAX1). The genetic trade-offs are comm on and greatly shape the evolutio n of drought resista nee in upland rice . In genomic regions associated with both productivity and drought resistance, signs of balancing selection were detected in upland rice, while signs of directional selection were detected in lowland rice, potentially contributing to their adaptive differentiation. Signs of balancing selection in upland rice resulted from bi-directional selection during its domestication in drought-prone upland agro-ecosystems.Using genome-wide association analysis, we ide ntified several valuable quantitative trait loci associated with drought resista nee, for which highly differentiated genes should be considered candidates. Bi-directional selection breaking tight linkages by accumulating recombination events would be applicable in breeding water-saving and droughtresistance rice. | Hui Xia Zhi Luo Jie Xiong Xiaosong Ma Qiaojun Lou Haibin Wei Jie Qiu Hua Yang Guolan Liu Longjiang Fan Liang Chen Lijun Luo | 2019 | Molecular Plant2019，12，2： | 16 |
| 2 | PlantcircBase: A Database for Plant Circular RNAs显示文摘 | Qinjie Chu Xingchen Zhang Xintian Zhu Chen Liu Lingfeng Mao Chuyu Ye Qian-Hao Zhu Longjiang Fan | 2017 | Molecular Plant2017，10，8： | 15 |
| 3 | Mapping epistasis and environment × QTX interaction based on four-omics genotypes for the detected QTX loci controlling complex traits in tobacco显示文摘Using newly developed methods and software, association mapping was conducted for chromium content and total sugar in tobacco leaf, based on four-omics datasets. Our objective was to collect data on genotype and phenotype for 60 leaf samples at four developmental stages, from three plant architectural positions and for three cultivars that were grown in two locations. Association mapping was conducted to detect genetic variants at quantitative trait SNP(QTS) loci, quantitative trait transcript(QTT) differences,quantitative trait protein(QTP) variability, and quantitative trait metabolite(QTM) changes,which can be summarized as QTX locus variation. The total heritabilities of the four-omics loci for both traits tested were 23.60% for epistasis and 15.26% for treatment interaction.Epistasis and environment × treatment interaction had important impacts on complex traits at all-omics levels. For decreasing chromium content and increasing total sugar in tobacco leaf, six methylated loci can be directly used for marker-assisted selection, and expression of ten QTTs, seven QTPs and six QTMs can be modified by selection or cultivation. | Liyuan Zhou Ruiyuan Li Longjiang Fan Yuewei Shi Zhihong Wang Shengdong Xie Yijie Gui Xueliang Ren Jun Zhu | 2013 | The Crop Journal2013，1，2： | 4 |
| 4 | 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 |
| 5 | Development of DArT markers for a linkage map of flue-cured tobacco显示文摘Tobacco(Nicotiana tabacum) is one of the most economically important nonfood crops,and flue-cured tobacco accounts for approximately 80% of world tobacco production.An extremely narrow genetic diversity in the tobacco pool has led to a low efficiency of PCR-based molecular markers(such as AFLP and SSR).Diversity Arrays Technology(DArT) is a high-throughput hybridisation-based marker system that has been developed in many plants including wheat,which,like tobacco,has a complex genome.In this study,we developed a tobacco DArT chip that included 7680 representative sequence tags based on typical tobacco accessions.The 1076 DArT markers of flue-cured tobacco were identified and most(82.1%) of their polymorphism information contents(PICs) were greater than 0.4.An integrated linkage map that included 851 markers(238 DArT and 613 SSR),which is the highest density map of flue-cured tobacco to date,was constructed.This chip-based DArT system provides an alternative in high-throughput marker genotyping for tobacco. | LU XiuPing GUI YiJie XIAO BingGuang LI YongPing TONG ZhiJun LIU Yun BAI XueFei WU WeiRen XIA Ling HUTTNER Eric KILIAN Adrzej FAN LongJiang | 2013 | Chinese Science Bulletin2013，58，6： | 4 |
