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 p...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.展开更多
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 quantitat...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.展开更多
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...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.展开更多
The growing global population presents a significant challenge to ensuring food security,further compounded by the increasing threat of salinity to agricultural productivity.Wheat,a major staple food providing 20%of t...The growing global population presents a significant challenge to ensuring food security,further compounded by the increasing threat of salinity to agricultural productivity.Wheat,a major staple food providing 20%of the total caloric intake for humans,is susceptible to salinity stress.Developing new salttolerant wheat cultivars using wheat breeding techniques and genetic modifications is crucial to addressing this issue while ensuring the sustainability and efficiency of wheat production systems within the prevailing climate trend.This review overviews the current landscape in this field and explores key mechanisms and associated genetic traits that warrant attention within breeding programs.We contend that traditional approaches to breeding wheat for Na^(+)exclusion have limited applicability across varying soil salinity levels,rendering them inefficient.Moreover,we question current phenotyping approaches,advocating for a shift from whole-plant assessments to cell-based phenotyping platforms.Finally,we propose a broader use of wild wheat relatives and various breeding strategies to tap into their germplasm pool for inclusion in wheat breeding programs.展开更多
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 ...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.展开更多
Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under ...Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern geneediting platforms. In particular, clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.展开更多
Rangelands worldwide have been subject to broadscale modification,such as widespread predator control,intro-duction of permanent livestock water and altered vegetation to improve grazing.In Australia,these landscape ch...Rangelands worldwide have been subject to broadscale modification,such as widespread predator control,intro-duction of permanent livestock water and altered vegetation to improve grazing.In Australia,these landscape changes have resulted in kangaroos(i.e.large macropods)populations increasing over the past 200 years.Kan-garoos are a key contributor to total grazing pressure and in conjunction with livestock and feral herbivores have been linked to land degradation.We used 22 years of aerial survey data to investigate whether the density of 3 macropod species in the southern rangelands of Western Australia was associated with:(i)land use,including type of livestock,total livestock,density of feral goats,type of land tenure,and kangaroo commercial harvest effort;(ii)predator management,including permitted dingo control effort,estimated dingo abundance,and presence of the State Barrier Fence(a dingo exclusion fence);and(iii)environmental variables:ruggedness,rainfall,fractional cover,and total standing dry matter.Red kangaroos(Osphranter rufus)were most abundant inflat,open vegetation,on pastoral land,where area permitted for dingo control was high,and numbers were positively associated with antecedent rainfall with a 12-month delay.Western grey kangaroos(Macropus fuliginosus)were most abundant onflat,agricultural land,but less abundant in areas with high permitted dingo control.Euros(Osphranter robustus)were most abundant in rugged pastoral land with open vegetation,where permitted dingo control was high.While environmental variables are key drivers of landscape productivity and kangaroo populations,anthropogenic factors such as land use and permitted dingo control are strongly associated with kangaroo abundance.展开更多
This article is the 13th contribution in the Fungal Diversity Notes series,wherein 125 taxa from four phyla,ten classes,31 orders,69 families,92 genera and three genera incertae sedis are treated,demonstrating worldwi...This article is the 13th contribution in the Fungal Diversity Notes series,wherein 125 taxa from four phyla,ten classes,31 orders,69 families,92 genera and three genera incertae sedis are treated,demonstrating worldwide and geographic distri-bution.Fungal taxa described and illustrated in the present study include three new genera,69 new species,one new com-bination,one reference specimen and 51 new records on new hosts and new geographical distributions.Three new genera,Cylindrotorula(Torulaceae),Scolecoleotia(Leotiales genus incertae sedis)and Xenovaginatispora(Lindomycetaceae)are introduced based on