Centromere repositioning and shifts in wheat evolution

The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat.Here,we comprehensively analyzed centromeres from the de novoassembled common wheat cultivar Aikang58(AK58),Chinese Spring(CS),and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing,whole-genome bisulfite sequencing,RNA sequencing,assay for transposase-accessible chromatin using sequencing,and comparative genomics.We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization.Centromeric repeats of wheat(CRWs)have undergone expansion during wheat evolution,with strong interweaving between the A and B subgenomes post tetraploidization.We found that CENH3 prefers to bind with younger CRWs,as directly supported by immunocolocalization on two chromosomes(1A and 2A)of wild emmer wheat with dicentromeric regions,only one of which bound with CENH3.In a comparison of AK58 with CS,obvious centromere repositioning was detected on chromosomes 1B,3D,and 4D.The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels.We also found that centromeric chromatin was more open than pericentromeric chromatin,with higher levels of gene expression but lower gene density.Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome.This study also showed that active wheat centromeres were genetically and epigenetically determined.

Low phosphorus promotes NSP1–NSP2 heterodimerization to enhance strigolactone biosynthesis and regulate shoot and root architecture in rice

Phosphorus is an essential macronutrient for plant development and metabolism,and plants have evolved ingenious mechanisms to overcome phosphate(Pi)starvation.However,the molecular mechanisms underlying the regulation of shoot and root architecture by low phosphorus conditions and the coordinated utilization of Pi and nitrogen remain largely unclear.Here,we show that Nodulation Signaling Pathway 1(NSP1)and NSP2 regulate rice tiller number by promoting the biosynthesis of strigolactones(SLs),a class of phytohormones with fundamental effects on plant architecture and environmental responses.We found that NSP1 and NSP2 are induced by Oryza sativa PHOSPHATE STARVATION RESPONSE2(OsPHR2)in response to low-Pi stress and form a complex to directly bind the promoters of SL biosynthesis genes,thus markedly increasing SL biosynthesis in rice.Interestingly,the NSP1/2–SL signaling module represses the expression of CROWN ROOTLESS 1(CRL1),a newly identified early SL-responsive gene in roots,to restrain lateral root density under Pi deficiency.We also demonstrated that GR24^(4DO) treatment under normal conditions inhibits the expression of OsNRTs and OsAMTs to suppress nitrogen absorption but enhances the expression of OsPTs to promote Pi absorption,thus facilitating the balance between nitrogen and phosphorus uptake in rice.Importantly,we found that NSP1p:NSP1 and NSP2p:NSP2 transgenic plants show improved agronomic traits and grain yield under low-and medium-phosphorus conditions.Taken together,these results revealed a novel regulatory mechanism of SL biosynthesis and signaling in response to Pi starvation,providing genetic resources for improving plant architecture and nutrient-use efficiency in low-Pi environments.

HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis

Integration of light signaling and diverse abiotic stress responses contribute to plant survival in a changing environment.Some reports have indicated that light signals contribute a plant’s ability to deal with heat,cold,and stress.However,the molecular link between light signaling and the saltresponse pathways remains unclear.We demonstrate here that increasing light intensity elevates the salt stress tolerance of plants.Depletion of HY5,a key component of light signaling,causes Arabidopsis thaliana to become salinity sensitive.Interestingly,the small heat shock protein(sHsp)family genes are upregulated in hy5-215 mutant plants,and HsfA 2 is commonly involved in the regulation of these sH sps.We found that HY5directly binds to the G-box motifs in the HsfA2promoter,with the cooperation of HISTONE DEACETYLASE 9(HDA9),to repress its expression.Furthermore,the accumulation of HDA9 and the interaction between HY5 and HDA9 are significantly enhanced by salt stress.On the contrary,high temperature triggers HY5 and HDA9 degradation,which leads to dissociation of HY5-HDA9from the HsfA2 promoter,thereby reducing salt tolerance.Under salt and heat stress conditions,fine tuning of protein accumulation and an interaction between HY5 and HDA9 regulate HsfA2 expression.This implies that HY5,HDA9,and HsfA2play important roles in the integration of light signaling with salt stress and heat shock response.

Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat

Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat(Triticum aestivum.L.,BBAADD)is hypothesized to increase its adaptability and/or plasticity.However,the molecular basis of expression divergence remains unclear.Squamosa promoter-binding protein-like(SPL)transcription factors are critical for a wide array of biological processes.In this study,we constructed expression regulatory networks by combining DAP-seq for 40 SPLs,ATACseq,and RNA-seq.Our findings indicate that a group of low-affinity SPL binding regions(SBRs)were targeted by diverse SPLs and caused different sequence preferences around the core GTAC motif.The SBRs including the low-affinity ones are evolutionarily conserved,enriched GWAS signals related to important agricultural traits.However,those SBRs are highly diversified among the cis-regulatory regions(CREs)of syntenic genes,with less than 8%SBRs coexisting in triad genes,suggesting that CRE variations are critical for subgenome differentiations.Knocking out of Ta SPL7A/B/D and Ta SPL15A/B/D subfamily further proved that both high-and low-affinity SBRs played critical roles in the differential expression of genes regulating tiller number and spike sizes.Our results have provided baseline data for downstream networks of SPLs and wheat improvements and revealed that CRE variations are critical sources for subgenome divergence in the allohexaploid wheat.

Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.

Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development

Development of wheat(Triticum aestivum L.)grain mainly depends on the processes of starch synthesis and storage protein accumulation,which are critical for grain yield and quality.However,the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear.Here,we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes.We found that the chromatin accessibility changes are tightly associated with differential transcriptomic expressions,and the proportion of distal ACRs was increased gradually during grain development.Specific transcription factor(TF)binding sites were enriched at different stages and were diversified among the 3 subgenomes.We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles.Overall,our findings have provided numerous resources and illustrated the regulatory network during wheat grain development,which would shed light on the improvement of wheat yields and qualities.

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat

Wheat(Triticum aestivum,BBAADD)is an allohexaploid species that originated from two polyploidization events.The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii,respectively.Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome.However,whether Ae.speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae.speltoides and the B subgenome remain unclear.Here,we assembled a high-quality reference genome for Ae.speltoides,resequenced 53 accessions from seven species(Aegilops bicornis,Aegilops longissima,Aegilops searsii,Aegilops sharonensis,Ae.speltoides,Aegilops mutica[syn.Amblyopyrum muticum],and Triticumdicoccoides)and revealed their genomic contributions to the wheat B subgenome.Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae.speltoides and the B subgenome.We classified five groups of conserved and non-conserved genes between Aegilops and Triticum,revealing their biological characteristics,differentiation in gene expression patterns,and collinear relationships between Ae.speltoides and the wheat B subgenome.We also identified gene families that expanded in Ae.speltoides during its evolution and 789 genes specific to Ae.speltoides.These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress.The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.

Tiller Bud Formation Regulators MOC1 and MOC3 Cooperatively Promote Tiller Bud Outgrowth by Activating F0N1 Expression in Rice

Tillering in rice is one of the most important agronomic traits.Rice tiller development can be divided into two main processes: the formation of the axillary bud and its subsequent outgrowth.Several genes critical for bud formation in rice have been identified by genetic studies;however,their molecular functions and relationships are still largely unknown.Here,we report that MONOCULM 1 (MOC1) and MONOCULM 3/ TILLERS ABSENT 1/STERILE AND REDUCED TILLERING 1 (MOC3/TAB1/SRT1),two vital regulators for tiller formation in rice,physically interact to regulate tiller bud outgrowth through upregulating the expression of FLORAL ORGAN NUMBER 1 (FON1),the homolog of CLAVATA1 in rice.We found that M0C3 is able to directly bind the promoter ofFONI and subsequently activate FON1 expression.MOC1 functions as a coactivator of MOC3,whereas it could not directly bind the FON1 promoter,and further activated FON1 expression in the presence of MOC3.Accordingly,FON1 is highly expressed at axillary meristems and shows remarkably decreased expression levels in mod and moc3 mutants.Loss-of-function mutants of FON1 exhibit normal bud formation but defective bud outgrowth and reduced tiller number.Collectively,these results shed light on a joint transcriptional regulatory mechanim by MOC1 and MOC3,and establish a new framework for the control of tiller bud formation and outgrowth.

MONOCULM 3,an Ortholog of WUSCHEL in Rice,Is Required for Tiller Bud Formation

WUSCHEL （WUS） plays an essential role for the maintenance of meristem activity in dicots, but its function is still elusive in monocots. We isolated a new monoculm mutant, monoculm 3 （moc3）, in which a point mutation causes the premature termination of rice O. sativa WUS （OsWUS）. Morphological observation revealed that the formation of tiller buds was disrupted in moc3. MOC3 was localized in the nuclear and could interact with TOPLESS-RELATED PROTEINS （TPRs）. The expression of MOC3 was induced by cytokinins and defection of MOC3 affected the expression of several two-component cytokinin response regulators, OsRRs and ORRs. Our results suggest that MOC3 is required for the formation of axillary buds and has a complex relationship with cytokinins.

Wheat genomic study for genetic improvement of traits in China

Bread wheat(Triticum aestivum L.)is a major crop that feeds 40%of the world’s population.Over the past several decades,advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat,and the genetic basis of agronomically important traits,which promote the breeding of elite varieties.In this review,we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield,end-use traits,flowering regulation,nutrient use efficiency,and biotic and abiotic stress responses,and various breeding strategies that contributed mainly by Chinese scientists.Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools,highthroughput phenotyping platforms,sequencing-based cloning strategies,high-efficiency genetic transformation systems,and speed-breeding facilities.These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process,ultimately contributing to more sustainable agriculture in China and throughout the world.