Starch is an essential commodity for humans and other animals.Future demands require qualitative and quantitative improvement by crop and post-harvest engineering that calls for comprehensive actions requiring increas...Starch is an essential commodity for humans and other animals.Future demands require qualitative and quantitative improvement by crop and post-harvest engineering that calls for comprehensive actions requiring increased fundamental knowledge on starch biosynthesis,development of advanced breeding strategies,efficient farming,and well-adapted and up scalable extraction protocols for diverse starch products.Recent staggering progress in molecular breeding techniques,especially genome editing,have enabled generation of higher starch yield and special functional qualities required to support such advancement.However,this necessitates fundamental biochemical and mechanistic understanding of starch biosynthesis and the variegated starch crop germplasms,all of which are closely linked to the relationships between starch molecular structures and functionality of various starch types as directed by the different capabilities of starch crop genotypes.We here review starch biosynthesis and its genetic foundation with a focus on increasing nutritional and health-promoting value of starch especially through bioengineering of the high amylose trait.展开更多
Drought is a natural disaster that profoundly impacts on global agricultural production,significantly reduces crop yields,and thereby poses a severe threat to worldwide food security.Addressing the challenge of effect...Drought is a natural disaster that profoundly impacts on global agricultural production,significantly reduces crop yields,and thereby poses a severe threat to worldwide food security.Addressing the challenge of effectively improving crop drought resistance(DR)to mitigate yield loss under drought conditions is a global issue.An optimal root system architecture(RSA)plays a pivotal role in enhancing the capacity of crops to efficiently uptake water and nutrients,which consequently strengthens their resilience against environmental stresses.In this review,we discuss the compositions and roles of crop RSA and summarize the most recent developments in augmenting drought tolerance in crops by manipulating RSA-related genes.Based on the current research,we propose the potential optimal RSA configuration that could be helpful in enhancing crop DR.Lastly,we discuss the existing challenges and future directions for breeding crops with enhanced DR capabilities through genetic improvements targeting RSA.展开更多
The plant germplasm resources harboring abundant genetic variations are necessary wealth in developing new cultivars adapted to various geographic and seasonal conditions.Unraveling the complex genetic architecture un...The plant germplasm resources harboring abundant genetic variations are necessary wealth in developing new cultivars adapted to various geographic and seasonal conditions.Unraveling the complex genetic architecture underlying phenotypic diversity in germplasm population is essential in studies on genetics,evolution and breeding plans for crop species.Mapping quantitative trait loci(QTLs)using molecular markers provide a basic tool for understanding the inheritance of quantitative traits,while the genomewide association study(GWAS)is a potential approach to detecting the whole-genome QTLs and their corresponding alleles in a germplasm population.The previous GWAS detects QTLs by taking high-density single-nucleotide polymorphism(SNP)markers to identify genotypephenotype associations,and has been extensively used for genetic dissection of quantitative traits in plants(Huang and Han 2014).展开更多
How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades,especially under an unpredicted climate change.Crop breeding,initiating from the phenotype-based sel...How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades,especially under an unpredicted climate change.Crop breeding,initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding,has played a critical role in securing the global food supply.However,regarding the changing environment and ever-increasing human population,can we breed outstanding crop varieties fast enough to achieve high productivity,good quality,and widespread adaptability?This review outlines the recent achievements in understanding cereal crop breeding,including the current knowledge about crop agronomic traits,newly developed techniques,crop big biological data research,and the possibility of integrating them for intelligence-driven breeding by design,which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops.This review focuses on the major cereal crops,including rice,maize,and wheat,to explain how intelligence-driven breeding by design is becoming a reality.展开更多
Crop phenomics has rapidly progressed in recent years due to the growing need for crop functional geno-mics,digital breeding,and smart cultivation.Despite this advancement,the lack of standards for the cre-ation and u...Crop phenomics has rapidly progressed in recent years due to the growing need for crop functional geno-mics,digital breeding,and smart cultivation.Despite this advancement,the lack of standards for the cre-ation and usage of crop phenomics technology and equipment has become a bottleneck,limiting the industry’s high-quality development.This paper begins with an overview of the crop phenotyping indus-try and presents an industrial mapping of technology and equipment for big data in crop phenomics.It analyzes the necessity and current state of constructing a standard framework for crop phenotyping.Furthermore,this paper proposes the intended organizational structure and goals of the standard frame-work.It details the essentials of the standard framework in the research and development of hardware and equipment,data acquisition,and the storage and management of crop phenotyping data.Finally,it discusses promoting the construction and evaluation of the standard framework,aiming to provide ideas for developing a high-quality standard framework for crop phenotyping.展开更多
The authors regret to report a mistake in the text and an associated change necessary to section 3.6 of the paper.On page 1766 in the right-hand column,line 4,the heading of subsection 3.6“GmWRKY40 represses the expr...The authors regret to report a mistake in the text and an associated change necessary to section 3.6 of the paper.On page 1766 in the right-hand column,line 4,the heading of subsection 3.6“GmWRKY40 represses the expression of PR genes”should be changed to“GmWRKY40 promotes the expression of PR genes”.The authors would like to apologize for any inconvenience caused.展开更多