distinct phylogenetic lineages and unique morphologies.Newly described species are Aspergillus lan-naensis,Cercophora dulciaquae,Cladophialophora aquatica,Coprinellus punjabensis,Cortinarius alutarius,C.mammil-latus,C.quercoflocculosus,Coryneum fagi,Cruentomycena uttarakhandina,Cryptocoryneum rosae,Cyathus uniperidiolus,Cylindrotorula indica,Diaporthe chamaeropicola,Didymella azollae,Diplodia alanphillipsii,Dothiora coronicola,Efibula rodriguezarmasiae,Erysiphe salicicola,Fusarium queenslandicum,Geastrum gorgonicum,G.hansagiense,Helicosporium sexualis,Helminthosporium chiangraiensis,Hongkongmyces kokensis,Hydrophilomyces hydraenae,Hygrocybe boertmannii,Hyphoderma australosetigerum,Hyphodontia yunnanensis,Khaleijomyces umikazeana,Laboulbenia divisa,Laboulbenia triarthronis,Laccaria populina,Lactarius pallidozonarius,Lepidosphaeria strobelii,Longipedicellata megafusiformis,Lophiotrema lincangensis,Marasmius benghalensis,M.jinfoshanensis,M.subtropicus,Mariannaea camelliae,Mel-anographium smilaxii,Microbotryum polycnemoides,Mimeomyces digitatus,Minutisphaera thailandensis,Mortierella solitaria,Mucor harpali,Nigrograna jinghongensis,Odontia huanrenensis,O.parvispina,Paraconiothyrium ajrekarii,Par-afuscosporella niloticus,Phaeocytostroma yomensis,Phaeoisaria synnematicus,Phanerochaete hainanensis,Pleopunctum thailandicum,Pleurotheciella dimorphospora,Pseudochaetosphaeronema chiangraiense,Pseudodactylaria albicolonia,Rhexoacrodictys nigrospora,Russula paravioleipes,Scolecoleotia eriocamporesi,Seriascoma honghense,Synandromyces makranczyi,Thyridaria aureobrunnea,Torula lancangjiangensis,Tubeufia longihelicospora,Wicklowia fusiformispora,Xenovaginatispora phichaiensis and Xylaria apiospora.One new combination,Pseudobactrodesmium stilboideus is pro-posed.A reference specimen of Comoclathris permunda is designated.New host or distribution records are provided for Acrocalymma fici,Aliquandostipite khaoyaiensis,Camarosporidiella laburni,Canalisporium caribense,Chaetoscutula juniperi,Chlorophyllum demangei,C.globosum,C.hortense,Cladophialophora abundans,Dendryphion hydei,Diaporthe foeniculina,D.pseudophoenicicola,D.pyracanthae,Dictyosporium pandanicola,Dyfrolomyces distoseptatus,Ernakula-mia tanakae,Eutypa flavovirens,E.lata,Favolus septatus,Fusarium atrovinosum,F.clavum,Helicosporium luteosporum,Hermatomyces nabanheensis,Hermatomyces sphaericoides,Longipedicellata aquatica,Lophiostoma caudata,L.clematidis-vitalbae,Lophiotrema hydei,L.neoarundinaria,Marasmiellus palmivorus,Megacapitula villosa,Micropsalliota globocys-tis,M.gracilis,Montagnula thailandica,Neohelicosporium irregulare,N.parisporum,Paradictyoarthrinium diffractum,Phaeoisaria aquatica,Poaceascoma taiwanense,Saproamanita manicata,Spegazzinia camelliae,Submersispora variabi-lis,Thyronectria caudata,T.mackenziei,Tubeufia chiangmaiensis,T.roseohelicospora,Vaginatispora nypae,Wicklowia submersa,Xanthagaricus necopinatus and Xylaria haemorrhoidalis.The data presented herein are based on morphological examination of fresh specimens,coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.展开更多
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 se...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.展开更多
Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation.Domestication and crop breeding often target the scaling traits in the opposite directions.The g...Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation.Domestication and crop breeding often target the scaling traits in the opposite directions.The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored.Here,we revisited a diverse barley(Hordeum vulgare L.)panel with genome-wide single-nucleotide polymorphisms(SNPs)profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling.Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit.Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network.We discovered seventeen novel SNPs(quantitative trait locus)conferring pleiotropic effect on plant height and seed weight,involving genes with function in diverse traits related to plant growth and development.Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome.We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley.Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.展开更多
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.Ho...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.展开更多
