Trehalose:A sugar molecule involved in temperature stress management in plants

Trehalose(Tre)is a non-reducing disaccharide found in many species,including bacteria,fungi,invertebrates,yeast,and even plants,where it acts as an osmoprotectant,energy source,or protein/membrane protector.Despite relatively small amounts in plants,Tre concentrations increase following exposure to abiotic stressors.Trehalose-6-phosphate,a precursor of Tre,has regulatory functions in sugar metabolism,crop production,and stress tolerance.Among the various abiotic stresses,temperature extremes(heat or cold stress)are anticipated to impact crop production worldwide due to ongoing climate changes.Applying small amounts of Tre can mitigate negative physiological,metabolic,and molecular responses triggered by temperature stress.Trehalose also interacts with other sugars,osmoprotectants,amino acids,and phytohormones to regulate metabolic reprogramming that underpins temperature stress adaptation.Transformed plants expressing Tre-synthesis genes accumulate Tre and show improved stress tolerance.Genome-wide studies of Tre-encoding genes suggest roles in plant growth,development,and stress tolerance.This review discusses the functions of Tre in mitigating temperature stress—highlighting genetic engineering approaches to modify Tre metabolism,crosstalk,and interactions with other molecules—and in-silico approaches for identifying novel Tre-encoding genes in diverse plant species.We consider how this knowledge can be used to develop temperature-resilient crops essential for sustainable agriculture.

Development of an Agrobacterium-mediated CRISPR/Cas9 system in pea(Pisum sativum L.)

Pea(Pisum sativum L.)is an annual cool-season legume crop.Owing to its role in sustainable agriculture as both a rotation and a cash crop,its global market is expanding and increased production is urgently needed.For both technical and regulatory reasons,neither conventional nor transgenic breeding techniques can keep pace with the demand for increased production.In answer to this challenge,CRISPR/Cas9 genome editing technology has been gaining traction in plant biology and crop breeding in recent years.However,there are currently no reports of the successful application of the CRISPR/Cas9 genome editing technology in pea.We developed a transient transformation system of hairy roots,mediated by Agrobacterium rhizogenes strain K599,to validate the efficiency of a CRISPR/Cas9 system.Further optimization resulted in an efficient vector,PsU6.3-tRNA-PsPDS3-en35S-PsCas9.We used this optimized CRISPR/Cas9 system to edit the pea phytoene desaturase(PsPDS)gene,causing albinism,by Agrobacterium-mediated genetic transformation.This is the first report of successful generation of gene-edited pea plants by this route.

Abiotic stress tolerance:Genetics,genomics,and breeding

1.Tenth anniversary of The Crop Journal The Crop Journal will be 10 years old in October 2023.The journal is sponsored by the Crop Science Society of China,the Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,and China Science Publishing&Media Group Ltd.(Science Press).It is published by Science Press and Ke Ai (founded by China Science Publishing&Media Ltd.and Elsevier).

Wheat leaf senescence and its regulatory gene network

Wheat leaf senescence is a developmental process that involves expressional changes in thousands of genes that ultimately impact grain protein content(GPC), grain yield(GY), and nitrogen use efficiency.The onset and rate of senescence are strongly influenced by plant hormones and environmental factors e.g. nitrogen availability. At maturity, decrease in nitrogen uptake could enhance N remobilization from leaves and stem to grain, eventually leading to leaf senescence. Early senescence is related to high GPC and somewhat low yield whereas late senescence is often related to high yield and somewhat low GPC. Early or late senescence is principally regulated by up and down-regulation of senescence associated genes. Integration of external and internal factors together with genotypic variation influence senescence associated genes in a developmental age dependent manner. Although regulation of genes involved in senescence has been studied in rice, Arabidopsis, maize, and currently in wheat, there are genotypespecific variations yet to explore. A major effort is needed to understand the interaction of positive and negative senescence regulators in determining the onset of senescence. In wheat, increasing attention has been paid to understand the role of positive senescence regulator, e.g. GPC-1, regulated gene network during early senescence time course. Recently, gene regulatory network involved early to late senescence time course revealed important senescence regulators. However, the known negative senescence regulator Ta NAC-S gene has not been extensively studied in wheat and little is known about its value in breeding. Existing data on senescence-related transcriptome studies and gene regulatory network could effectively be used for functional study in developing nitrogen efficient wheat varieties.