The NAC(NAM,ATAF1/2,and CUC2)is a defense-associated transcription factor(TF)family that positively regulates defense responses to pathogen infection.TaNAC069 positively regulates resistance in wheat to Puccinia triti...The NAC(NAM,ATAF1/2,and CUC2)is a defense-associated transcription factor(TF)family that positively regulates defense responses to pathogen infection.TaNAC069 positively regulates resistance in wheat to Puccinia triticina(Pt).However,the molecular mechanism of its interaction with a Pt effector is not clear.We found that Pt effector Pt-1234 interacts with TaNAC069 to subvert host immunity during Pt infection.Quantitative real-time PCR analysis showed that expression of Pt-1234 was significantly upregulated during the early stage of Pt infection.Protein-mediated cell death assays in wheat showed that the Pt-1234 protein was unable to induce cell death in wheat near-isogenic lines carrying different leaf rust resistance genes,whereas it suppressed BAX-induced cell death in leaves of Nicotiana benthamiana.Silencing of Pt-1234 by host-induced gene silencing(HIGS)significantly reduced the virulence of Pt in the susceptible wheat variety Thatcher.The C subdomain of TaNAC069 was responsible for its interaction with Pt-1234,and the E subdomain was required for TaNAC069-mediated defense responses to Pt in planta.These findings indicate that Pt utilizes Pt-1234 to interact with wheat transcription factor TaNAC069 through its C subdomain,thereby modulating wheat immunity.展开更多
Mutations and rearrangements of mitochondrial genes cause plant cytoplasmic male sterility. It is a significant way to utilize hybrid vigor to enhance crop yield. Ogu cytoplasmic male sterility(CMS) is a natural cytop...Mutations and rearrangements of mitochondrial genes cause plant cytoplasmic male sterility. It is a significant way to utilize hybrid vigor to enhance crop yield. Ogu cytoplasmic male sterility(CMS) is a natural cytoplasmic male sterility type discovered in radishes, being successfully transferred to rapeseed and cruciferous vegetables. However, current studies lack depth in exploring the molecular mechanisms of its male sterility. This study confirmed that orf138 is the causal gene for Ogu CMS through the genetic transformation in Arabidopsis. Transcriptome analysis of aborted anthers in different stages suggested that differentially expressed genes(DEGs) are mainly enriched in pathways such as glycerophospholipid metabolism and arginine and proline metabolism. It reveals that key genes involved in lipid metabolism pathways are significantly down-regulated in the sterile line(OguA), including BnaGPAT1, localized within the tapetum mitochondrial and endoplasmic reticulum. This could lead to changes in the metabolism of substances like acylglycerols within the tapetum, causing disruptions in lipid metabolism. This is consistent with morphological and subcellular structural changes in the tapetum and microspore cells, as observed in the transmission electron microscopy. This abnormal lipid metabolism may trigger specific reactive oxygen species(ROS) accumulation in an oxidative stress response, ultimately leading to an aborted microspore. Our study based on transcriptome has deepened our understanding of the molecular mechanisms in Ogu CMS.展开更多
Phenotypic prediction is a promising strategy for accelerating plant breeding.Data from multiple sources(called multi-view data)can provide complementary information to characterize a biological object from various as...Phenotypic prediction is a promising strategy for accelerating plant breeding.Data from multiple sources(called multi-view data)can provide complementary information to characterize a biological object from various aspects.By integrating multi-view information into phenotypic prediction,a multi-view best linear unbiased prediction(MVBLUP)method is proposed in this paper.To measure the importance of multiple data views,the differential evolution algorithm with an early stopping mechanism is used,by which we obtain a multi-view kinship matrix and then incorporate it into the BLUP model for phenotypic prediction.To further illustrate the characteristics of MVBLUP,we perform the empirical experiments on four multi-view datasets in different crops.Compared to the single-view method,the prediction accuracy of the MVBLUP method has improved by 0.038–0.201 on average.The results demonstrate that the MVBLUP is an effective integrative prediction method for multi-view data.展开更多
Banana fruit ripening is a highly regulatory process involving various layers consisting of transcriptional regulation,epigenetic factor,and post-translational modification.Previously,we reported that MaERF11 cooperat...Banana fruit ripening is a highly regulatory process involving various layers consisting of transcriptional regulation,epigenetic factor,and post-translational modification.Previously,we reported that MaERF11 cooperated with MaHDA1 to precisely regulate the transcription of ripening-associated genes via histone deacetylation.However,whether MaERF11 is subjected to post-translational modification during banana ripening is largely unknown.In this study,we found that MaERF11 targeted a subset of starch degradation-related genes using the DNA affinity purification sequence(DAP-Seq)approach.Electrophoretic mobility shift assay(EMSA)and dual-luciferase reporter assay(DLR)demonstrated that MaERF11 could specifically bind and repress the expression of the starch degradation-related genes MaAMY3,MaBAM2 and MaGWD1.Further analyses of yeast two-hybrid(Y2H),bimolecular fluorescence complementation(BiFC)and Luciferase complementation imaging(LCI)assays indicated that MaERF11 interacted with the ubiquitin E3 ligase MaRFA1,and this interaction weakened the MaERF11-mediated transcriptional repression capacity.Collectively,our results suggest an additional regulatory layer in which MaERF11 regulates banana fruit ripening and expands the regulatory network in fruit ripening at the post-translational modification level.展开更多
Polyembryony has posed a significant impediment to the advancement of citrus hybrid breeding.FhRWP is widely regarded as a pivotal factor governing asexual reproduction in citrus,and prior research has demonstrated th...Polyembryony has posed a significant impediment to the advancement of citrus hybrid breeding.FhRWP is widely regarded as a pivotal factor governing asexual reproduction in citrus,and prior research has demonstrated that FhARID1,acting as an upstream regulator,modulates FhRWP expression.In this study,we performed a genome-wide characterization of the ARID-HMG-related genes using the short juvenile minicitrus Fortunella hindsii.A total of 20 ARID-HMG-related genes were identified.Protein interaction network and enrichment analysis suggested that ARID-HMG-related proteins might might be involved in chromatin remodeling complexes.Knockout of FhARID1 in F.hindsii did not induce the conversion from polyembryony to monoembryony.However,fharid1 plants in T1 generation exhibited abnormal proliferation at axillary buds,which is similar to phenotype of fhrwp plants.Expression analysis of fharid1 ovary tissues revealed the downregulation of FhRWP.The results indicated that FhARID1,as an upstream regulator of FhRWP,has an effect on the development of citrus axillary buds.Expression analysis of overexpressed leaves of FhARID1 lines showed that no significant up-regulation of FhRWP,indicating that FhARID1 is not the sole upstream regulatory factor of FhRWP.Only FhARID2 showed a correlation in expression with FhARID1 among the ARID-related genes,further supporting the notion that this gene may be involved in complex formation rather than acting alone.Yeast two-hybrid and MS/MS spectra further indicated that FhARID1 function requires casein kinase II-mediated post-transcriptional phosphorylation.This study elucidated the function of FhARID1 in citrus apomixis and axillary bud development,providing a fundamental basis for understanding the role of ARID-HMG-related genes.展开更多