| 6 | Elimination of a Retrotransposon for Quenching Genome Instability in Modern Rice显示文摘Transposable elements(TEs)constitute the most abundant portions of plant genomes and can dramatically shape host genomes during plant evolution.They also play important roles in crop domestication.However,whether TEs themselves are also selected during crop domestication has remained unknown.Here,we identify an active long terminal repeat(LTR)retrotransposon,HUO,as a potential target of selection during rice domestication and breeding.HUO is a low-copy-number LTR retrotransposon,and is active under natural growth conditions and transmitted through male gametogenesis,preferentially inserting into genomic regions capable of transcription.HUO exists in all wild rice accessions and about half of the archaeological rice grains(1200–7000 years ago)and landraces surveyed,but is absent in almost all modern varieties,indicating its gradual elimination during rice domestication and breeding.Further analyses showed that HUO is subjected to strict gene silencing through the RNA-directed DNA methylation pathway.Our results also suggest that multiple HUO copies may trigger genomic instability through altering genome-wide DNA methylation and small RNA biogenesis and changing global gene expression,resulting in decreased disease resistance and yield,coinciding with its elimination during rice breeding.Together,our study suggests that negative selection of an active retrotransposon might be important for genome stability during crop domestication and breeding. | Yu Peng Yingying Zhang Yijie Gui Dong An Junzhong Liu Xun Xu Qun Li Junmin Wang Wen Wang Chunhai Shi Longjiang Fan Baorong Lu Yiwen Deng Sheng Teng Zuhua He | 2019 | Molecular Plant2019，12，10： | 2 |
| 7 | Rice bioinformatics in the genomic era: Status and perspectives显示文摘Rice is one of cereal crops and a model species for monocots.Since the release of the first draft rice genome sequences in 2002,considerable progress has been achieved in rice genomic researches,thanks to rapid development and efficient utilization of bioinformatics methods and tools.In this review,we summarize the progress of studies of rice genome sequencing and other omics and introduce the wellmaintained bioinformatics databases and tools developed for rice genome resources and breeding.After reviewing the history of rice bioinformatics,we use single-cell sequencing and machine learning as examples showing how bioinformatics integrates emerging technologies and how it continues to develop for future rice research. | Lei Jia Lingjuan Xie Sangting Lao Qian-Hao Zhu Longjiang Fan | 2021 | The Crop Journal2021，9，3： | 2 |
| 8 | Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence显示文摘Rice (Oryza sativa) was first domesticated in the lower and middle Yangtze regions of China, and rice remains have been found in many Chinese archaeological sites. Until now, only phenotypic archeobotanical evidence, such as the spikelet bases of ancient grains, has been used to speculate on the domestication process and domestication rate of rice. In this study, we sequenced 4 genomic segments from rice remains in Tianluoshan, a site of the local Hemudu Neolithic culture in the low Yangtze and two other archaeological sites (~2400 and 1200 BC, respectively). We compared our sequences with those of the current domesticated and wild rice (O. rufipogon) populations. At least two genotypes were found in the remains from each site, suggesting a heterozygotic state of the rice seeds. One ancient genotype was not found in the current domesticated population and might have been lost. The rice remains belonged to the japonica group, and most if not all were japonica-type, suggesting that the remains might be at an early stage of indica-japonica divergence or an indica-japonica mixture. We also identified sequences with significant similarity to those from species of Sapindales, Zygophyllales, and Brassicales, which is consistent with the identification of other plant remains in the Tianluoshan site and the common rice field weeds such as mustards in southern China. | FAN LongJiang GUI YiJie ZHENG YunFei WANG Yu CAI DaGuang YOU XiuLing | 2011 | Chinese Science Bulletin2011，56，28： | 2 |
| 9 | Identification of NBS-Type Resistance Gene Homologs in Tobacco Genome显示文摘 | Xiaodong Leng Bingguang Xiao Sheng Wang Yijie Gui Yu Wang Xiuping Lu Jiahua Xie Yongping Li Longjiang Fan | 2010 | Plant Molecular Biology Reporter2010，，1： | 1 |
| 10 | When domestication bottleneck meets weed显示文摘DOMESTICATION OF CROPS BY TWO DIFFERENT SCENARIOS Crop domestication is a unique pattern of plant evolution,commonly referred to as the process of generation of cultivated crops from wild specles due to morphological and gen-etic transformation as a result of human intervention and selec-tion.Studies on the relationship between weeds and crops in archaeology,evolutionary biology,and genetics have revolution-ized our understanding of the role of weeds in the agroecosystem and of the intricacy of crop domestication.Weeds,generally be-ing effective competitors of crops,are not the targets of human cultivation;however,like crops,they can adapt to human-made habitats and thereby are under unintentional human selection.The peculiar environment of the agricultural system alows some arable weeds to develop domestication syndrome,Le.,to mimic crop characteristics,such as plant architecture and seed size,to escape being detected and eradicated. | Yanqing Sun Longbiao Guo Qian-Hao Zhu Longjiang Fan | 2022 | Molecular Plant2022，15，9： | 1 |
