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| 1 | 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 |
| 2 | Opportunities for graphene,single-walled and multi-walled carbon nanotube applications in agriculture:A review显示文摘Nanotechnology is an important driver leading to the revolution in the fields of agriculture.Here,we presented insights into the application of carbon nanomaterials(single-and multi-walled carbon nanotubes and graphene)in biomolecule delivery for crop breeding.We also reviewed the application of graphene to biosensors and the utilization efficiency of water,fertilizers and insecticides in agriculture to better manage environmental stresses.Finally,potential molecular interaction mechanisms between graphene and plant roots were discussed.It can be expected that carbon nanomaterials will hold strong promise in developing a more efficient agricultural production system. | Zhiwen Chen Jianguo Zhao Junfeng Cao Yongyan Zhao Jinquan Huang Zishou Zheng Weijia Li Shang Jiang Jun Qiao Baoyan Xing Jin Zhang | 2022 | Crop Design2022，1，1： | 1 |
| 3 | CTREP-finder:A web service for quick identification and visualization of clean transgenic and genome-edited plants显示文摘To feed 10 billion people in 30 years from now will heavily depend on new higher yield,yet safe,biotech crop varieties,which are developed using biotechnologies,particularly genetic transformation and genome editing.A clean transgenic plant(CTP)contains only the defined transgene,whilst a clean edited plant(CEP)is transgene-free.Currently,it is difficult and time-consuming to identify and locate transgenes within plant genomes due to the complex nature of transfer DNA(T-DNA)or plasmid backbone integration,which has led to a major obstacle in mass scale production of clean transgenic/edited plants(CTREPs).Here we have built a web-based portal,CTREP-finder,for fast detection,characterization and visualization of foreign DNA fragments in plants,based on next-generation whole genome sequencing data.We invented a novel bioinformatics strategy to handle three scenarios of transgene integration and successfully identified CTREPs by testing 132 samples.Furthermore,we compared the CTREP-finder with three public programs,FED,transgeneR and TDNAscan,and it showed that the CTREP-finder outperforms those programs particularly on the localization of transgene integration.The use of CTREP-finder needs little requirement for bioinformatics expertise.Therefore,it is a user-friendly web-based portal that could be used by plant breeders and regulatory agencies for the rapid selection/detection of CTREPs for crop breeding and production. | San-Ling Wu Yuan-Yuan Tan Yang Zhao Long-Jiang Fan Qi-Kang Gao Angharad M.R.Gatehouse Qing-Yao Shu | 2022 | Crop Design2022，1，1： | 0 |
| 4 | Divergence of two cultivated allotetraploid cottons unveiled by single-molecule long-read expression sequencing显示文摘Allotetraploid Gossypium hirsutum and G.barbadense are two major cultivated cotton species that have different fiber traits.Research into the molecular basis of those differences is limited by a lack of accurate,complete transcript profiles.Here we adopted joint PacBio Iso-seq and RNA-seq to investigate genome-wide transcript profiles and uncover differences in the expression between G.hirsutum acc.TM-1 and G.barbadense cv.Hai7124.We obtained 178,867 full-length transcripts covering 60.0%of gene loci in the TM-1 reference annotation,including 7846 transcription factors and 3122 lncRNAs.Moreover,we identified 304 and 610 high-confidence(HC)species-specific transcripts in TM-1 and Hai7124,respectively,along with 4156 and 4381 tissue-specific transcripts.Our results update the reference genome annotation and also provide potential resources for studying the molecular mechanisms of fiber development.We are thus able to promote improvements in cotton fiber quality. | Yan Hu Jiedan Chen Lei Fang Fan Dai Gaofu Mei Qiong Wang Tianzhen Zhang | 2022 | Crop Design2022，1，1： | 0 |
| 5 | New windows of crop breeding:FTIPs-mediated protein trafficking in plant reproduction and stress tolerance显示文摘FT-INTERACTING PROTEIN(FTIP)family is the member of multiple C2 domain and transmembrane region proteins(MCTPs).So far thirteen OsFTIPs in rice and sixteen MCTPs in Arabidopsis have been identified,each of which contains three or four C2 domains at N-terminus and one to four transmembrane regions at the C-terminus[1].These FTIPs play key roles in plant reproductive growth and stresses response in addition to the function in macromolecular trafficking in various plant species,which means that FTIPs have tremendous implication value for crop breeding due to their role in the involvement of some reproduction or stress-related proteins transport[2-6]. | Fan Zhang Liang Zhang Lijun Xie Shiyong Song | 2022 | Crop Design2022，1，1： | 0 |