Aegilops speltoides,the closest ancestor of the wheat B subgenome,has been well studied genomically.However,the epigenetic landscape of Ae.speltoides and the effects of epigenetics on its growth and development remain...Aegilops speltoides,the closest ancestor of the wheat B subgenome,has been well studied genomically.However,the epigenetic landscape of Ae.speltoides and the effects of epigenetics on its growth and development remain poorly understood.Here,we present a comprehensive multi-omics atlas of leaves and roots in Ae.speltoides,encompassing transcriptome,DNA methylation,histone modifications,and small RNA profiling.Divergent DNA methylation levels were detected between leaves and roots,and were associated with differences in accumulated 24-nt siRNAs.DNA methylation changes in promoters and gene bodies showed strong connections with altered expression between leaves and roots.Transcriptional regulatory networks(TRN)reconstructed between leaves and roots were driven by tissue-specific TF families.DNA methylation and histone modification act together as switches that shape root and leaf morphogenesis by modulating the binding of tissue-specific TFs to their target genes.The TRNs in leaves and roots reshaped during wheat polyploidization were associated with alterations in epigenetic modi-fications.Collectively,these results not only shed light on the critical contribution of epigenetic regulation in the morphogenesis of leaves and roots in Ae.speltoides but also provide new insights for future investigations into the complex interplay of genetic and epigenetic factors in the developmental biology of common wheat.展开更多
The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported...The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.展开更多
Asian cultivated rice is one of the most important cereal crops globally,feeding approximately 50%of the world's population.Increasing rice nitrogen use efficiency(NUE)is crucial for achieving high yields with low...Asian cultivated rice is one of the most important cereal crops globally,feeding approximately 50%of the world's population.Increasing rice nitrogen use efficiency(NUE)is crucial for achieving high yields with low nitrogen inputs(Xu et al.,2012;Hu et al.,2023).However,modern cultivars are typically bred for high yields through excessive nitrogen fertilizer use,leading to the loss of beneficial alleles associated with high NUE during the breeding process(Wang and Peng,2017;Hu et al.,2023).Genetic improvement for high NUE should be a key strategy in breeding“Green Super Rice”(GSR)(Yu et al.,2021)and water-saving and drought-resistance rice(WDR)(Luo,2010;Xia et al.,2022)for sustainable agriculture.Asian cultivated rice is highly diverse and harbors vital genetic variants essential for adaptation to different environments(Wing et al.,2018).展开更多
Reducing water consumption in rice production in China without affecting grain yield and quality is a significant challenge.This study explored how various dry cultivation methods could improve rice quality while bala...Reducing water consumption in rice production in China without affecting grain yield and quality is a significant challenge.This study explored how various dry cultivation methods could improve rice quality while balancing yield to maintain sustainable rice production.A japonica upland rice cultivar and a japonica paddy rice cultivar were cultivated in the field with three cultivation methods:plastic film mulching dry cultivation(PFMC),bare dry cultivation(BC),and continuous flooding cultivation(CF)as control.There was no significant difference in upland rice yield between PFMC and BC,nor in paddy rice yield between PFMC and CF.Compared with CF,the two varieties'yields decreased significantly with BC.Dry cultivation,especially PFMC,could decrease the active filling period,chalky rice rate,chalkiness,amylose content,gel consistency,breakdown viscosity,the ratio of glutelin to prolamin,and leaf senescence while increasing water use efficiency,protein components content,setback viscosity,grain starch branching enzyme(Q-enzyme)activity,and average filling rate.Compared with paddy rice,upland rice had a lower yield,shorter active filling period,lower chalkiness grain rate and gel consistency,higher amylose content,breakdown viscosity,protein components content,and average filling rate.Grain Q-enzyme activity and grain-filling parameters were closely related to rice quality.Reasonable dry cultivation methods could balance yield and quality,especially by improving rice's nutritional and appearance quality.展开更多
Ascorbic acid, also referred to as vitamin C(Vc), is an important nutrient found in fruits and vegetables that promotes produce quality and human health. Rosa roxburghii is an underutilized natural fruit that contains...Ascorbic acid, also referred to as vitamin C(Vc), is an important nutrient found in fruits and vegetables that promotes produce quality and human health. Rosa roxburghii is an underutilized natural fruit that contains very high levels of Vc. However, the Vc content of R. roxburghii varies considerably during plant development and ripening. To better understand the molecular mechanisms that underlie fluctuations in Vc content of R. roxburghii fruit at different developmental stages, we performed transcriptomic and metabolomic analyses and identified two significant gene networks/modules and 168 transcription factors directly involved in Vc synthesis. Promoter analysis of two core genes involved in Vc synthesis, RrGGP and RrGalUR, revealed the presence of a retroviral long terminal repeat(LTR) insert in the RrGalUR promoter. Using yeast one-hybrid and dual-luciferase assays, we demonstrated that the transcription factors RrHY5H and RrZIP9 bind to the promoter of RrGGP to promote its expression. RrZIP6 and RrWRKY4 bind to the LTR in the RrGalUR promoter to promote its expression. Our results reveal a molecular mechanism that controls Vc synthesis and accumulation in R. roxburghii fruit.展开更多
