Dear Editor Circular RNAs （circRNAs） are a kind of non-coding RNAs; they were first found over 35 years ago but have only become a research hotspot in recent years. CircRNAs are covalently closed loops derived from ...Dear Editor Circular RNAs （circRNAs） are a kind of non-coding RNAs; they were first found over 35 years ago but have only become a research hotspot in recent years. CircRNAs are covalently closed loops derived from precursor mRNAs by non-sequential back-splicing. Based on their genomic location, circRNAs can be classified into exonic, intronic, intergenic, and exon-intronic circRNAs （Chen, 2016）. By taking advantages of recent advances in bioinformatics algorithms, a large number of circRNAs have been detected among diverse organisms,展开更多
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 diffe...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.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
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 tiss...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).展开更多
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 pheno...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.展开更多
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...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.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
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 ...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.展开更多
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 g...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.展开更多
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 ...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.展开更多
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 ...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.展开更多
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 develo...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.展开更多
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...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).展开更多
In recent years,with the development of artificial intelligence,especially deep learning technology,researches on automatic detection of cerebrovascular diseases on medical images have made tremendous progress and the...In recent years,with the development of artificial intelligence,especially deep learning technology,researches on automatic detection of cerebrovascular diseases on medical images have made tremendous progress and these models are gradually entering into clinical practice.However,because of the complexity and flexibility of the deep learning algorithms,these researches have great variability on model building,validation process,performance description and results interpretation.The lack of a reliable,consistent,standardized design protocol has,to a certain extent,affected the progress of clinical translation and technology development of computer aided detection systems.After reviewing a large number of literatures and extensive discussion with domestic experts,this position paper put forward recommendations of standardized design on the key steps of deep learning-based automatic image detection models for cerebrovascular diseases.With further research and application expansion,this position paper would continue to be updated and gradually extended to evaluate the generalizability and clinical application efficacy of such tools.展开更多
基金This work was supported by the National Science Foundation of China （91435111）, the National Basic Research Program of China （2015CB150200）, Shanghai Municipal Commission of Agriculture （2014- 7-1-4）, and Jiangsu Collaborative Innovation Center for Modern Crop Production （JCIC-MCP）.
文摘Dear Editor Circular RNAs （circRNAs） are a kind of non-coding RNAs; they were first found over 35 years ago but have only become a research hotspot in recent years. CircRNAs are covalently closed loops derived from precursor mRNAs by non-sequential back-splicing. Based on their genomic location, circRNAs can be classified into exonic, intronic, intergenic, and exon-intronic circRNAs （Chen, 2016）. By taking advantages of recent advances in bioinformatics algorithms, a large number of circRNAs have been detected among diverse organisms,
基金the National Key R&D Programe of China (grant no. 2017YFD0300100)Shanghai Agriculture Applied Technology Development Program, China (grant no. G2016060107)+4 种基金Shanghai Natural Science Foundation (17ZR1425500)National High-Tech Research and Development Program of China (863 Plan (grant no.2014AA10A603)Shan ghai Agriculture Applied Tech no logy Developme nt Program, China (grant no. 2017-02-08-00-08-F00071)National Natural Science Foundation of China (grant no. 31501270)Shared Platform of Crop Germplasm Resources in Shanghai (18DZ2293700).
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.
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.
基金supported by the China Postdoctoral Science Foundation(2019M662066)the National Postdoctoral Program for Innovative Talents(BX20200301)+1 种基金the National Natural Science Foundation of China(91740108)the Jiangsu Collaborative Innovation Center for Modern Crop.
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).
基金supported by the National Basic Research Program of China (2011CB109306 and 2009CB118404)the Program of Introducing Talents of Discipline to Universities of China ("111" Project, B06014)Research Programs (CNTC-D2011100, CNTC-[2012]146, NY-[2011]3047, QKHRZ [2013] 02)
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.
基金This work was supported by grants from the Zhejiang Natural Science Foundation(LZ17C130001)the Jiangsu Collaborative Innovation Center for Modern Crop Production,111 Project(B17039).
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.
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This work was funded in part by the National Natural Science Foundation of China(31971865)the Zhejiang Natural Science Foundation(LZ17C130001)the Innovation Method Project of China(2018IM0301002).
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.
基金This work was supported by the National Natural Science Foundation(grant 9143511)Department of Science and Technology of Zhejiang Province(grant 2020C02002)+1 种基金the Zhejiang Natural Science Foundation(grant LZ17C130001)the Jiangsu Collaborative Innovation Center for Modern Crop Production,and the 111 Project(grant B17039)to L.F.
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.
基金supported by the National Natural Science Foundation(grant no.9143511)the Department of Science and Technology of Zhejiang Province(grant no.2020c02002)+2 种基金the Zhejiang Natural Science Foundation(grant no.LZ17C130001)the JiangsuCollaborative Innovation Center for Modern Crop Productionthe 111 Project(grant no.B17039)to L.F.
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.
基金grants from the Chinese Academy of Sciences(XDB27040201)the National Natural Science Foundation of China(91640114).
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.
基金supported by the National Natural Science Foundation of China(31971865)Zhejiang Natural Science Foundation(LZ17C130001)+1 种基金the Innovation Method Project of China(2018IM0301002)the Jiangsu Collaborative Innovation Center for Modern Crop Production。
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.
基金funded by in part by the National Natural Science Foundation(31971865)Jiangsu Collaborative Innovation Center for Modern Crop Production,and 111 Project(B17039)to L.F.Weedy rice research by K.M.O.is supported by the NSF Plant Genome Research Program(IOS-1947609).
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).
基金Project supported by the Key Program of the National Natural Sci-ence Foundation of China(Grant Nos.81830057 and 82230068)the Young Scientists Fund of the National Natural Science Foundation of China(Grant No.82102155).
文摘In recent years,with the development of artificial intelligence,especially deep learning technology,researches on automatic detection of cerebrovascular diseases on medical images have made tremendous progress and these models are gradually entering into clinical practice.However,because of the complexity and flexibility of the deep learning algorithms,these researches have great variability on model building,validation process,performance description and results interpretation.The lack of a reliable,consistent,standardized design protocol has,to a certain extent,affected the progress of clinical translation and technology development of computer aided detection systems.After reviewing a large number of literatures and extensive discussion with domestic experts,this position paper put forward recommendations of standardized design on the key steps of deep learning-based automatic image detection models for cerebrovascular diseases.With further research and application expansion,this position paper would continue to be updated and gradually extended to evaluate the generalizability and clinical application efficacy of such tools.