| 6 | The Launch of the Journal Crop Design显示文摘Humans’pursuit of healthy diets has not changed since ancient times.Agriculture remains the foundational guarantee for the sustainable,healthy,open,and happy development of mankind in the future.Nature provides human beings with healthy water,air and domesticated plant resources to meet their needs.Humans have never stopped observing,exploring and transforming nature,and the passion for our future selves has grown exceptionally in 2022. | Xueying Guan Varshney Rajeev Tianzhen Zhang | 2022 | Crop Design2022，1，1： | 0 |
| 7 | The complex interplay between plant-microbe and virus interactions in sustainable agriculture: Harnessing phytomicrobiomes for enhanced soil health, designer plants, resource use efficiency, and food security显示文摘The present-day climate change scenario represents a substantial peril to the global population concerning food security,given the potential impacts on agricultural productivity,food availability,and accessibility.The excessive use of agrochemicals,such as fertilizers and pesticides,leads to the deterioration of soil health as well.Sustainable land-use practices without perturbing the soil ecosystem are achievable only with a comprehensive mechanism.The current need for sustainable agriculture is fulfilled by harnessing the noble services of plantmicrobial association.Microhabitats around plant roots represent the region of maximum microbial activity.Microbiomes play a functional role in affecting plant growth,soil fertility and biogeochemical cycles.Plantmicrobe interactions are highly specific to the host controlled by root exudates,metabolites,environmental factors and symbiotic associations e.g.legume-rhizobia and plant-fungi association.Proper strategies for the use of microbial inoculants will certainly facilitate the various crop improvement programs.The present review,therefore,exemplifies the various studies on the potential of plant microbiomes for sustainable agricultural ecosystems coupled with assuring food security.The review also summarizes recent trends in plant microbiome diversity,the relationship between host plant and microbe,transgenic plants,designer plants and their role in mitigating soil stress.Nevertheless,the future of the global population and food production rely on the prospects of plant microbiome ingenuity. | Ashim Das Astapati Soumitra Nath | 2023 | Crop Design2023，2，1： | 0 |
| 8 | Phytoremediation,stress tolerance and bio fortification in crops through soilless culture显示文摘Crop improvement through soilless cultivation opens up challenges of crop breeding,plant tissue culture and gene manipulation.The plant growing in soilless culture in a closed system,vertical farming,and protected cultivation under controlled climatic factors has immense potential for crop improvement in different aspects of phytoremediation,stress tolerance and bio fortification.The water-based culture and substrate-based culture induce classified stress tolerance in crops such as disease stress,water stress,salt stress under controlled climatic factors and can also be utilized to develop bio fortified crops.The scope and possibilities of crop improvement through water-based culture and substrate-based culture with respect to phytoremediation,stress tolerance,bio fortifi-cation,mechanisms of crop improvement and the challenges in crop improvement through soilless culture are reviewed in this paper.The soilless culture has enormous tools to combat problem of crop improvement and call for soilless green revolution.The comparative and non-comparative investigations of metabolomics,phenomics,genomics and proteomics,Donald concept-plant ideotype and Mendel theory-oligogenic and polygenic inheritance are essential to examine in natural&artificial system through soilless crop improvement. | Avinash Sharma Himanshu Pandey V.S.Devadas Bhagya D.Kartha Amit Vashishth | 2023 | Crop Design2023，2，1： | 0 |