This study aimed to investigate the effects of dietary guanidinoacetic acid on growth performance,meat quality,antioxidant activity,and antioxidant-related gene expression in ducks.Total 48042-day-old female ducks wer...This study aimed to investigate the effects of dietary guanidinoacetic acid on growth performance,meat quality,antioxidant activity,and antioxidant-related gene expression in ducks.Total 48042-day-old female ducks were randomly divided into four groups with six replicates and 20 ducks per replicate and fed the basal diet to the control group.The experimental groups were fed the basal diet with 400,600 and 800 mg·kg^(-1) guanidinoacetic acid,respectively.The trial lasted 48 days.Compared with the control group,(1)the body weight at 90 days and average daily gain were increased(P<0.05),the feed conservation ratio was decreased(P<0.05);(2)the dressing percentage and breast muscle percentage were increased(P<0.05);(3)the total amino acid content,polyunsaturated fatty acids to monounsaturated fatty acids ratio were increased(P<0.05)in breast and thigh muscles;(4)activities of superoxide dismutase,catalase and glutathione peroxidase enzyme were increased(P<0.05)in thigh muscles;(5)the relative expressions of superoxide dismutase 1,glutathione peroxidase 1,and catalase were significantly increased(P<0.05)in the liver.In this study,the optimum dosage of 600 mg·kg^(-1) guanidinoacetic acid improved the growth performance,meat quality,antioxidant activity,and antioxidant-related gene expression in ducks.展开更多
Pigment accumulation is an important trait related to wheat domestication,but there remains a limited understanding of its molecular mechanism.The genetic control of the red glume trait by a dominant allele,Rg-B1,on 1...Pigment accumulation is an important trait related to wheat domestication,but there remains a limited understanding of its molecular mechanism.The genetic control of the red glume trait by a dominant allele,Rg-B1,on 1BS was reported in the last century,but the underlying gene and its molecular basis remained elusive.Here,we identified TraesTSP1B01G005700(G57)encoding an R2R3-MYB transcription factor(TF)as the candidate Rg-B1 gene controlling red glume color by a combination of genome-wide association study(GWAS),bulked segregant RNA-sequencing(BSR-Seq),map-based cloning,and RNAseq.The Rg-B1 locus had zero to five duplicate copies only one of which had high transcriptional activity.Genetic evidence suggested that promoter sequence variation in G57 in the glume leads to high expression of G57,resulting in the red glume phenotype.G57 could bind to the promoters of anthocyanin synthesis genes TaCHS,TaF3'H,and TaUFGT,activating their expression and contributing to anthocyanin accumulation in wheat glume.G57 also played a pivotal role in up-regulating expression of genes TaDREB1C and TaFLO2 associated with increased grain weight,thereby causing increased grain weight.Our research offers a better understanding of the molecular basis of red glume in bread wheat.展开更多
Pear fruit corking disorder is a non-infectious physiological condition that primarily occurs during the late developmental stages of pear and significantly impacts fruit quality and economic value in several major cu...Pear fruit corking disorder is a non-infectious physiological condition that primarily occurs during the late developmental stages of pear and significantly impacts fruit quality and economic value in several major cultivars.As the underlying mechanism remains unclear,effective prevention strategies and genetic improvements continue to present major challenges.In this study,‘Akizuki’pear was used as experimental material,and the lignin content in cork-affected tissue was found to be significantly higher than in healthy tissue.Exogenous abscisic acid(ABA)treatment induced cork formation and promoted lignin biosynthesis,a major structural component,in both pear fruits and calli.Through integrated RNA-seq and expression analyses,we identified the ABA-responsive gene PbrMYB8,which was differentially expressed between healthy and diseased tissues and associated with lignin biosynthesis during corking disorder.Stable transformation of PbrMYB8 into pear calli and Arabidopsis confirmed its role in promoting lignin biosynthesis.Notably,PbrMYB8 not only activated lignin biosynthesis genes independently but also interacted with PbrMYB169 to form a protein complex that co-regulated their expression.These findings improve our understanding of lignin biosynthesis in pear fruit corking disorder by identifying a key regulator and its interaction network and provide a theoretical foundation for future strategies aimed at improving pear fruit quality.展开更多
The TSJT1 protein belongs to the class-II glutamine amidotransferase(GATase)superfamily.Research on the functions and underlying mechanisms of TSJT1 in plants is limited.In this study,the abscisic acid(ABA)-inducible ...The TSJT1 protein belongs to the class-II glutamine amidotransferase(GATase)superfamily.Research on the functions and underlying mechanisms of TSJT1 in plants is limited.In this study,the abscisic acid(ABA)-inducible gene IbTSJT1 was isolated from drought-tolerant sweetpotato line Xushu 55-2.Its expression was strongly induced by PEG6000 and ABA.The IbTSJT1 protein was localized in the nucleus and cell membrane.IbTSJT1-overexpressing sweetpotato plants exhibited significantly enhanced drought tolerance.Their ABA and proline contents and superoxide dismutase(SOD)and peroxidase(POD)activities were increased,and their reactive oxygen species(ROS)scavenging-related genes were upregulated under drought stress.The stomatal aperture assay confirmed that the IbTSJT1-overexpressing plants had greater sensitivity to ABA.The results of yeast onehybrid(Y1H)assay,electrophoretic mobility shift assay(EMSA),luciferase reporter assay and ChIP-qPCR assay indicated that IbABF2 can directly bind to the cis-acting ABA-responsive element(ABRE)in the IbTSJT1 promoter to activate the expression of IbTSJT1.These findings suggest that IbTSJT1 mediates ABA-dependent drought stress responses and enhances drought tolerance by inducing stomatal closure and activating the ROS scavenging system in transgenic sweetpotato.Our study provides a novel gene for improving drought tolerance in sweetpotato and other plants.展开更多
文摘Starch is an essential commodity for humans and other animals.Future demands require qualitative and quantitative improvement by crop and post-harvest engineering that calls for comprehensive actions requiring increased fundamental knowledge on starch biosynthesis,development of advanced breeding strategies,efficient farming,and well-adapted and up scalable extraction protocols for diverse starch products.Recent staggering progress in molecular breeding techniques,especially genome editing,have enabled generation of higher starch yield and special functional qualities required to support such advancement.However,this necessitates fundamental biochemical and mechanistic understanding of starch biosynthesis and the variegated starch crop germplasms,all of which are closely linked to the relationships between starch molecular structures and functionality of various starch types as directed by the different capabilities of starch crop genotypes.We here review starch biosynthesis and its genetic foundation with a focus on increasing nutritional and health-promoting value of starch especially through bioengineering of the high amylose trait.