Salinity affects more than 6%of the world’s total land area,causing massive losses in crop yield.Salinity inhibits plant growth and development through osmotic and ionic stresses;however,some plants exhibit adaptatio...Salinity affects more than 6%of the world’s total land area,causing massive losses in crop yield.Salinity inhibits plant growth and development through osmotic and ionic stresses;however,some plants exhibit adaptations through osmotic regulation,exclusion,and translocation of accumulated Na+or Cl-.Currently,there are no practical,economically viable methods for managing salinity,so the best practice is to grow crops with improved tolerance.Germination is the stage in a plant’s life cycle most adversely affected by salinity.Barley,the fourth most important cereal crop in the world,has outstanding salinity tolerance,relative to other cereal crops.Here,we review the genetics of salinity tolerance in barley during germination by summarizing reported quantitative trait loci(QTLs)and functional genes.The homologs of candidate genes for salinity tolerance in Arabidopsis,soybean,maize,wheat,and rice have been blasted and mapped on the barley reference genome.The genetic diversity of three reported functional gene families for salt tolerance during barley germination,namely dehydration-responsive element-binding(DREB)protein,somatic embryogenesis receptor-like kinase and aquaporin genes,is discussed.While all three gene families show great diversity in most plant species,the DREB gene family is more diverse in barley than in wheat and rice.Further to this review,a convenient method for screening for salinity tolerance at germination is needed,and the mechanisms of action of the genes involved in salt tolerance need to be identified,validated,and transferred to commercial cultivars for field production in saline soil.展开更多
Frost damage is one of the major concerns for crop growers as it can impact the growth of the plants and hence,yields.Early detection of frost can help farmers mitigating its impact.In the past,frost detection was a m...Frost damage is one of the major concerns for crop growers as it can impact the growth of the plants and hence,yields.Early detection of frost can help farmers mitigating its impact.In the past,frost detection was a manual or visual process.Image-based techniques are increasingly being used to understand frost development in plants and automatic assessment of damage resulting from frost.This research presents a comprehensive survey of the state-of the-art methods applied to detect and analyse frost stress in plants.We identify three broad computational learning approaches i.e.,statistical,traditional machine learning and deep learning,applied to images to detect and analyse frost in plants.We propose a novel taxonomy to classify the existing studies based on several attributes.This taxonomy has been developed to classify the major characteristics of a significant body of published research.In this survey,we profile 80 relevant papers based on the proposed taxonomy.We thoroughly analyse and discuss the techniques used in the various approaches,i.e.,data acquisition,data preparation,feature extraction,computational learning,and evaluation.We summarise the current challenges and discuss the opportunities for future research and development in this area including in-field advanced artificial intelligence systems for real-time frost monitoring.展开更多
Dogtooth tuna,Gymnosarda unicolor were sampled off the east coast of Australia(southwest Pacific Ocean)from 2007 to 2012.Ages were determined by examining thin transverse sections of their sagittal otoliths and were b...Dogtooth tuna,Gymnosarda unicolor were sampled off the east coast of Australia(southwest Pacific Ocean)from 2007 to 2012.Ages were determined by examining thin transverse sections of their sagittal otoliths and were based on counts of alternating opaque and translucent zones(annual growth increments).Growth was rapid during the first year of life,after which growth in length was much reduced.Parameters of the constrained von Bertalanffy growth function(fork length-at-age)were L∞=1164.77(mm,FL)and K=0.44 year^(-1).Preliminary estimates of longevity indicate a maximum observed age of at least 20 years.There was a high degree of variation in the observed length and age of sexual maturity for G.unicolor.Despite this variation,the size at 50%maturity for female G.unicolor estimated in this study was 713 mm FL(<2 years of age).The diet of G.unicolor is very broad and covers a range of fish species.The life history characteristics of G.unicolor overall,indicate that this species may be somewhat resilient to fishing.However,reports of localised depletions,in association with heavy targeting by sports fishers,low effective population sizes and patchy recruitment indicate that this species is particularly vulnerable to overfishing.展开更多
基金The research is supported by the Australian Grain Research and Development Corporation(UMU00049 and UMU00050).
文摘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.
基金Australian Grains Research and Development Corporation(GRDC)grant IDUmu00046Graduate Research Funds from Murdoch University。
文摘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.
基金supported by the Australian Grain Research and Development Corporation(UMU00047)。
文摘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.