| 11 | Population genomic analysis reveals domestication of cultivated rye from weedy rye显示文摘Rye(Secale cereale)is an important crop with multiple uses and a valuable genetic resource for wheat breeding.However,due to its complex genome and outcrossing nature,the origin of cultivated rye remains elusive.The geneticist N.I.Vavilov proposed that cultivated rye had been domesticated from weedy rye,rather than directly from wild species like other crops.Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds.To this end,in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild,weedy,and cultivated rye,and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans.We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits,including shattering,grain yield,and disease resistance.Furthermore,we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye.Taken together,our findings unravel the domestication history of cultivated rye,suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale,and provide an important resource for future rye and wheat breeding. | Yanqing Sun Enhui Shen Yiyu Hu Dongya Wu Yu Feng Sangting Lao Chenfeng Dong Tianyu Du Wei Hua Chu-Yu Ye Jinhuan Zhu Qian-Hao Zhu Daguang Cai Lidia Skuza Jie Qiu Longjiang Fan | 2022 | Molecular Plant2022，15，3： | 1 |
| 12 | PlantscRNAdb: A database for plant single-cell RNA analysis显示文摘Dear Editor,Many functional characteristics of plant tissue attribute to highly specialized cells in the tissue.Dissecting cell types and profiling the transcriptome and proteome of individual cell types of plant tissues are important for understanding cellular activities underlying plant development and stress adaptation(Shaw et al.,2021).Single-cell RNA sequencing(scRNA-seq)provides such a tool for studying the transcriptional activities of individual cell types at single-cell resolution in any given organism(Rich-Griffin et al.,2020). | Hongyu Chen Xinxin Yin Longbiao Guo Jie Yao Yiwen Ding Xiaoxu Xu Lu Liu Qian-Hao Zhu Qinjie Chu Longjiang Fan | 2021 | Molecular Plant2021，14，6： | 1 |
| 13 | Orphan Crops and their Wild Relatives in the Genomic Era显示文摘More than half of the calories consumed by humans are provided by three major cereal crops(rice,maize,and wheat).Orphan crops are usually well adapted to low-input agricultural conditions,and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide.Interestingly,many wild relatives of orphan crops are important weeds of major crops.Although orphan crops and their wild relatives have received little attentions from researchers for many years,genomic studies have recently been performed on these plants.Here,we provide an overview of genomic studies on orphan crops,with a focus on orphan cereals and their wild relatives.The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced.In addition to genomic benefits for orphan crop breeding,we discuss the potential ways for mutual utilization of genomic data from major crops,orphan crops,and their wild relatives(including weeds)and provide perspectives on genetic improvement of both orphan and major crops(including de novo domestication of orphan crops)in the coming genomic era. | Chu-Yu Ye Longjiang Fan | 2021 | Molecular Plant2021，14，1： | 1 |
| 14 | The Absence of TIR-Type Resistance Gene Analogues in the Sugar Beet (Beta vulgaris L.) Genome显示文摘 | Yanyan Tian Longjiang Fan Tim Thurau Christian Jung Daguang Cai | 2004 | Journal of Molecular Evolution2004，，1： | 1 |
| 15 | Removal of sulfur compounds by a copper-based metal organic framework under ambient conditions显示文摘 | Li Ye Wang Longjiang Fan Huiling | 2015 | Energ Fuels2015，29，5： | 1 |