基金supported by the Key Technologies Research and Development Program,China(2022YFE0100500)the National Natural Science Foundation of China(31971954,31960405,32061143031)+2 种基金Hainan Yazhou Bay Seed Lab and China National Seed Group(B23YQ1510)Gansu Province Industrial Support Plan(2022CYZC-46)Postdoctoral Fellowship Program of CPSF(GZC20230909).
文摘Drought is a natural disaster that profoundly impacts on global agricultural production,significantly reduces crop yields,and thereby poses a severe threat to worldwide food security.Addressing the challenge of effectively improving crop drought resistance(DR)to mitigate yield loss under drought conditions is a global issue.An optimal root system architecture(RSA)plays a pivotal role in enhancing the capacity of crops to efficiently uptake water and nutrients,which consequently strengthens their resilience against environmental stresses.In this review,we discuss the compositions and roles of crop RSA and summarize the most recent developments in augmenting drought tolerance in crops by manipulating RSA-related genes.Based on the current research,we propose the potential optimal RSA configuration that could be helpful in enhancing crop DR.Lastly,we discuss the existing challenges and future directions for breeding crops with enhanced DR capabilities through genetic improvements targeting RSA.
基金supported by the National Natural Science Foundation of China(31701447)the National R&D Program of China(2016YFD0100201,2016YFD0100304,2017YFD0100500,and 2017YFD0102002)+4 种基金the 111 Project of Ministry of Education,China(B08025)the Program for Changjiang Scholars and Innovative Research Team in University,China(PCSIRT_17R55)the earmarked fund for China Agriculture Research System(CARS-04)the Fundamental Research Funds for the Central Universities,China(KYT201801)the Jiangsu Collaborative Innovation Center for Modern Crop Production,China。
文摘The plant germplasm resources harboring abundant genetic variations are necessary wealth in developing new cultivars adapted to various geographic and seasonal conditions.Unraveling the complex genetic architecture underlying phenotypic diversity in germplasm population is essential in studies on genetics,evolution and breeding plans for crop species.Mapping quantitative trait loci(QTLs)using molecular markers provide a basic tool for understanding the inheritance of quantitative traits,while the genomewide association study(GWAS)is a potential approach to detecting the whole-genome QTLs and their corresponding alleles in a germplasm population.The previous GWAS detects QTLs by taking high-density single-nucleotide polymorphism(SNP)markers to identify genotypephenotype associations,and has been extensively used for genetic dissection of quantitative traits in plants(Huang and Han 2014).
基金supported by the National Science Foundation of China(32341029)Science and Technology Innovation 2030 Major Projects(2023ZD0406804)Outstanding Youth Team Cultivation Project of Center Universities(2662023PY007)。
文摘How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades,especially under an unpredicted climate change.Crop breeding,initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding,has played a critical role in securing the global food supply.However,regarding the changing environment and ever-increasing human population,can we breed outstanding crop varieties fast enough to achieve high productivity,good quality,and widespread adaptability?This review outlines the recent achievements in understanding cereal crop breeding,including the current knowledge about crop agronomic traits,newly developed techniques,crop big biological data research,and the possibility of integrating them for intelligence-driven breeding by design,which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops.This review focuses on the major cereal crops,including rice,maize,and wheat,to explain how intelligence-driven breeding by design is becoming a reality.
基金supported by the National Key R&D Program of China(2022YFD2002300)the Construction of Collaborative Innovation Center of Beijing Academy of Agricultural and Forestry Sciences(KJCX20240406)+1 种基金the National Natural Science Foundation of China(32071891)the earmarked fund(CARS-02 and CARS-054).
文摘Crop phenomics has rapidly progressed in recent years due to the growing need for crop functional geno-mics,digital breeding,and smart cultivation.Despite this advancement,the lack of standards for the cre-ation and usage of crop phenomics technology and equipment has become a bottleneck,limiting the industry’s high-quality development.This paper begins with an overview of the crop phenotyping indus-try and presents an industrial mapping of technology and equipment for big data in crop phenomics.It analyzes the necessity and current state of constructing a standard framework for crop phenotyping.Furthermore,this paper proposes the intended organizational structure and goals of the standard frame-work.It details the essentials of the standard framework in the research and development of hardware and equipment,data acquisition,and the storage and management of crop phenotyping data.Finally,it discusses promoting the construction and evaluation of the standard framework,aiming to provide ideas for developing a high-quality standard framework for crop phenotyping.
文摘The authors regret to report a mistake in the text and an associated change necessary to section 3.6 of the paper.On page 1766 in the right-hand column,line 4,the heading of subsection 3.6“GmWRKY40 represses the expression of PR genes”should be changed to“GmWRKY40 promotes the expression of PR genes”.The authors would like to apologize for any inconvenience caused.
基金funded by State Key Laboratory of North China Crop Improvement and Regulation(NCCIR2023ZZ-10)the National Natural Science Foundation of China(32172384 and 31501623)+1 种基金the Natural Science Foundation of Hebei(C2020204028)the Science and Technology Research Project of Higher Education of Hebei(ZC2023178).