基金supported by Australian Research Council,Australia grants to Sergey Shabala and Kadambot H.M.Siddique。
文摘The growing global population presents a significant challenge to ensuring food security,further compounded by the increasing threat of salinity to agricultural productivity.Wheat,a major staple food providing 20%of the total caloric intake for humans,is susceptible to salinity stress.Developing new salttolerant wheat cultivars using wheat breeding techniques and genetic modifications is crucial to addressing this issue while ensuring the sustainability and efficiency of wheat production systems within the prevailing climate trend.This review overviews the current landscape in this field and explores key mechanisms and associated genetic traits that warrant attention within breeding programs.We contend that traditional approaches to breeding wheat for Na^(+)exclusion have limited applicability across varying soil salinity levels,rendering them inefficient.Moreover,we question current phenotyping approaches,advocating for a shift from whole-plant assessments to cell-based phenotyping platforms.Finally,we propose a broader use of wild wheat relatives and various breeding strategies to tap into their germplasm pool for inclusion in wheat breeding programs.
基金generous support of Western Crop Genetics Alliance,Murdoch University,Western Australiaawarded a Murdoch International Postgraduate Scholarship。
文摘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.
文摘Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern geneediting platforms. In particular, clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.
文摘Rangelands worldwide have been subject to broadscale modification,such as widespread predator control,intro-duction of permanent livestock water and altered vegetation to improve grazing.In Australia,these landscape changes have resulted in kangaroos(i.e.large macropods)populations increasing over the past 200 years.Kan-garoos are a key contributor to total grazing pressure and in conjunction with livestock and feral herbivores have been linked to land degradation.We used 22 years of aerial survey data to investigate whether the density of 3 macropod species in the southern rangelands of Western Australia was associated with:(i)land use,including type of livestock,total livestock,density of feral goats,type of land tenure,and kangaroo commercial harvest effort;(ii)predator management,including permitted dingo control effort,estimated dingo abundance,and presence of the State Barrier Fence(a dingo exclusion fence);and(iii)environmental variables:ruggedness,rainfall,fractional cover,and total standing dry matter.Red kangaroos(Osphranter rufus)were most abundant inflat,open vegetation,on pastoral land,where area permitted for dingo control was high,and numbers were positively associated with antecedent rainfall with a 12-month delay.Western grey kangaroos(Macropus fuliginosus)were most abundant onflat,agricultural land,but less abundant in areas with high permitted dingo control.Euros(Osphranter robustus)were most abundant in rugged pastoral land with open vegetation,where permitted dingo control was high.While environmental variables are key drivers of landscape productivity and kangaroo populations,anthropogenic factors such as land use and permitted dingo control are strongly associated with kangaroo abundance.
基金the Thailand Research Fund(Grant No.TRG6180001)the Mae Fah Luang University Fund(Grant No.631C15001)+42 种基金Plant Genetic Conserva-tion Project under the Royal Initiation of Her Royal Highness Princess Maha Chakri Sirindhorn-Mae Fah Luang Universitythe Mushroom Research Foundation.Kevin D.Hyde thanks the 2019 high-end foreign expert introduction plan to Kunming Institute of Botany(Granted by the Ministry of Science and Technology of the People’s Republic of China,Grant No.G20190139006)the future of specialist fungi in a changing climate:baseline data for generalist and specialist fungi associated with ants,Rhododendron species and Dra-caena species(Grant No.DBG6080013)Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion(Grant No.RDG6130001)Dhanushka Wanasinghe thanks CAS President’s International Fellowship