Harness the power of genomic selection and the potential of germplasm in crop breeding for global food security in the era with rapid climate change

Crop genetic improvements catalysed population growth,which in turn has increased the pressure for food security.We need to produce 70%more food to meet the demands of 9.5 billion people by 2050.Climate changes have posed challenges for global food supply,while the narrow genetic base of elite crop cultivars has further limited our capacity to increase genetic gain through conventional breeding.The effective utilization of genetic resources in germplasm collections for crop improvement is crucial to increasing genetic gain to address challenges in the global food supply.Genomic selection(GS)uses genome-wide markers and phenotype information from observed populations to establish associations,followed by genome-wide markers to predict phenotypic values in test populations.Characterizing an extensive germplasm collection can serve a dual purpose in GS,as a reference population for predicting model,and mining desirable genetic variants for incorporation into elite cultivars.New technologies,such as high-throughput genotyping and phenotyping,machine learning,and gene editing,have great potential to contribute to genomeassisted breeding.Breeding programmes integrating germplasm characterization,GS and emerging technologies offer promise for accelerating the development of cultivars with improved yield and enhanced resistance and tolerance to biotic and abiotic stresses.Finally,scientifically informed regulations on new breeding technologies,and increased sharing of genetic resources,genomic data,and bioinformatics expertise between developed and developing economies will be the key to meeting the challenges of the rapidly changing climate and increased demand for food.

Genome-wide association studies reveal QTL hotspots for grain brightness and black point traits in barley

Grain kernel discoloration(KD)in cereal crops leads to down-grading grain quality and substantial economic losses worldwide.Breeding KD tolerant varieties requires a clear understanding of the genetic basis underlying this trait.Here,we generated a high-density single nucleotide polymorphisms(SNPs)map for a diverse barley germplasm and collected trait data from two independent field trials for five KD related traits:grain brightness(TL),redness(Ta),yellowness(Tb),black point impact(Tbpi),and total black point in percentage(Tbpt).Although grain brightness and black point is genetically correlated,the grain brightness traits(TL,Ta,and Tb)have significantly higher heritability than that of the black point traits(Tbpt and Tbpi),suggesting black point traits may be more susceptible to environmental influence.Using genome-wide association studies(GWAS),we identified a total of 37 quantitative trait loci(QTL),including two major QTL hotspots on chromosomes 4H and 7H,respectively.The two QTL hotspots are associated with all five KD traits.Further genetic linkage and gene transcription analyses identified candidate genes for the grain KD,including several genes in the flavonoid pathway and plant peroxidase.Our study provides valuable insights into the genetic basis for the grain KD in barley and would greatly facilitate future breeding programs for improving grain KD resistance.

Barley and Wheat Share the Same Gene Controlling the Short Basic Vegetative Period

Basic vegetative period（BVP） is an important trait for determining flowering time and adaptation to variable environments.A short BVP barley mutant is about 30 d shorter than its wild type.Genetic analysis using 557 F 2 individuals revealed that the short BVP is governed by a single recessive gene（BVP-1） and was further validated in 2 090 F 3 individuals.The BVP-1 gene was first mapped to barley chromosome 1H using SSR markers.Comparative genomic analysis demonstrated that the chromosome region of BVP-1 is syntenic to rice chromosome 5 and Brachypodium chromosome 2.Barley ESTs/genes were identified after comparison with candidate genes in rice and Brachypodium;seven new gene-specific markers were developed and mapped in the mapping populations.The BVP-1 gene co-segregated with the Mot1 and Ftsh4 genes and was flanked by the gene-specific markers AK252360（0.2 cM） and CA608558（0.5 cM）.Further analysis demonstrated that barley and wheat share the same short BVP gene controlling early flowering.