文摘The NAC(NAM,ATAF1/2,and CUC2)is a defense-associated transcription factor(TF)family that positively regulates defense responses to pathogen infection.TaNAC069 positively regulates resistance in wheat to Puccinia triticina(Pt).However,the molecular mechanism of its interaction with a Pt effector is not clear.We found that Pt effector Pt-1234 interacts with TaNAC069 to subvert host immunity during Pt infection.Quantitative real-time PCR analysis showed that expression of Pt-1234 was significantly upregulated during the early stage of Pt infection.Protein-mediated cell death assays in wheat showed that the Pt-1234 protein was unable to induce cell death in wheat near-isogenic lines carrying different leaf rust resistance genes,whereas it suppressed BAX-induced cell death in leaves of Nicotiana benthamiana.Silencing of Pt-1234 by host-induced gene silencing(HIGS)significantly reduced the virulence of Pt in the susceptible wheat variety Thatcher.The C subdomain of TaNAC069 was responsible for its interaction with Pt-1234,and the E subdomain was required for TaNAC069-mediated defense responses to Pt in planta.These findings indicate that Pt utilizes Pt-1234 to interact with wheat transcription factor TaNAC069 through its C subdomain,thereby modulating wheat immunity.
基金supported by the National Natural Science Foundation of China (31930032)。
文摘Mutations and rearrangements of mitochondrial genes cause plant cytoplasmic male sterility. It is a significant way to utilize hybrid vigor to enhance crop yield. Ogu cytoplasmic male sterility(CMS) is a natural cytoplasmic male sterility type discovered in radishes, being successfully transferred to rapeseed and cruciferous vegetables. However, current studies lack depth in exploring the molecular mechanisms of its male sterility. This study confirmed that orf138 is the causal gene for Ogu CMS through the genetic transformation in Arabidopsis. Transcriptome analysis of aborted anthers in different stages suggested that differentially expressed genes(DEGs) are mainly enriched in pathways such as glycerophospholipid metabolism and arginine and proline metabolism. It reveals that key genes involved in lipid metabolism pathways are significantly down-regulated in the sterile line(OguA), including BnaGPAT1, localized within the tapetum mitochondrial and endoplasmic reticulum. This could lead to changes in the metabolism of substances like acylglycerols within the tapetum, causing disruptions in lipid metabolism. This is consistent with morphological and subcellular structural changes in the tapetum and microspore cells, as observed in the transmission electron microscopy. This abnormal lipid metabolism may trigger specific reactive oxygen species(ROS) accumulation in an oxidative stress response, ultimately leading to an aborted microspore. Our study based on transcriptome has deepened our understanding of the molecular mechanisms in Ogu CMS.
基金supported by National Natural Science Foundation of China(32122066,32201855)STI2030—Major Projects(2023ZD04076).
文摘Phenotypic prediction is a promising strategy for accelerating plant breeding.Data from multiple sources(called multi-view data)can provide complementary information to characterize a biological object from various aspects.By integrating multi-view information into phenotypic prediction,a multi-view best linear unbiased prediction(MVBLUP)method is proposed in this paper.To measure the importance of multiple data views,the differential evolution algorithm with an early stopping mechanism is used,by which we obtain a multi-view kinship matrix and then incorporate it into the BLUP model for phenotypic prediction.To further illustrate the characteristics of MVBLUP,we perform the empirical experiments on four multi-view datasets in different crops.Compared to the single-view method,the prediction accuracy of the MVBLUP method has improved by 0.038–0.201 on average.The results demonstrate that the MVBLUP is an effective integrative prediction method for multi-view data.
基金financially supported by the National Natural Science Foundation of China(Grant Nos.31830071,32202561)the earmarked fund for CARS(Grant No.CARS-31)。
文摘Banana fruit ripening is a highly regulatory process involving various layers consisting of transcriptional regulation,epigenetic factor,and post-translational modification.Previously,we reported that MaERF11 cooperated with MaHDA1 to precisely regulate the transcription of ripening-associated genes via histone deacetylation.However,whether MaERF11 is subjected to post-translational modification during banana ripening is largely unknown.In this study,we found that MaERF11 targeted a subset of starch degradation-related genes using the DNA affinity purification sequence(DAP-Seq)approach.Electrophoretic mobility shift assay(EMSA)and dual-luciferase reporter assay(DLR)demonstrated that MaERF11 could specifically bind and repress the expression of the starch degradation-related genes MaAMY3,MaBAM2 and MaGWD1.Further analyses of yeast two-hybrid(Y2H),bimolecular fluorescence complementation(BiFC)and Luciferase complementation imaging(LCI)assays indicated that MaERF11 interacted with the ubiquitin E3 ligase MaRFA1,and this interaction weakened the MaERF11-mediated transcriptional repression capacity.Collectively,our results suggest an additional regulatory layer in which MaERF11 regulates banana fruit ripening and expands the regulatory network in fruit ripening at the post-translational modification level.
基金funded by the National Key Research and Development Program of China(Grant No.2022YFF1003100)Modern Citrus Industry Technology System of China(Grant No.CARS-26).
文摘Polyembryony has posed a significant impediment to the advancement of citrus hybrid breeding.FhRWP is widely regarded as a pivotal factor governing asexual reproduction in citrus,and prior research has demonstrated that FhARID1,acting as an upstream regulator,modulates FhRWP expression.In this study,we performed a genome-wide characterization of the ARID-HMG-related genes using the short juvenile minicitrus Fortunella hindsii.A total of 20 ARID-HMG-related genes were identified.Protein interaction network and enrichment analysis suggested that ARID-HMG-related proteins might might be involved in chromatin remodeling complexes.Knockout of FhARID1 in F.hindsii did not induce the conversion from polyembryony to monoembryony.However,fharid1 plants in T1 generation exhibited abnormal proliferation at axillary buds,which is similar to phenotype of fhrwp plants.Expression analysis of fharid1 ovary tissues revealed the downregulation of FhRWP.The results indicated that FhARID1,as an upstream regulator of FhRWP,has an effect on the development of citrus axillary buds.Expression analysis of overexpressed leaves of FhARID1 lines showed that no significant up-regulation of FhRWP,indicating that FhARID1 is not the sole upstream regulatory factor of FhRWP.Only FhARID2 showed a correlation in expression with FhARID1 among the ARID-related genes,further supporting the notion that this gene may be involved in complex formation rather than acting alone.Yeast two-hybrid and MS/MS spectra further indicated that FhARID1 function requires casein kinase II-mediated post-transcriptional phosphorylation.This study elucidated the function of FhARID1 in citrus apomixis and axillary bud development,providing a fundamental basis for understanding the role of ARID-HMG-related genes.