Initiative(PIFI)for funding his postdoctoral research(Grant No.2021FYB0005)the Postdoctoral Fund from Human Resources and Social Security Bureau of Yunnan Province.the National Natural Science Foundation of China(Nos.31870011,31750001,31770028 and 31970017).CAS President’s International Fellowship Initiative(PIFI)for young staff(Grant No.Y9215811Q1)Provincial Science and Tech-nology Department(grant no.202003AD150004)Yunnan Provincial Key Programs of Yunnan Eco-friendly Food International Cooperation Research Center(Grant No.2019ZG00908)Key Research Program of Frontier Sciences“Response of Asian mountain ecosystems to global change”,CAS,Grant No.QYZDY-SSWSMC014”the Agreement ENDESA and San Ignacio de Huinay Foundations and Consejo Superior de Investiga-ciones Científicas,CSIC(Projects No.2011HUIN10,2013CL0012)and DGICYT projects CGL2005-01192/BOS,CGL2009-07231,CGL2015-67459-P,CSIC project PIE202030E059the Polish Ministry of Science and Higher Education(grant No.N N305299640)the support from UIDB/04046/2020 and UIDP/04046/2020 Centre grants from FCT,Portugal(to BioISI).the University of Southern Queensland and the Grains Research and Development Corporation projects DAQ00186 and DAQ00194the Japan Society for the Promotion of Science(JSPS)for the award of post-doctoral fellowship and the research grants(No.185701000001 and No.18-06620)the National Natural Science Foundation of China(Nos.31500013,30770013)Talent Introduction Scientific Research Special Project of Hebei Agricultural University(YJ201849)the Ear-marked Fund for Hebei Edible Fungi Innovation Team of Modern Agro-industry Technology Research System(Project ID:HBCT2018050205).SERB,Department of Science and Technology,Government of India,for funding a project(SERB/SB/SO/PS/18/2014 dt.19.5.2015)the Department of Biotechnology,Pondicherry Univer-sity for facilitiesSERB,Department of Science and Technology,Government of India for providing financial support under the project YSS/2015/001590the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program[Grant No.2019QZKK0503]the open research project of“Cross Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences[Grant No.292019312511043]Science and Technology Ser-vice Network Initiative,Chinese Academy of Sciences[KFJ-STS-QYZD-171]S.N.Wijesinghe would like to acknowledge Mae Fah Luang University,National Science Foundation of China(NSFC)pro-ject code 31851110759National Natural Science Foundation of China(No.31972222,31560489)Program of Introducing Talents of Discipline to Universities of China(111 Program,D20023)Talent Project of Guizhou Science and Technology Cooperation Platform([2017]5788-5,[2019]5641 and[2020]5001)Guizhou Science,Tech-nology Department International Cooperation Basic project([2018]5806)the National Natural Science Foundation of China(Project ID:31970021 and 32060005)Fungal Diversity Conservation and Utilization Innovation Team of Dali University(ZKLX2019213)for financial support.the National Natural Sci-ence Foundation of China(NSFC 32060013)Youth Science and Technology Talent Development Project from Guizhou Provincial Department of Education(QJHKYZ[2021]263)Dan-Feng Bao would like to thank the National Natural Science Foundation of China(Project ID:31660008 and 31860006)Fungal diversity conservation and uti-lization innovation team(ZKLX2019213)the Thailand Research Fund grant“impact of climate change on fungal diversity and bioge-ography in the Greater Mekong Sub-region(RDG6130001)”for finan-cial and laboratory support.Higher Educa-tion Commission,Pakistan for financial support through NRPU research project no.20-3383/NRPU/R&D/HEC/14/184.the Széchenyi 2020 Programme(Grant No.GINOP 2.2.1-15-2017-00042)the FWF and the Land Tirol for funding the MICINSNOW project(P31038)the Ministry of Ecology and Environment of China(Project No.2019HJ2096001006)the Science and Technology Support Project of Guizhou Province(Project No.20192451-2)for research support.Yusufjon Gafforov acknowledges Ministry of Innovative Development of the Republic of Uzbekistan(Project no.P3-2014-0830174425 and PЗ-20170921183)CAS President’s International Fellowship Initiative(PIFI)for a Visiting Scientist grant(no.:2018VBB0021).
