Fine mapping and characterization of a major QTL for grain length,QGl.cau-2D.1,that has pleiotropic effects in synthetic allohexaploid wheat

Grain size is one of the determinants of grain yield,and identifying the genetic loci that control grain size will be helpful for increasing grain yield.In our previous study,a quantitative trait locus(QTL)for grain length(GL),QGl.cau-2D.1,was identified from an F2 population developed from the cross between the natural(TAA10)and synthetic(XX329)allohexaploid wheat.In the present study,we mainly fine mapped and validated its genetic effects.To this end,multiple near-isogenic lines(NILs)were obtained through marker-assisted selection with TAA10 as the recurrent parent.The secondary populations derived from 25 heterozygous recombinants were used for fine mapping of QGl.cau-2D.1,and the allele from XX329 significantly increased GL,thousand-grain weight(TGW),total spikelet number per spike(TSN)and spike compactness(SC).Using NILs for XX329(2D+)and TAA10(2D−),we determined the genetic and pleiotropic effects of QGl.cau-2D.1.The target sequences were aligned with the wheat reference genome RefSeq v2.1 and spanned an~0.9 Mb genomic region.TraesCS2D03G0114900(ortholog of Os03g0594700)was predicted as the candidate gene based on whole-genome re-sequencing and expression analyses.In summary,the map-based cloning of QGl.cau-2D.1 will be useful for improving grain weight with enhanced GL and TSN.

Mapping of powdery mildew resistance genes transferred to common wheat from wild emmer wheat revealed three functional Pm60 haplotypes

Powdery mildew(PM),caused by Blumeria graminis f.sp.tritici(Bgt),is one of the destructive wheat diseases worldwide.Wild emmer wheat(Triticum turgidum ssp.dicoccoides,WEW),a tetraploid progenitor of common wheat,is a valuable genetic resource for wheat disease resistance breeding programs.We developed three hexaploid pre-breeding lines with PM resistance genes derived from three WEW accessions.These resistant pre-breeding lines were crossed with susceptible common wheat accessions.Segregations in the F2populations were 3 resistant:1 susceptible,suggesting a single dominant allele in each resistant parent.Mapping of the resistance gene in each line indicated a single locus on the long arm of chromosome 7A,at the approximate location of previously cloned Pm60 from T.urartu.Sanger sequencing revealed three different Pm60 haplotypes(Hap 3,Hap 5,and Hap 6).Co-segregating diagnostic markers were developed for identification and selection of each haplotype.The resistance function of each haplotype was verified by the virus-induced gene silencing(VIGS).Common wheat lines carrying each of these Pm60 haplotypes were resistant to most Bgt isolates and differences in the response arrays suggested allelic variation in response.

Changes in concentrations and transcripts of plant hormones in wheat seedling roots in response to Fusarium crown rot

Fusarium crown rot(FCR) is a soilborne disease causing severe yield losses in many wheat-growing areas of the world. Diseased plants show browning and necrosis of roots and stems causing white heads at maturity. Little is known about the molecular processes employed by wheat roots to respond to the disease. We characterized morphological, transcriptional and hormonal changes in wheat seedling roots following challenge with Fusarium pseudograminearum(Fp), the main pathogen of FCR. The pathogen inhibited root development to various extents depending on plants' resistance level. Many genes responsive to FCR infection in wheat roots were enriched in plant hormone pathways. The contents of compounds involved in biosynthesis and metabolism of jasmonic acid, salicylic acid, cytokinin and auxin were drastically changed in roots at five days post-inoculation. Presoaking seeds in methyl jasmonate for 24 h promoted FCR resistance, whereas presoaking with cytokinin 6-benzylaminopurine made plants more susceptible. Overexpression of TaOPR3, a gene involved in jasmonic acid biosynthesis, enhanced plant resistance as well as root and shoot growth during infection.