| 9 | Transcriptome analysis of chickpea during heat stress unveils the signatures of long intergenic non-coding RNAs (lincRNAs) and mRNAs in the heat-QTL region显示文摘In plants, besides the role of messenger RNAs (mRNAs) in gene expression, long intergenic non-coding RNAs(lincRNAs) play a key role in regulating various biological processes. Chickpea (Cicer arietinum L.), an importantlegume crop, is sensitive to extreme temperature regimes. Here, we identified the lincRNAs and mRNAs in threechickpea genotypes contrasting for heat stress response (two tolerant- ICC 1356, ICC 15614;one sensitive- ICC4567) and investigated their role in heat stress. A total of 894 putative lincRNAs and 61,110 mRNAs wereidentified from leaf and root tissues at the vegetative and reproductive stages of the plant under control and heatstress conditions. Co-expression studies revealed the significant association of lincRNAs with mRNAs which areattributed to heat stress leaf samples at the reproductive stage. Further, mRNAs encoding heat shock transcriptionfactors (HSFs), heat shock proteins (HSPs), starch, and sucrose metabolism pathway genes played an essential rolein mitigating heat stress. Furthermore, three key lincRNAs underlying chickpea's heat-quantitative trait locus(QTL) region were identified. This study provided new insights into the regulation of heat stress tolerance inchickpea by identifying candidate lincRNAs and mRNAs. | Sailaja Bhogireddy Himabindu Kudapa Prasad Bajaj Vanika Garg Annapurna Chitikineni Sourav Nayak Rajeev K.Varshney | 2023 | Crop Design2023，2，1： | 0 |
| 10 | Genome-wide landscapes of genes and repeatome reveal the genomic differences between the two subspecies of peanut (Arachis hypogaea)显示文摘Distribution and structural features of genes,repeat elements and transposable elements(TEs)were studied to identify the genomic differences between the two subspecies(ssp.hypogaea and ssp.fastigiata)of peanut(Arachis hypogaea L.).A total of 67128 predicted genes,2738666 copies of TEs and 162361 tandem repeats from the reference genome of Tifrunner were employed for this study.Of the 67128 genes,33622 were reading on the plus strand,while 33506 were traced on the minus strand.Though B03 had the highest number of genes(4524),A08 recorded the highest density(53 genes/Mb)of genes in the genome.Telomeric regions had the highest density of genes.The average length of the genes was 3971 bp with majority of the genes(39228)containing one to five exons.The gene Arahy.11.0DU9MH had the insertion of 28 different types of TEs,and was the longest gene in the peanut genome.A total of 15731 genes were monomorphic in terms of SNPs across 179 accessions,while 7401 genes showed polymorphism at one nucleotide,indicating very low allelic variation at these genes.Remaining 66%of the genes had two or more SNPs,and therefore showed relatively high allelic variation.Among the 101 unique types of TEs,the Retro elements(869279)followed by CACTA(272596)and Mu(250248)TEs were most predominant.Telomeric regions showed less density of TEs than the regions.On an average,each gene contained 1.8 copies of TEs,and 35706 genes did not have the insertion of any TEs.A QTL-Seq approach could identify 186 SNPs and 26 gene differences between the two subspecies of A.hypogaea.Two of the 26 genes showed allelic variation in terms of SNPs and TEs. | R.S.Bhat K.Shirasawa S.S.Gangurde M.G.Rashmi K.Sahana M.K.Pandey | 2023 | Crop Design2023，2，1： | 0 |
| 11 | An efficient method to quantify silique(fruit)parameters in rapeseed and other crops显示文摘In addition to protecting the developing seeds,rapeseed(Brassica napus L.)silique also plays a major role in providing nutrition for the seeds inside[1–3].Proper silique traits with higher yield potential are favorable in rapeseed breeding.As a three-dimensional object,the silique can be evaluated by its length,width and thickness.A common procedure to quantify the silique length is to measure the replum length of mature siliques by manual,which is labor-intensive and time-consuming.As for the width and thickness,they are often ignored by researchers because of the lack of proper quantifying methods.Here we provide a simple,accurate,and high-throughput method to quantify silique parameters of rapeseed,including the silique length,width,and thickness. | Yushun Jiao Baoling Liang Xiang Li Dawei Zhao Guangsheng Yang Dengfeng Hong | 2023 | Crop Design2023，2，1： | 0 |
| 12 | Core photomorphogenic regulators connect waterlogging response with DNA methylation in Brassica napus显示文摘Light is a pivotal environmental cue for plant development as well as crop yield,and over many years of study,the basic scheme of light signal transduction has been well established.Light signal is perceived by a group of proteins called photoreceptors which can change their conformation or status after sensing light to initiate downstream signaling cascades[1].One group of photoreceptors are phytochromes,the red(R)/far-red(FR)light photoreceptors,which are encoded by PHYA,PHYB,PHYC,PHYD,and PHYE genes in Arabidopsis[1,2].Phytochromes can switch between two conformational states,the inactive R-absorbing(Pr)form and the active FR-absorbing(Pfr)form,which is light-dependent[2].The switch between Pr and Pfr of phytochromes ensures precise response to light intensity and quality to optimize plant growth under fluctuating light conditions. | Yiyi Guo Ting Zhao Jie Dong | 2023 | Crop Design2023，2，1： | 0 |