Fine-mapping and characterisation of genes on barley(Hordeum vulgare)chromosome 2H for salinity stress tolerance during germination

Salinity causes a detrimental impact on plant growth,particularly when the stress occurs during germination and early development stages.Barley is one of the most salt-tolerant crops;previously we mapped two quantitative trait loci(QTL)for salinity tolerance during germination on the short arm of chromosome 2 H using a CM72/Gairdner doubled haploid(DH)population.Here,we narrowed down the major QTL to a region of 0.341 or 0.439 Mb containing 9 or 24 candidate genes belonging to 6 or 20 functional gene families according to barley reference genomes v1 and v3 respectively,using two DH populations of CM72/Gairdner and Skiff/CM72,F_(2)and F;generations of CM72/Gairdner/;Spartacus CL,Two Receptorlike kinase 4(RLPK4)v1 or Receptor-like kinase(RLK)v3 could be the candidates for enhanced germination under salinity stress because of their upregulated expression in salt-tolerant variety CM72.Besides,several insertion/deletion polymorphisms were identified within the 3 rd exon of the genes between CM72 and Gairdner.The sequence variations resulted in shifted functional protein domains,which may be associated with differences in salinity tolerance.Two molecular markers were designed for selecting the locus with receptor-like protein kinase 4,and one was inside HORVU2 Hr1 G111760.1 or HORVU.MOREX.r3.2 HG0202810.1.The diagnostic markers will allow for pyramiding of 2 H locus in barley varieties and facilitate genetic improvement for saline soils.Further,validation of the genes to elucidate the mechanisms involved in enhancing salinity tolerance at germination and designing RLPK4 specific markers is proposed.For this publication,all the analysis was based on barley reference genome of2017(v1),and it was used throughout for consistence.However,the positions of the markers and genes identified were updated according to new genome(v3)for reference.

Non-escaping frost tolerant QTL linked genetic loci at reproductive stage in six wheat DH populations

Reproductive stage frost poses a major constraint for wheat production in countries such as Australia.However,little progress has been made in identifying key genes to overcome the constraint.In the present study,a severe frost event hit two large-scale field trials consisting of six doubled haploid(DH)wheat populations at reproductive stage(young microspore stage)in Western Australia,leading to the identification of 30 robust frost QTL on 17 chromosomes.The major 18 QTL with the phenotype variation over 9.5%were located on 13 chromosomes including 2 A,2 B,2 D,3 A,4 A,4 B,4 D,5 A,5 D,6 D,7 A,7 B and7 D.Most frost QTL were closely linked to the QTL of anthesis,maturity,Zadok stages as well as linked to anthesis related genes.Out of those,six QTL were repetitively detected on the homologous regions on 2 B,4 B,4 D,5 A,5 D,7 A in more than two populations.Results showed that the frost damage is associated with alleles of Vrn-A1 a,Vrn-D1 a,Rht-B1 b,Rht-D1 b,and the high copy number of Ppd-B1.However,anthesis QTL and anthesis related genes of Vrn-B1 a and Ta FT3-1 B on chromosomes 5 B and 1 B did not lead to frost damage,indicating that these early-flowering phenotype related genes are compatible with frost tolerance and thus can be utilised in breeding.Our results also indicate that wild-type alleles Rht-B1 a and Rht-D1 a can be used when breeding for frost-tolerant varieties without delaying flowering time.