基于轻量级无锚点深度卷积神经网络的树上苹果检测模型

为提高现有苹果目标检测模型在硬件资源受限制条件下的性能和适应性,实现在保持较高检测精度的同时,减轻模型计算量,降低检测耗时,减少模型计算和存储资源占用的目的,本研究通过改进轻量级的MobileNetV3网络,结合关键点预测的目标检测网络(CenterNet),构建了用于苹果检测的轻量级无锚点深度学习网络模型(M-CenterNet),并通过与CenterNet和单次多重检测器(Single Shot Multibox Detector,SSD)网络比较了模型的检测精度、模型容量和运行速度等方面的综合性能。对模型的测试结果表明,本研究模型的平均精度、误检率和漏检率分别为88.9%、10.9%和5.8%;模型体积和帧率分别为14.2MB和8.1fps;在不同光照方向、不同远近距离、不同受遮挡程度和不同果实数量等条件下有较好的果实检测效果和适应能力。在检测精度相当的情况下,所提网络模型体积仅为CenterNet网络的1/4;相比于SSD网络,所提网络模型的AP提升了3.9%,模型体积降低了84.3%;本网络模型在CPU环境中的运行速度比CenterNet和SSD网络提高了近1倍。研究结果可为非结构环境下果园作业平台的轻量化果实目标检测模型研究提供新的思路。

Wheat powdery mildew resistance gene Pm64 derived from wild emmer (Triticum turgidum var.dicoccoides) is tightly linked in repulsion with stripe rust resistance gene Yr5

Stripe rust and powdery mildew are both devastating diseases for durum and common wheat.Pyramiding of genes conferring resistance to one or more diseases in a single cultivar is an important breeding approach to provide broader spectra of resistances in wheat improvement. A new powdery mildew resistance gene originating from wild emmer(Triticum turgidum var.dicoccoides) backcrossed into common wheat(T. aestivum) line WE35 was identified. It conferred an intermediate level of resistance to Blumeria graminis f. sp. tritici isolate E09 at the seedling stage and a high level of resistance at the adult plant stage. Genetic analysis showed that the powdery mildew resistance in WE35 was controlled by a dominant gene designated Pm64. Bulked segregant analysis(BSA) and molecular mapping indicated that Pm64 was located in chromosome bin 2 BL4-0.50–0.89. Polymorphic markers were developed from the corresponding genomic regions of Chinese Spring wheat and wild emmer accession Zavitan to delimit Pm64 to a 0.55 cM genetic interval between markers WGGBH1364 and WGGBH612, corresponding to a 15 Mb genomic region on Chinese Spring and Zavitan 2 BL, respectively. The genetic linkage map of Pm64 is critical for fine mapping and cloning. Pm64 was completely linked in repulsion with stripe rust resistance gene Yr5. Analysis of a larger segregating population might identify a recombinant line with both genes as a valuable resource in breeding for resistance to powdery mildew and stripe rust.

Genetic improvement of heat tolerance in wheat:Recent progress in understanding the underlying molecular mechanisms

As a cool season crop, wheat(Triticum aestivum L.) has an optimal daytime growing temperature of 15 ℃ during the reproductive stage. With global climate change, heat stress is becoming an increasingly severe constraint on wheat production. In this review, we summarize recent progress in understanding the molecular mechanisms of heat tolerance in wheat. We firstly describe the impact of heat tolerance on morphology and physiology and its potential effect on agronomic traits. We then review recent discoveries in determining the genetic and molecular factors affecting heat tolerance, including the effects of phytohormone signaling and epigenetic regulation. Finally, we discuss integrative strategies to improve heat tolerance by utilization of existing germplasm including modern cultivars, landraces and related species.

Integrated transcriptome and metabolite profiling highlights the role of benzoxazinoids in wheat resistance against Fusarium crown rot