基金supported by the National Key Research and Development Program of China(2023YFD1200403).
文摘Aegilops speltoides,the closest ancestor of the wheat B subgenome,has been well studied genomically.However,the epigenetic landscape of Ae.speltoides and the effects of epigenetics on its growth and development remain poorly understood.Here,we present a comprehensive multi-omics atlas of leaves and roots in Ae.speltoides,encompassing transcriptome,DNA methylation,histone modifications,and small RNA profiling.Divergent DNA methylation levels were detected between leaves and roots,and were associated with differences in accumulated 24-nt siRNAs.DNA methylation changes in promoters and gene bodies showed strong connections with altered expression between leaves and roots.Transcriptional regulatory networks(TRN)reconstructed between leaves and roots were driven by tissue-specific TF families.DNA methylation and histone modification act together as switches that shape root and leaf morphogenesis by modulating the binding of tissue-specific TFs to their target genes.The TRNs in leaves and roots reshaped during wheat polyploidization were associated with alterations in epigenetic modi-fications.Collectively,these results not only shed light on the critical contribution of epigenetic regulation in the morphogenesis of leaves and roots in Ae.speltoides but also provide new insights for future investigations into the complex interplay of genetic and epigenetic factors in the developmental biology of common wheat.
基金supported by the National Natural Science Foundation of China(32201873)the Key Research and Development Plan of Hubei Province(2023BBB050)。
文摘The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.
基金supported by Joint Funds of National Natural Science Foundation of China(U24A20399)Natural Science Foundation of Shanghai(23JC1403500,22ZR1455300)+2 种基金Specific university discipline construction project(2023B10564002,2023B10564004)Shanghai Agricultural Science and Technology Innovation Program(2024-02-08-00-12-F00028)Earmarked Fund for China Agriculture Research System(CARS-01).
文摘Asian cultivated rice is one of the most important cereal crops globally,feeding approximately 50%of the world's population.Increasing rice nitrogen use efficiency(NUE)is crucial for achieving high yields with low nitrogen inputs(Xu et al.,2012;Hu et al.,2023).However,modern cultivars are typically bred for high yields through excessive nitrogen fertilizer use,leading to the loss of beneficial alleles associated with high NUE during the breeding process(Wang and Peng,2017;Hu et al.,2023).Genetic improvement for high NUE should be a key strategy in breeding“Green Super Rice”(GSR)(Yu et al.,2021)and water-saving and drought-resistance rice(WDR)(Luo,2010;Xia et al.,2022)for sustainable agriculture.Asian cultivated rice is highly diverse and harbors vital genetic variants essential for adaptation to different environments(Wing et al.,2018).
基金he National Key Research and Development Program of China(2022YFD2300304)the National Natural Science Foundation of China(31671617)a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD),China。
文摘Reducing water consumption in rice production in China without affecting grain yield and quality is a significant challenge.This study explored how various dry cultivation methods could improve rice quality while balancing yield to maintain sustainable rice production.A japonica upland rice cultivar and a japonica paddy rice cultivar were cultivated in the field with three cultivation methods:plastic film mulching dry cultivation(PFMC),bare dry cultivation(BC),and continuous flooding cultivation(CF)as control.There was no significant difference in upland rice yield between PFMC and BC,nor in paddy rice yield between PFMC and CF.Compared with CF,the two varieties'yields decreased significantly with BC.Dry cultivation,especially PFMC,could decrease the active filling period,chalky rice rate,chalkiness,amylose content,gel consistency,breakdown viscosity,the ratio of glutelin to prolamin,and leaf senescence while increasing water use efficiency,protein components content,setback viscosity,grain starch branching enzyme(Q-enzyme)activity,and average filling rate.Compared with paddy rice,upland rice had a lower yield,shorter active filling period,lower chalkiness grain rate and gel consistency,higher amylose content,breakdown viscosity,protein components content,and average filling rate.Grain Q-enzyme activity and grain-filling parameters were closely related to rice quality.Reasonable dry cultivation methods could balance yield and quality,especially by improving rice's nutritional and appearance quality.
基金supported in part by the Priority Academic Program Development of Jiangsu Higher Education Institutions and the State Key Laboratory of Crop Genetics and Germplasm Enhancement (Grant No. ZW201813)supported by the high-performance computing platform at the Bioinformatics Center of Nanjing Agricultural University。
文摘Ascorbic acid, also referred to as vitamin C(Vc), is an important nutrient found in fruits and vegetables that promotes produce quality and human health. Rosa roxburghii is an underutilized natural fruit that contains very high levels of Vc. However, the Vc content of R. roxburghii varies considerably during plant development and ripening. To better understand the molecular mechanisms that underlie fluctuations in Vc content of R. roxburghii fruit at different developmental stages, we performed transcriptomic and metabolomic analyses and identified two significant gene networks/modules and 168 transcription factors directly involved in Vc synthesis. Promoter analysis of two core genes involved in Vc synthesis, RrGGP and RrGalUR, revealed the presence of a retroviral long terminal repeat(LTR) insert in the RrGalUR promoter. Using yeast one-hybrid and dual-luciferase assays, we demonstrated that the transcription factors RrHY5H and RrZIP9 bind to the promoter of RrGGP to promote its expression. RrZIP6 and RrWRKY4 bind to the LTR in the RrGalUR promoter to promote its expression. Our results reveal a molecular mechanism that controls Vc synthesis and accumulation in R. roxburghii fruit.