| 16 | Mid-infrared active metasurface based on Si/VO_(2) hybrid meta-atoms显示文摘Active metasurfaces whose optical properties can be tuned by an external stimulus have attracted great research interest recently. Introduction of VO_(2)phase change material in all-dielectric metasurfaces has been demonstrated to modulate the resonance wavelength and amplitude in the visible to near-infrared wavelength range. In this study, we report a mid-infrared active metasurface based on Si∕VO_(2)hybrid meta-atoms. By incorporating VO_(2)thin films in different locations of Si∕VO_(2)all-dielectric nanodisks, we demonstrate different modulation amplitude of the electric or magnetic resonance scattering cross sections, leading to drastically different transmission spectrum upon VO_(2)insulator to metal phase transition. The physical mechanism is originated from the field profiles of the resonance modes, which interact with VO_(2)differently depending on its locations. Based on this mechanism, we experimentally demonstrated a large modulation of the transmittance from 82% to 28% at the 4.6 μm wavelength. Our work demonstrates a promising potential of VO_(2)-based active all-dielectric metasurface for mid-infrared photonic applications such as infrared camouflage, chemical/biomedical sensing, optical neuromorphic computing, and multispectral imaging. | Tongtong Kang Boyu Fan Jun Qin Weihao Yang Shuang Xia Zheng Peng Bo Liu Sui Peng Xiao Liang Tingting Tang Longjiang Deng Yi Luo Hanbin Wang Qiang Zhou Lei Bi | 2022 | Photonics Research2022，10，2： | 1 |
| 17 | Weedy rice, a hidden gold mine in the paddy field显示文摘Weedy rice(Oryza spp.)is an increasingly invasive paddy weed,which mimics cultivated rice at the seedling stage but is distinguished from cultivated rice with strong seed shattering and seed dormancy,which are typical phenotypic characteristics of wild rice.On the origins of this conspecific form of cultivated rice(Oryza sativa),four hypotheses have been proposed and debated for decades:(1)origination from wild rice(Oryza rufipogon or possibly other wild Oryza species);(2)origination following hybridization between wild and cultivated rice;(3)direct descent from escaped cultivated rice;and(4)intervarietal hybridization between different domesticated rice varieties(Ellstrand et al.,2010).Recent population genomic investigations based on whole-genome variation provide powerful phylogenetic and demographic evidence for the de-domestication origination of weedy rice(Li et al.,2017;Qiu et al.,2017,Qiu et al.,2020;Sun et al.,2019). | Dongya Wu Jie Qiu Jian Sun Beng-Kah Song Kenneth M.Olsen Longjiang Fan | 2022 | Molecular Plant2022，15，4： | 0 |
| 18 | Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants显示文摘Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster(BGC)in maize.Data mining of 41 high-quality grass genomes identified complete Bx clusters(containing genes Bx1–Bx5 and Bx8)in three genera(Zea,Echinochloa,and Dichanthelium)of Panicoideae and partial clusters in Triticeae.The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes.An ancient Bx cluster that included additional Bx genes(e.g.,Bx6)is presumed to have been present in ancestral Panicoideae.The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer(HT)from the ancestral Panicoideae and later separated into multiple segments on different chromosomes.Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae,as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays,moved to other chromosomes in Echinochloa,and even lost in Dichanthelium.Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family.This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs. | Dongya Wu Bowen Jiang Chu-Yu Ye Michael P.Timko Longjiang Fan | 2022 | Plant Communications2022，3，3： | 0 |
| 19 | PlantcircBase 7.0:Full-length transcripts and conservation of plant circRNAs显示文摘Circular RNA(circRNA)is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants.Five years ago,we developed a comprehensive plant circRNA database(PlantcircBase),which has attracted much attention from the plant circRNA community.Here,we report an updated PlantcircBase(v.7.0),which contains 171,118 circRNAs from 21 plant species.Over 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing(RNAseq)datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study.A plant multiple conservation score(PMCS),based on the conservation of both sequence and expression profiles,was calculated for each circRNA to quantify and compare the conservation of all circRNAs.A new parameter,plant circRNA confidence level(PCCL),is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the circRNA.All this information and other details of circRNAs can be browsed,searched,and downloaded from PlantcircBase 7.0,which also provides online bioinformatics tools for visualization and sequence alignment.PlantcircBase 7.0 is publicly and freely accessible at http://gffzzbe43f054107d49d7hww69fxn5xpwu6xw9.ffgz.tsg.suse.edu.cn/plantcircbase/. | Xiaoxu Xu Tianyu Du Weihua Mao Xiaohan Li Chu-Yu Ye Qian-Hao Zhu Longjiang Fan Qinjie Chu | 2022 | Plant Communications2022，3，4： | 0 |
| 20 | 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 |
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