Fast integration and accumulation of beneficial breeding alleles through an AB–NAMIC strategy in wheat

Wheat(Triticum aestivum)is among the most important staple crops for safeguarding the food security of the growing world population.To bridge the gap between genebank diversity and breeding programs,we developed an advanced backcross-nested association mapping plus inter-crossed population(AB-NAMIC)by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core collection.Selective backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB-NAMIC population.We performed phenotyping of 590 AB-NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP array.Genome-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in AB-NAMIC.Notably,genome-wide association studies in AB-NAMIC detected the candidate gene TaSWEET6-7B(TraesCS7B03G1216700),which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield traits.The commercial release of two derived AB-NAMIC lines attests to its direct applicability in wheat improvement.Valuable information on genome-wide association studymapping,candidate genes,and their haplotypes for breeding traits are available through WheatGAB.Our research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.

Back to wild relatives for future breeding through super-pangenome

Crop wild relatives(CWRs)deliver untapped genetic diversity,as they contain valuable breeding traits absent in the cultivated pool,e.g.,traits imparting climate resilience.Facilitating genetic material from CWRs to breeding programs can advance effective traits and broaden the genetic base of cultivated crops(Bohra et al.,2022).The availability of genetic diversity in crop breeding programs is important for accelerating crop production while safeguarding food safety and agricultural sustainability.Crop domestication and artificial selection have paved the way for crop cultivars tailored to evolving human requirements and modern cultivation practices.However,domestication and breeding have significantly reduced genetic diversity in modern crops(Khan et al.,2020;Bohra et al.,2022).Owing to the extensive genetic and phenotypic variability,CWRs serve as valuable genetic reservoirs for crop improvement(Bohra et al.,2022;Li et al.,2023).The use of CWRs in breeding programs is not that straightforward,as linkage drags often remain difficult to overcome.

Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction

The first paradigm of plant breeding involves direct selection-based phenotypic observation,followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and,more recently,by incorporation of molecular marker genotypes.However,plant performance or phenotype(P)is determined by the combined effects of genotype(G),envirotype(E),and genotype by environment interaction(GEI).Phenotypes can be predicted more precisely by training a model using data collected from multiple sources,including spatiotemporal omics(genomics,phenomics,and enviromics across time and space).Integration of 3D information profiles(G-P-E),each with multidimensionality,provides predictive breeding with both tremendous opportunities and great challenges.Here,we first review innovative technologies for predictive breeding.We then evaluate multidimensional information profiles that can be integrated with a predictive breeding strategy,particularly envirotypic data,which have largely been neglected in data collection and are nearly untouched in model construction.We propose a smart breeding scheme,integrated genomic-enviromic prediction(iGEP),as an extension of genomic prediction,using integrated multiomics information,big data technology,and artificial intelligence(mainly focused on machine and deep learning).We discuss how to implement iGEP,including spatiotemporal models,environmental indices,factorial and spatiotemporal structure of plant breeding data,and cross-species prediction.A strategy is then proposed for prediction-based crop redesign at both the macro(individual,population,and species)and micro(gene,metabolism,and network)scales.Finally,we provide perspectives on translating smart breeding into genetic gain through integrative breeding platforms and open-source breeding initiatives.We call for coordinated efforts in smart breeding through iGEP,institutional partnerships,and innovative technological support.

CRISPR/Cas9 gene editing and natural variation analysis demonstrate the potential for HvARE1 in improvement of nitrogen use efficiency in barley

Nitrogen is a major determinant of grain yield and quality.As excessive use of nitrogen fertilizer leads to environmental pollution and high production costs,improving nitrogen use efficiency(NUE)is fundamental for a sustainable agriculture.Here,we dissected the role of the barley abnormal cytokinin response1 repressor 1(Hv ARE1)gene,a candidate for involvement in NUE previously identified in a genome-wide association study,through natural variation analysis and clustered regularly interspacedshort palindromic repeats(CRISPR)/CRISPRassociated protein 9(Cas9)-mediated gene editing.Hv ARE1 was predominantly expressed in leaves and shoots,with very low expression in roots under low nitrogen conditions.Agrobacterium-mediated genetic transformation of immature embryos(cv.Golden Promise)with single guide RNAs targeting Hv ARE1 generated 22 T0 plants,from which four T1 lines harbored missense and/or frameshift mutations based on genotyping.Mutant are1 lines exhibited an increase in plant height,tiller number,grain protein content,and yield.Moreover,we observed a 1.5-to2.8-fold increase in total chlorophyll content in the flag leaf at the grain filling stage.Delayed senescence by 10–14 d was also observed in mutant lines.Barley are1 mutants had high nitrogen content in shoots under low nitrogen conditions.These findings demonstrate the potential of ARE1 in NUE improvement in barley.