Fusarium crown rot(FCR), caused by Fusarium spp., is a chronic and severe plant disease worldwide. In the last years, the incidence and severity of FCR in China has increased to the point that it is now considered a threat to local wheat crops. In this study, for the first time, the metabolites and transcripts responsive to FCR infection in the partial resistant wheat cultivar 04 Zhong 36(04 z36) and susceptible cultivar Xinmai 26(XM) were investigated and compared at 20 and 25 days post inoculation(dpi). A total of 443 metabolites were detected, of which 102 were significantly changed because of pathogen colonization.Most of these 102 metabolites belonged to the flavonoid, phenolic acid, amino acid and derivative classes.Some metabolites, such as proline betaine, lauric acid, ribitol, and arabitol, were stably induced by Fusarium pseudograminearum(Fp) infection at two time points and may have important roles in FCR resistance. In line with the reduced seedling height of 04 z36 and XM plants, RNA-seq analysis revealed that FCR infection significantly affected the photosynthesis activities in two cultivars. Furthermore, 15 jasmonate ZIM-domain genes(JAZ) in the significantly enriched ‘regulation of jasmonic acid mediated signaling pathway’ in 04 z36 were down-regulated. The down-regulation of these JAZ genes in 04 z36 may cause a strong activation of the jasmonate signaling pathway. Based on combined data from gene expression and metabolite profiles, two metabolites, benzoxazolin-2-one(BOA) and 6-methoxy-benzoxazolin-2-one(MBOA), involved in the benzoxazinoid-biosynthesis pathway, were tested for their effects on FCR resistance. Both BOA and MBOA significantly reduced fungal growth in vitro and in vivo, and, thus, a higher content of BOA and MBOA in 04 z36 may contribute to FCR resistance. Above all, the current analysis extends our understanding of the molecular mechanisms of FCR resistance/susceptibility in wheat and will benefit further efforts for the genetic improvement of disease resistance.

Characterization of a new hexaploid triticale 6D(6A) substitution line with increased grain weight and decreased spikelet number

Hexaploid triticale(×Triticosecale,AABBRR)is an important forage crop and a promising energy plant.Transferring D-genome chromosomes or segments from common wheat(Triticum aestivum)into hexaploid triticale is attractive in improving its economically important traits.Here,a hexaploid triticale 6D(6A)substitution line Lin 456 derived from the cross between the octoploid triticale line H400 and the hexaploid wheat Lin 56 was identified and analyzed by genomic in situ hybridization(GISH),fluorescence in situ hybridization(FISH),and molecular markers.The GISH analysis showed that Lin 456 is a hexaploid triticalewith 14 rye(Secale cereale)chromosomes and 28 wheat chromosomes,whereas non-denaturing fluorescence in situ hybridization(ND-FISH)and molecular marker analysis revealed that it is a 6D(6A)substitution line.In contrast to previous studies,the signal of Oligo-pSc119.2 was observed at the distal end of 6DL in Lin 456.The wheat chromosome 6D was associatedwith increased grain weight and decreased spikelet number using the genotypic data combined with the phenotypes of the F2 population in the three environments.The thousand-grain weight and grain width in the substitution individuals were significantly higher than those in the non-substitution individuals in the F2 population across the three environments.We propose that the hexaploid triticale 6D(6A)substitution line Lin 456 can be a valuable and promising donor stock for genetic improvement during triticale breeding.

A k-mer-based pangenome approach for cataloging seed-storage-protein genes in wheat to facilitate genotype-to-phenotype prediction and improvement of end-use quality

Wheat is a staple foodfor more than 35%of the world's population,with wheatflourused to make hundreds of baked goods.Superior end-use quality is a major breeding target;however,improving it is especially time-consuming and expensive.Furthermore,genes encoding seed-storage proteins(ssPs)form multigene families and are repetitive,with gaps commonplace in several genome assemblies.To overcome these barriers and efficiently identify superior wheat SSP alleles,we developed"PanSK"(Pan-SSP k-mer)for genotype-to-phenotype prediction based on an SsP-based pangenome resource.PanSK uses 29-mer sequences that represent each ssP gene at the pangenomic level to reveal untapped diversity across landraces and modern cultivars.Genome-wide association studies with k-mers identified 23 Ssp genes associated with end-use quality that represent novel targets for improvement.We evaluated the effect of rye secalin genes on end-use quality and found that removal of w-secalins from 1BL/1RS wheat translocation lines is associated with enhanced end-use quality.Finally,using machine-learning-based prediction inspired by PanSK,we predicted the quality phenotypes with high accuracy from genotypes alone.This study provides an effective approach for genome design based on ssP genes,enabling the breeding of wheat varieties with superior processing capabilities and improved end-use quality.