文摘This article is the 13th contribution in the Fungal Diversity Notes series,wherein 125 taxa from four phyla,ten classes,31 orders,69 families,92 genera and three genera incertae sedis are treated,demonstrating worldwide and geographic distri-bution.Fungal taxa described and illustrated in the present study include three new genera,69 new species,one new com-bination,one reference specimen and 51 new records on new hosts and new geographical distributions.Three new genera,Cylindrotorula(Torulaceae),Scolecoleotia(Leotiales genus incertae sedis)and Xenovaginatispora(Lindomycetaceae)are introduced based on distinct phylogenetic lineages and unique morphologies.Newly described species are Aspergillus lan-naensis,Cercophora dulciaquae,Cladophialophora aquatica,Coprinellus punjabensis,Cortinarius alutarius,C.mammil-latus,C.quercoflocculosus,Coryneum fagi,Cruentomycena uttarakhandina,Cryptocoryneum rosae,Cyathus uniperidiolus,Cylindrotorula indica,Diaporthe chamaeropicola,Didymella azollae,Diplodia alanphillipsii,Dothiora coronicola,Efibula rodriguezarmasiae,Erysiphe salicicola,Fusarium queenslandicum,Geastrum gorgonicum,G.hansagiense,Helicosporium sexualis,Helminthosporium chiangraiensis,Hongkongmyces kokensis,Hydrophilomyces hydraenae,Hygrocybe boertmannii,Hyphoderma australosetigerum,Hyphodontia yunnanensis,Khaleijomyces umikazeana,Laboulbenia divisa,Laboulbenia triarthronis,Laccaria populina,Lactarius pallidozonarius,Lepidosphaeria strobelii,Longipedicellata megafusiformis,Lophiotrema lincangensis,Marasmius benghalensis,M.jinfoshanensis,M.subtropicus,Mariannaea camelliae,Mel-anographium smilaxii,Microbotryum polycnemoides,Mimeomyces digitatus,Minutisphaera thailandensis,Mortierella solitaria,Mucor harpali,Nigrograna jinghongensis,Odontia huanrenensis,O.parvispina,Paraconiothyrium ajrekarii,Par-afuscosporella niloticus,Phaeocytostroma yomensis,Phaeoisaria synnematicus,Phanerochaete hainanensis,Pleopunctum thailandicum,Pleurotheciella dimorphospora,Pseudochaetosphaeronema chiangraiense,Pseudodactylaria albicolonia,Rhexoacrodictys nigrospora,Russula paravioleipes,Scolecoleotia eriocamporesi,Seriascoma honghense,Synandromyces makranczyi,Thyridaria aureobrunnea,Torula lancangjiangensis,Tubeufia longihelicospora,Wicklowia fusiformispora,Xenovaginatispora phichaiensis and Xylaria apiospora.One new combination,Pseudobactrodesmium stilboideus is pro-posed.A reference specimen of Comoclathris permunda is designated.New host or distribution records are provided for Acrocalymma fici,Aliquandostipite khaoyaiensis,Camarosporidiella laburni,Canalisporium caribense,Chaetoscutula juniperi,Chlorophyllum demangei,C.globosum,C.hortense,Cladophialophora abundans,Dendryphion hydei,Diaporthe foeniculina,D.pseudophoenicicola,D.pyracanthae,Dictyosporium pandanicola,Dyfrolomyces distoseptatus,Ernakula-mia tanakae,Eutypa flavovirens,E.lata,Favolus septatus,Fusarium atrovinosum,F.clavum,Helicosporium luteosporum,Hermatomyces nabanheensis,Hermatomyces sphaericoides,Longipedicellata aquatica,Lophiostoma caudata,L.clematidis-vitalbae,Lophiotrema hydei,L.neoarundinaria,Marasmiellus palmivorus,Megacapitula villosa,Micropsalliota globocys-tis,M.gracilis,Montagnula thailandica,Neohelicosporium irregulare,N.parisporum,Paradictyoarthrinium diffractum,Phaeoisaria aquatica,Poaceascoma taiwanense,Saproamanita manicata,Spegazzinia camelliae,Submersispora variabi-lis,Thyronectria caudata,T.mackenziei,Tubeufia chiangmaiensis,T.roseohelicospora,Vaginatispora nypae,Wicklowia submersa,Xanthagaricus necopinatus and Xylaria haemorrhoidalis.The data presented herein are based on morphological examination of fresh specimens,coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.
基金supported by Murdoch University and the Australia Grains Research&Development Corporation(GRDC)(grant number UMU00048)the Department of Primary Industries and Regional Development(DPIRD),Western AustraliaKalyx Australia Pty Ltd。
文摘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.
基金supported by the Australian Grain Research and Development Corporation(UMU00049).