| 13 | Rice dep1 variety maintains larger stomatal conductance to enhance photosynthesis under low nitrogen conditions显示文摘The DEP1 gene,which corresponds to the erect panicle architecture,shows a pleiotropic effect in increasing grain yield and nitrogen use efficiency in rice.Nevertheless,it remains unclear how nitrogen nutrition affects the photosynthesis in dep1 variety.In the study,we used W7,which carries the gain-of-function dep1 allele and its counterpart wild type plants,in pot trials under two nitrogen conditions.We investigated the differences in photosynthesis,stomatal conductance,and other photosynthetic parameters between the two rice varieties at different levels of nitrogen supply.Our results indicate that dep1 has a higher photosynthetic capacity under low nitrogen conditions due to the larger stomatal conductance.This work reveals that dep1 is more adaptable under a low nitrogen environment by analysis from the perspective of photosynthesis,stomatal function,and nitrogen uptake and assimilation,which provides a theoretical basis for revealing the photosynthetic efficiency of dep1 variety under low nitrogen conditions. | Yihong Li Xiachen Lv Mengmeng Rui Jiang Hu Vadim SVolkov Dali Zeng Yizhou Wang | 2023 | Crop Design2023，2，1： | 0 |
| 14 | Precise and graded regulation of target protein expression in plants显示文摘To ensure the accuracy of developmental programs and maintain a stable intracellular environment,organisms utilize regulatory elements to finely regulate protein expression at various levels.Upstream open reading frames(uORFs),located in the 50 untranslated regions(UTRs)of primary open reading frames(pORFs),are an mRNA regulatory element that primarily regulates the translation initiation of downstream pORFs in a cis-manner by competitively binding with ribosomes,thereby suppressing pORF translation[1]. | Jinpeng Zou Kejian Wang | 2023 | Crop Design2023，2，1： | 0 |
| 15 | Unveiling novel genes in Fern genomes for the design of stress tolerant crops显示文摘Ferns are the second largest vascular plant lineage after angiosperms,shaping the plant biodiversity on our planet for more than 360 million years.Understanding the biological function of fern genes and their potential uses for agriculture,environment and health has been hampered by the lack of high-quality genome sequence of fern.The last five years have seen the assembly of reference fern genomes of Salvinia cucullata(0.26 Gb,n=9),Azolla filiculoides(0.75 Gb,n=22),Adiantum capillus-veneris(4.83 Gb,n=30),Alsophila spinulosa(6.27 Gb,n=69)and Ceratopteris richardii(7.46 Gb,n=39).These high-quality genome sequences will make significant contribution to the better understanding of evolution,ecology,functional genomics,and the diverse applications of ferns.Here,I review the physiological and some aspects of limited molecular mechanisms of abiotic(mainly heavy metal,drought,and shade)and biotic(pests and pathogens)tolerance in different fern species.The potential use of the fern genome toward crop abiotic and biotic stress tolerance is suggested.Thus,deciphering the genetic diversity and novel functional genes of ferns will provide tremendous boost to the knowledge advancement and the biotechnological applications of unique fern genes and proteins for sustainable agricultural production and environmental protection. | Zhong-Hua Chen | 2022 | Crop Design2022，1，2： | 0 |
| 16 | Research progresses on rice leaf color mutants显示文摘Rice leaf color variation is a morphological phenotype that is valuable in studying plant metabolism and physiology.Besides,the rice leaf color phenotype can also be utilized in the breeding process.Rice plants with color mutations typically have less efficient photosynthesis,which can result in poor growth and yield reduction.Studies of rice leaf color mutants have led to important findings about the metabolic and regulatory mechanisms of pigment synthesis and accumulation,chloroplast biogenesis and differentiation,photosynthesis,stress response,etc.In this mini-review,we summarized the current progress in the identification and study of rice leaf color mutants,and we also discussed on the limitations and perspectives of the current research about these rice leaf color mutants. | Weiran Li Yuchan Zhang Md.Anisur Rahman Mazumder Ronghui Pan Delara Akhter | 2022 | Crop Design2022，1，2： | 0 |