Genomic insights into the origin and evolution of spelt(Triticum spelta L.)as a valuable gene pool for modern wheat breeding

Spelt(Triticum aestivum ssp.spelta)is an important wheat subspecies mainly cultivated in Europe before the 20th century that has contributed to modern wheat breeding as a valuable genetic resource.However,relatively little is known about the origins and maintenance of spelt populations.Here,using resequencing data from 416 worldwide wheat accessions,including representative spelt wheat,we demonstrate that Eu-ropean spelt emerged when primitive hexaploid wheat spread to the west and hybridized with pre-settled domesticated emmer,the putative maternal donor.Genomic introgression regions from domesticated emmer confer spelt’s primitive morphological characters used for species taxonomy,such as tenacious glumes and laterflowering.We propose a haplotype-based"spelt index"to identify spelt-type wheat vari-eties and to quantify utilization of the spelt gene pool in modern wheat cultivars.This study reveals the ge-netic basis for the establishment of the spelt wheat subspecies in a specific ecological niche and the vital role of the spelt gene pool as a unique germplasm resource in modern wheat breeding.

Innovative computational tools provide new insights into the polyploid wheat genome

Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.

lcQTH:Rapid quantitative trait mapping by tracing parental haplotypes with ultra-low-coverage sequencing

Dear Editor,Gene cloning has a fundamental role in crop research but has long been hindered by high costs and labor requirements,which have limited the numbers of genes that have been functionally characterized,especially in wheat(Liang et al.,2021).Quantitative trait locus(QTL)mapping is the first step in gene cloning,enabling the localization of genomic loci that show significant associations with quantitative traits.One commonly used strategy is based on single-nucleotide polymorphism(SNP)arrays(Sun et al.,2020).

Invitationto Contributeto Frontiers of Agricultural Science and Engineering

Colleagues,It is our great pleasure to introduce you to the Frontiers of Agricultural Science and Engineering(FASE),an international journal launched in 2014.FASE was founded jointly by the Chinese Academy of Engineering,China Agricultural University and Higher Education Press of China.Our goal is to use FASE as a platform to foster scientific information flow,stimulate transdisciplinary inquiries that have strong multi-disciplinary connections,and cultivate research and idea exchanges that address agricultural sustainability challenges regionally and globally.

Invitation to Contribute to Frontiers of Agricultural Science and Engineering

Colleagues,It is our great pleasure to introduce you to the Frontiers of Agricultural Science and Engineering(FASE), an international journal launched in 2014. FASE was founded jointly by the Chinese Academy of Engineering, China Agricultural University and Higher Education Press of China.

Phosphorylation of KAT-2B by WKS1/Yr36 redirects the lipid flux to jasmonates to enhance resistance against wheat stripe rust

Wheat(Triticum aestivum)is one of the most essential human energy and protein sources.However,wheat production is threatened by devastating fungal diseases such as stripe rust,caused by Puccinia striiformis Westend.f.sp.tritici(Pst).Here,we reveal that the alternations in chloroplast lipid profiles and the accumulation of jasmonate(JA)in the necrosis region activate JA signaling and trigger the host defense.The collapse of chloroplasts in the necrosis region results in accumulations of polyunsaturated membrane lipids and the lipid-derived phytohormone JA in transgenic lines of Yr36 that encodes Wheat Kinase START 1(WKS1),a high-temperature-dependent adult plant resistance protein.WKS1.1,a protein encoded by a full-length splicing variant of WKS1,phosphorylates and enhances the activity of keto-acyl thiolase(KAT-2B),a critical enzyme catalyzing theβ-oxidation reaction in JA biosynthesis.The premature stop mutant,kat-2b,accumulates less JA and shows defects in the host defense against Pst.Conversely,overexpression of KAT-2B results in a higher level of JA and limits the growth of Pst.Moreover,JA inhibits the growth and reduces pustule densities of Pst.This study illustrates the WKS1.1-KAT-2B-JA pathway for enhancing wheat defense against fungal pathogens to attenuate yield loss.

A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement

Gene regulation is central to all aspects of organism growth,and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops.However,the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking.In this study,we constructed a wheat integrative gene regulatory network(wGRN)by combining an updated genome annotation and diverse complementary functional datasets,including gene expression,sequence motif,transcription factor(TF)binding,chromatin accessibility,and evolutionarily conserved regulation.wGRN contains 7.2 million genome-wide interactions covering 5947 TFs and 127439 target genes,which were further verified using known regulatory relationships,condition-specific expression,gene functional information,and experiments.We used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies.In addition,wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks.We further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions.Finally,we developed an interactive webserver,wGRN(http://wheat.cau.edu.cn/wGRN),for the community to explore gene regulation and discover trait-associated genes.Collectively,this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.