大麦芽期耐盐相关的同源和候选基因

土壤盐害影响了全球6%以上的陆地面积,并导致了大量的农作物减产。盐害主要通过渗透和离子胁迫抑制植物的生长和发育,而植物相应地通过渗透调节、转移或外排积累的钠和氯离子以增强适应性。目前,生产上尚未有实用、经济的方法治理盐害,因而最为可行的途径是增强植物自身的耐盐性。盐胁迫严重抑制种子萌发,而作为全球第四大禾谷类作物的大麦与其他谷物相比耐盐性更强。本文综述了大麦芽期耐盐性的遗传机制,总结了已报道的相关数量性状位点和功能基因,比对了拟南芥、大豆、玉米、小麦和水稻中耐盐候选基因在大麦中的同源基因并映射到参考基因组。此外,本文还讨论了三个耐盐功能基因家族的遗传多样性,包括脱水应答元件结合蛋白(DREB)、类体细胞胚胎发生受体激酶和水通道蛋白。上述三个基因家族在植物中都存在丰富的多样性,但DREB家族在大麦中的多样性高于水稻和小麦。后续研究中,芽期耐盐性的简便筛选方法仍有待开发,耐盐基因及相关机理机制仍需鉴定、验证,并整合到栽培品种中,以实现盐土上作物的生产。

Wheat gluten protein and its impacts on wheat processing quality

Before the advent of the wheat genomic era, a wide range of studies were conducted to understand the chemistry and functions of the wheat storage proteins,which are the major determinants of wheat flour the suitability of wheat flour for various end products, such as bread, noodles and cakes.Wheat grain protein is divided into gluten and non-gluten fractions and the wheat processing quality mainly depends on the gluten fractions.Gluten provides the unique extensibility and elasticity of dough that are essential for various wheat end products.Disulfide bonds are formed between cysteine residues,which is the chemical bases for the physical properties of dough.Based on the SDS-extractability, grain protein is divided into SDS-unextractable polymeric protein(UPP)and SDS-extractable polymeric protein.The percentage of UPP is positively related to the formation of disulfide bonds in the dough matrix.In the wheat genomic era, new glutenins with long repetitive central domains that contain a high number of consensus hexapeptide and nonapeptide motifs as well as high content of cysteine and glutamine residues should be targeted.

Highly efficient and genotype-independent barley gene editing based on anther culture

Recalcitrance to tissue culture and genetic transformation is the major bottleneck for gene manipulation in crops.In barley,immature embryos of Golden Promise have typically been used as explants for transformation.However,the genotype dependence of this approach limits the genetic modification of commercial varieties.Here,we developed an anther culture-based system that permits the effective creation of transgenic and gene-edited plants from commercial barley varieties.The protocol was tested in Golden Promise and four Australian varieties,which differed in phenology,callus induction,and green plant regeneration responses.Agrobacterium-mediated transformation was performed on microspore-derived callus to target the HvPDS gene,and T0 albinos with targeted mutations were successfully obtained from commercial varieties.Further editing of three targets was achieved with an average mutation rate of 53%in the five varieties.In 51 analyzed T0 individuals,Cas9 induced a large proportion(69%)of single-base indels and two-base deletions in the target sites,with variable mutation rates among targets and varieties.Both ontarget and off-target activities were detected in T1 progenies.Compared with immature embryo protocols,this genotype-independent platformcan deliver a high editing efficiency and more regenerant plants within a similar time frame.It shows promise for functional genomics and the application of CRISPR technologies for the precise improvement of commercial varieties.