文摘Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation.Domestication and crop breeding often target the scaling traits in the opposite directions.The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored.Here,we revisited a diverse barley(Hordeum vulgare L.)panel with genome-wide single-nucleotide polymorphisms(SNPs)profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling.Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit.Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network.We discovered seventeen novel SNPs(quantitative trait locus)conferring pleiotropic effect on plant height and seed weight,involving genes with function in diverse traits related to plant growth and development.Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome.We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley.Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.
基金supported by the Western Australian Department of Primary Industries and Regional Developmentthe Western Australian State Agricultural Biotechnology Center,Murdoch University.
文摘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.
文摘Salinity affects more than 6%of the world’s total land area,causing massive losses in crop yield.Salinity inhibits plant growth and development through osmotic and ionic stresses;however,some plants exhibit adaptations through osmotic regulation,exclusion,and translocation of accumulated Na+or Cl-.Currently,there are no practical,economically viable methods for managing salinity,so the best practice is to grow crops with improved tolerance.Germination is the stage in a plant’s life cycle most adversely affected by salinity.Barley,the fourth most important cereal crop in the world,has outstanding salinity tolerance,relative to other cereal crops.Here,we review the genetics of salinity tolerance in barley during germination by summarizing reported quantitative trait loci(QTLs)and functional genes.The homologs of candidate genes for salinity tolerance in Arabidopsis,soybean,maize,wheat,and rice have been blasted and mapped on the barley reference genome.The genetic diversity of three reported functional gene families for salt tolerance during barley germination,namely dehydration-responsive element-binding(DREB)protein,somatic embryogenesis receptor-like kinase and aquaporin genes,is discussed.While all three gene families show great diversity in most plant species,the DREB gene family is more diverse in barley than in wheat and rice.Further to this review,a convenient method for screening for salinity tolerance at germination is needed,and the mechanisms of action of the genes involved in salt tolerance need to be identified,validated,and transferred to commercial cultivars for field production in saline soil.
基金This work was supported by a Murdoch University Digital Agriculture Connectivity PhD scholarship to Sayma Shammi.
文摘Frost damage is one of the major concerns for crop growers as it can impact the growth of the plants and hence,yields.Early detection of frost can help farmers mitigating its impact.In the past,frost detection was a manual or visual process.Image-based techniques are increasingly being used to understand frost development in plants and automatic assessment of damage resulting from frost.This research presents a comprehensive survey of the state-of the-art methods applied to detect and analyse frost stress in plants.We identify three broad computational learning approaches i.e.,statistical,traditional machine learning and deep learning,applied to images to detect and analyse frost in plants.We propose a novel taxonomy to classify the existing studies based on several attributes.This taxonomy has been developed to classify the major characteristics of a significant body of published research.In this survey,we profile 80 relevant papers based on the proposed taxonomy.We thoroughly analyse and discuss the techniques used in the various approaches,i.e.,data acquisition,data preparation,feature extraction,computational learning,and evaluation.We summarise the current challenges and discuss the opportunities for future research and development in this area including in-field advanced artificial intelligence systems for real-time frost monitoring.
文摘Dogtooth tuna,Gymnosarda unicolor were sampled off the east coast of Australia(southwest Pacific Ocean)from 2007 to 2012.Ages were determined by examining thin transverse sections of their sagittal otoliths and were based on counts of alternating opaque and translucent zones(annual growth increments).Growth was rapid during the first year of life,after which growth in length was much reduced.Parameters of the constrained von Bertalanffy growth function(fork length-at-age)were L∞=1164.77(mm,FL)and K=0.44 year^(-1).Preliminary estimates of longevity indicate a maximum observed age of at least 20 years.There was a high degree of variation in the observed length and age of sexual maturity for G.unicolor.Despite this variation,the size at 50%maturity for female G.unicolor estimated in this study was 713 mm FL(<2 years of age).The diet of G.unicolor is very broad and covers a range of fish species.The life history characteristics of G.unicolor overall,indicate that this species may be somewhat resilient to fishing.However,reports of localised depletions,in association with heavy targeting by sports fishers,low effective population sizes and patchy recruitment indicate that this species is particularly vulnerable to overfishing.