Deciphering the evolution and complexity of wheat germplasm from a genomic perspective

Bread wheat provides an essential fraction of the daily calorific intake for humanity.Due to its huge and complex genome,progress in studying on the wheat genome is substantially trailed behind those of the other two major crops,rice and maize,for at least a decade.With rapid advances in genome assembling and reduced cost of high-throughput sequencing,emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research.Here,we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome.New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress,genomic variations at multiple scales contributing to the diversity of wheat germplasm,and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat.Genomics databases and bioinformatics tools meeting the urgent needs of wheat ge-nomics research are also summarized.The ever-increasing omics data,along with advanced tools and well-structured databases,are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.

TaMADS29 interacts with TaNF-YB1 to synergistically regulate early grain development in bread wheat

Grain development is a crucial determinant of yield and quality in bread wheat(Triticum aestivum L.).However,the regulatory mechanisms underlying wheat grain development remain elusive.Here we report how Ta MADS29 interacts with Ta NF-YB1 to synergistically regulate early grain development in bread wheat.The tamads29 mutants generated by CRISPR/Cas9 exhibited severe grain filling deficiency,coupled with excessive accumulation of reactive oxygen species(ROS)and abnormal programmed cell death that occurred in early developing grains,while overexpression of Ta MADS29 increased grain width and1,000-kernel weight.Further analysis revealed that Ta MADS29 interacted directly with Ta NF-YB1;null mutation in Ta NF-YB1caused grain developmental deficiency similar to tamads29 mutants.The regulatory complex composed of Ta MADS29 and Ta NF-YB1 exercises its possible function that inhibits the excessive accumulation of ROS by regulating the genes involved in chloroplast development and photosynthesis in early developing wheat grains and prevents nucellar projection degradation and endosperm cell death,facilitating transportation of nutrients into the endosperm and wholly filling of developing grains.Collectively,our work not only discloses the molecular mechanism of MADS-box and NF-Y TFs in facilitating bread wheat grain development,but also indicates that caryopsis chloroplast might be a central regulator of grain development rather than merely a photosynthesis organelle.More importantly,our work offers an innovative way to breed high-yield wheat cultivars by controlling the ROS level in developing grains.

CRISPR-mediated acceleration of wheat improvement:advances and perspectives

Common wheat(Triticum aestivum)is one of the most widely cultivated and consumed crops globally.In the face of limited arable land and climate changes,it is a great challenge to maintain current and increase future wheat production.Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition.However,clustered regularly interspaced short palindromic repeat(CRISPR)/CRISPR-associ-ated nuclease(Cas)genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species,thereby opening up new possibilities for biotechnology and breeding.In this review,we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat,emphasizing recent breakthroughs in precise and multiplex genome editing.We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells.Furthermore,we summarize the recent applications and ad-vancements of CRISPR/Cas technologies for wheat improvement.Lastly,we discuss the remaining chal-lenges specific to wheat genome editing and its future prospects.

TaACTIN7-D regulates plant height and grain shape in bread wheat

Exploitation of new gene resources and genetic networks contributing to the control of crop yield-related traits,such as plant height,grain size,and shape,may enable us to breed modern high-yielding wheat varieties through molecular methods.In this study,via ethylmethanesulfonate mutagenesis,we identify a wheat mutant plant,mu-597,that shows semi-dwarf plant architecture and round grain shape.Through bulked segregant RNA-seq and map-based cloning,the causal gene for the semi-dwarf phenotype of mu-597 is located.We find that a single-base mutation in the coding region of TaACTIN7-D(TaACT7-D),leading to a Gly-to-Ser(G65S)amino acid mutation at the 65th residue of the deduced TaACT7-D protein,can explain the semi-dwarfism and round grain shape of mu-597.Further evidence shows that the G65S mutation in TaACT7-D hinders the polymerization of actin from monomeric(G-actin)to filamentous(F-actin)status while attenuates wheat responses to multiple phytohormones,including brassinosteroids,auxin,and gibberellin.Together,these findings not only define a new semi-dwarfing gene resource that can be potentially used to design plant height and grain shape of bread wheat but also establish a direct link between actin structure modulation and phytohormone signal transduction.