基金Supported by Hainan Provincial Natural Science Foundation of China(322MS134)。
文摘This study aimed to investigate the effects of dietary guanidinoacetic acid on growth performance,meat quality,antioxidant activity,and antioxidant-related gene expression in ducks.Total 48042-day-old female ducks were randomly divided into four groups with six replicates and 20 ducks per replicate and fed the basal diet to the control group.The experimental groups were fed the basal diet with 400,600 and 800 mg·kg^(-1) guanidinoacetic acid,respectively.The trial lasted 48 days.Compared with the control group,(1)the body weight at 90 days and average daily gain were increased(P<0.05),the feed conservation ratio was decreased(P<0.05);(2)the dressing percentage and breast muscle percentage were increased(P<0.05);(3)the total amino acid content,polyunsaturated fatty acids to monounsaturated fatty acids ratio were increased(P<0.05)in breast and thigh muscles;(4)activities of superoxide dismutase,catalase and glutathione peroxidase enzyme were increased(P<0.05)in thigh muscles;(5)the relative expressions of superoxide dismutase 1,glutathione peroxidase 1,and catalase were significantly increased(P<0.05)in the liver.In this study,the optimum dosage of 600 mg·kg^(-1) guanidinoacetic acid improved the growth performance,meat quality,antioxidant activity,and antioxidant-related gene expression in ducks.
基金supported by the National Natural Science Foundation of China(31991210)the National Key Research and Development Program of China(2021YFD1200104)。
文摘Pigment accumulation is an important trait related to wheat domestication,but there remains a limited understanding of its molecular mechanism.The genetic control of the red glume trait by a dominant allele,Rg-B1,on 1BS was reported in the last century,but the underlying gene and its molecular basis remained elusive.Here,we identified TraesTSP1B01G005700(G57)encoding an R2R3-MYB transcription factor(TF)as the candidate Rg-B1 gene controlling red glume color by a combination of genome-wide association study(GWAS),bulked segregant RNA-sequencing(BSR-Seq),map-based cloning,and RNAseq.The Rg-B1 locus had zero to five duplicate copies only one of which had high transcriptional activity.Genetic evidence suggested that promoter sequence variation in G57 in the glume leads to high expression of G57,resulting in the red glume phenotype.G57 could bind to the promoters of anthocyanin synthesis genes TaCHS,TaF3'H,and TaUFGT,activating their expression and contributing to anthocyanin accumulation in wheat glume.G57 also played a pivotal role in up-regulating expression of genes TaDREB1C and TaFLO2 associated with increased grain weight,thereby causing increased grain weight.Our research offers a better understanding of the molecular basis of red glume in bread wheat.
基金funded by the National Science Foundation of China(32230097)the Earmarked Fund for China Agriculture Research System(CARS-28)the Project of Zhongshan Biological Breeding Laboratory(Grant No.ZSBBL-KY2023-08).
文摘Pear fruit corking disorder is a non-infectious physiological condition that primarily occurs during the late developmental stages of pear and significantly impacts fruit quality and economic value in several major cultivars.As the underlying mechanism remains unclear,effective prevention strategies and genetic improvements continue to present major challenges.In this study,‘Akizuki’pear was used as experimental material,and the lignin content in cork-affected tissue was found to be significantly higher than in healthy tissue.Exogenous abscisic acid(ABA)treatment induced cork formation and promoted lignin biosynthesis,a major structural component,in both pear fruits and calli.Through integrated RNA-seq and expression analyses,we identified the ABA-responsive gene PbrMYB8,which was differentially expressed between healthy and diseased tissues and associated with lignin biosynthesis during corking disorder.Stable transformation of PbrMYB8 into pear calli and Arabidopsis confirmed its role in promoting lignin biosynthesis.Notably,PbrMYB8 not only activated lignin biosynthesis genes independently but also interacted with PbrMYB169 to form a protein complex that co-regulated their expression.These findings improve our understanding of lignin biosynthesis in pear fruit corking disorder by identifying a key regulator and its interaction network and provide a theoretical foundation for future strategies aimed at improving pear fruit quality.
基金supported by the earmarked fund for CARS-10-Sweetpotato and the Beijing Food Crops Innovation Consortium Program,China(BJLSTD03)。
文摘The TSJT1 protein belongs to the class-II glutamine amidotransferase(GATase)superfamily.Research on the functions and underlying mechanisms of TSJT1 in plants is limited.In this study,the abscisic acid(ABA)-inducible gene IbTSJT1 was isolated from drought-tolerant sweetpotato line Xushu 55-2.Its expression was strongly induced by PEG6000 and ABA.The IbTSJT1 protein was localized in the nucleus and cell membrane.IbTSJT1-overexpressing sweetpotato plants exhibited significantly enhanced drought tolerance.Their ABA and proline contents and superoxide dismutase(SOD)and peroxidase(POD)activities were increased,and their reactive oxygen species(ROS)scavenging-related genes were upregulated under drought stress.The stomatal aperture assay confirmed that the IbTSJT1-overexpressing plants had greater sensitivity to ABA.The results of yeast onehybrid(Y1H)assay,electrophoretic mobility shift assay(EMSA),luciferase reporter assay and ChIP-qPCR assay indicated that IbABF2 can directly bind to the cis-acting ABA-responsive element(ABRE)in the IbTSJT1 promoter to activate the expression of IbTSJT1.These findings suggest that IbTSJT1 mediates ABA-dependent drought stress responses and enhances drought tolerance by inducing stomatal closure and activating the ROS scavenging system in transgenic sweetpotato.Our study provides a novel gene for improving drought tolerance in sweetpotato and other plants.
