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| 1 | CRISPR/Cas9 gene editing and natural variation analysis demonstrate the potential for HvARE1 in improvement of nitrogen use efficiency in barley显示文摘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. | Sakura D.Karunarathne Yong Han Xiao-Qi Zhang Chengdao Li | 2022 | Journal of Integrative Plant Biology2022，64，3： | 4 |
| 2 | 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显示文摘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. | Tianhua He Chengdao Li | 2020 | The Crop Journal2020，8，5： | 3 |
| 3 | Highly efficient and genotype-independent barley gene editing based on anther culture显示文摘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. | Yong Han Sue Broughton Li Liu Xiao-Qi Zhang Jianbin Zeng Xiaoyan He Chengdao Li | 2021 | Plant Communications2021，2，2： | 3 |
| 4 | Development of gene-specific markers for acid soil/aluminium tolerance in barley ( Hordeum vulgare L.)显示文摘 | Miao Bian Irene Waters Sue Broughton Xiao-Qi Zhang Meixue Zhou Reg Lance Dongfa Sun Chengdao Li | 2013 | Molecular Breeding2013，，1： | 1 |
| 5 | Genetic solutions through breeding counteract climate change and secure barley production in Australia显示文摘Climate changes threaten global sustainable food supply by reducing crop yield.Estimates of future crop production under climate change have rarely considered the capacity of genetic improvement in breeding high-yielding and stress-tolerant crop varieties.We believe that technological advancements and developing climate-resilient crop varieties may offset the adverse effects of climate change.In this study,we examined the historical record of barley breeding and yield,and the trends of climate changes over the past 70 years in Australia.We related the selection of fast development varieties to yield improvement,and revealed the genetic connections of fast development and yield potential through genome-wide association studies.Historical records show that Australia's barley yield has experienced a steady growth despite that the seasonal production window has been shortened due to increased risk of frost damage at flowering stage and terminal heat during maturity since the 1970s.The increase in yield is largely the result of higher yield capacity of the more recently developed varieties that develop faster to counteract the impact of increased terminal heat.We also show that the changing temperature may soon reach a critical point that dramatically changes the barley flowering behaviour to impact yield by pushing its growth beyond the seasonal production window to face increasing frost damage.For the first time,we provide evidence that the effects of climate change on crop production might be less severe than what is currently believed because the advancement of technologies and development of climate-resilient crop varieties may mitigate the adverse effect of climate change to some extent.The greater use of genetic techniques in crop breeding will play a vital role in sustainable global food production in the era of climate change. | Tianhua He Tefera Angessa Camilla B.Hill Xiao-Qi Zhang Paul Telfer Sharon Westcott Chengdao Li | 2022 | Crop Design2022，1，1： | 1 |
| 6 | Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison显示文摘 | Peixiang Ni Michael Francki | 2004 | Functional and IntegrativeGenomics2004，4，2： | 1 |
| 7 | Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison显示文摘 | Chengdao Li Peixiang Ni Michael Francki Adam Hunter Yong Zhang David Schibeci Heng Li Allen Tarr Jun Wang Mehmet Cakir Jun Yu Matthew Bellgard Reg Lance Rudi Appels | 2004 | Functional & Integrative Genomics2004，，2： | 1 |
| 8 | Breeding crops by design for future agriculture显示文摘Plant breeding is both the science and art of developing elite crop cultivars by creating and reassembling desirable inherited traits for human benefit.From the bulk selection of wild plants for cultivation during early civilization to Mendelian genetics and genomics-assisted breeding in modern society,breeding methodologies have evolved over the last thousand years.In the past few decades,the“Green Revolution”through breeding of semi-dwarf wheat and rice varieties,and the use of heterosis and transgenic crops have dramatically enhanced crop productivity and helped prevent widespread famine(Hickey et al.,2019).Integration of these technologies can significantly improve breeding efficiency in the development of super crop varieties(Li et al.,2018). | Chengdao LI | 2020 | Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)2020，21，6： | 1 |
| 9 | Genome-wide association studies reveal QTL hotspots for grain brightness and black point traits in barley显示文摘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. | Yong Jia Sharon Westcott Tianhua He Lee Anne McFawn Tefera Angessa Camila Hill Cong Tan Xiaoqi Zhang Gaofeng Zhou Chengdao Li | 2021 | The Crop Journal2021，9，1： | 1 |
| 10 | Molecular approaches unravel the mechanism of acid soil tolerance in plants显示文摘Acid soil is a worldwide problem to plant production. Acid toxicity is mainly caused by a lack of essential nutrients in the soil and excessive toxic metals in the plant root zone. Of the toxic metals, aluminum(Al) is the most prevalent and most toxic. Plant species have evolved to variable levels of tolerance to aluminum enabling breeding of high Al-tolerant cultivars.Physiological and molecular approaches have revealed some mechanisms of Al toxicity in higher plants. Mechanisms of plant tolerance to Al stress include: 1) exclusion of Al from the root tips, and 2) absorbance, but tolerance of Al in root cells. Organic acid exudation to chelate Al is a feature shared by many higher plants. The future challenge for Al tolerance studies is the identification of novel tolerance mechanisms and the combination of different mechanisms to achieve higher tolerance. Molecular approaches have led to significant progress in explaining mechanisms and detection of genes responsible for Al tolerance.Gene-specific molecular markers offer better options for marker-assisted selection in breeding programs than linked marker strategies. This paper mainly focuses on recent progress in the use of molecular approaches in Al tolerance research. | Miao Bian Meixue Zhou Dongfa Sun Chengdao Li | 2013 | The Crop Journal2013，1，2： | 1 |
| 11 | Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance显示文摘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. | Sakura KARUNARATHNE Esther WALKER Darshan SHARMA Chengdao LI Yong HAN | 2023 | Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)2023，24，12： | 0 |
| 12 | Fine-mapping and characterisation of genes on barley(Hordeum vulgare)chromosome 2H for salinity stress tolerance during germination显示文摘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. | Edward Mwando Yong Han Tefera Angessa Xiao-Qi Zhang Chengdao Li | 2022 | The Crop Journal2022，10，3： | 0 |
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