| 17 | Present and future prospects of crop synthetic biology显示文摘Affected by the explosion of the world's population,climate changes and resource depletion,crop design and utilization call for revolution.Alongside the rapid development of plant genomics,metabolomics,and new techniques,synthetic biology has now expanded from single-celled microbes to complex plant systems.Thus,much progress has been made in agriculture to meet the increasing demands for food,medicine,and energy.Here we reviewed the successful applications in crop synthetic biology,including crop production,nutrient quality,stress resistance,natural products,and biomedical.At last,we will discuss the challenges and future prospects in crop synthetic biology. | Bo Bi Wei Li Yushu Jiang Hao Du | 2022 | Crop Design2022，1，2： | 0 |
| 18 | Identification of drought tolerant entries based on stress tolerant indices and physiological traits in RIL population of cotton (Gossypium hirsutum)显示文摘The present investigation was taken up in a recombinant inbred population of cotton at advanced stage(F_(10))derived from the cross MCU 5 x TCH 1218 in order to identify drought tolerance lines based on stress tolerant indices and physiological traits.To achieve these objectives,220 recombinant inbred lines,parents and check KC3 were evaluated across two locations viz.,Coimbatore and Aruppukottai in a randomized block design with two replications during Kharif 2018 and stress tolerant indices were estimated from single plant yield under both locations while physiological traits were recorded at rainfed condition alone.Based on different multivariant analyses,18 RILs viz.,RIL 16,20,60,71,73,74,116,131,134,137,139,143,146,147,148,149,164 and 168 were identified as best performers under rainfed condition for yield traits which also exhibited lowest mean rank for physiological traits.Among these entries,RIL 74 and RIL 73 had low percentage of injury and high relative water content respectively.Association analysis revealed that tolerance index,yield reduction ratio,stress tolerance index and stress susceptibility index were significant and positively correlated among themselves.Negative correlation was noticed for yield under stress(YS)with tolerance index(TOL),yield reduction ratio(Yr)and stress susceptibility index(SSI).So,these indices are used to identify the susceptible genotypes,while remaining indices exhibit significant and positive association with yield under stress and normal condition.This implies remaining traits are used to discriminate tolerant genotypes. | K.Nandhini R.Saraswathi N.Premalatha | 2022 | Crop Design2022，1，2： | 0 |
| 19 | Establishment of an artificial inoculation system for the efficient induction of rice bakanae disease显示文摘Bakanae disease,mainly caused by Fusarium fujikuroi,can lead to yield losses ranging from 10 to 20%.The lack of systematic researches on efficient propagation of pathogenic F.fujikuroi,artificial inoculation technology and the pathogenic conditions presents a critical technological gap that has severely hampered research on rice resistance to bakanae disease.This study first explored the sporulation conditions of F.fujikuroi in mung bean liquid medium,and determined that F.fujikuroi cultured in 40 g/L mung bean liquid medium for 2–6 days could efficiently produce pathogenic spores in large quantity.On this basis,we further establish an artificial inoculation system to induce bakanae disease.The main steps and parameters include:Soak rice seeds in a F.fujikuroi spore solution with a concentration of 1×10^(6) conidia/mL for 2 days;let imbibed seeds germinate,and choose germinating seeds with buds of a grain length and cultivate them on half strength MS medium(1/2 MS,pH 5.8-6.8)for about a week.The characteristic bakanae symptoms of excessively elongated seedlings could thus be induced.Furthermore,we found that the bakanae disease symptoms became more profound when a small amount of PDA(0.5%)was added to 1/2 MS medium.Hence our study established a technical system for the artificial induction of bakanae disease involving the use of mung bean medium for rapid propagation of F.fujikuroi spores,seed inoculation and cultivation of seedlings in 1/2 MS medium added with 0.5%PDA.This system will enable quick assessment of bakanae disease resistance and thus will be useful for rice breeding. | Yu-xin Yan Xiao-yan Zhang Yuan-yuan Tan Jian-zhong Huang Ljupcho Jankuloski Qing-yao Shu | 2022 | Crop Design2022，1，2： | 0 |
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