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Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

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Plant Communications 2024年第5期5卷 57-74页

作者： Guo Ai Chao He Siteng Bi Ziru Zhou Ankui Liu Xin Hu Yanyan Liu Liujie Jin JiaCheng Zhou Heping Zhang Dengxiang Du Hao Chen Xin Gong Sulaiman Saeed Handong Su Caixia Lan Wei Chen Qiang Li Hailiang Mao Lin Li Hao Liu Dijun Chen Kerstin Kaufmann Khaled FAlazab Wenhao Yan National key laboratory of crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China Shenzhen Institute of Nutrition and Health Huazhong Agricultural UniversityWuhan 430070China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenomeAnalysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China State key laboratory of Pharmaceutical biotechnology School of Life SciencesNanjing UniversityNanjing 210023China Department for Plant Cell and Molecular Biology Institute for BiologyHumboldt-Universitat Zu Berlin10115 BerlinGermany Plant Research Department Nuclear Research CenterEgyptian Atomic Energy AuthorityCairo 13759Egypt

Spike architecture inﬂuences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat(Triticum aestivum L.).However,the complex wheat genome and the inﬂuence of various environmental factors pose challenges in mapping the causal genes that affect spike ***,we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in *** identified 170 loci that are responsible for variations in spike length,spikelet number per spike,and grain number per spike through genome-wide association study and meta-QTL *** constructed gene regulatory networks for young inﬂorescences at the double ridge stage and theﬂoret primordium stage,in which the spikelet meristem and theﬂoret meristem are predominant,respec-tively,by integrating transcriptome,histone modification,chromatin accessibility,eQTL,and protein–pro-tein interactome *** these networks,we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike *** functions of TaZF-B1,VRT-B2,and TaSPL15-A/D in establishment of wheat spike architecture were *** study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

关键词： bread wheat spike traits genetic variation protein–protein interaction gene regulatory network

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Correction:Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

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Journal of Cotton Research 2024年第2期7卷 219-222页

作者： SHUI Guangling LIN Hairong MA Xiaomei ZHU Bo HAN Peng AINI Nurimanguli GUO Chunping WU Yuanlong PAN Zhenyuan YOU Chunyuan SONG Guoli NIE Xinhui key laboratory of Oasis Ecology Agricultural of xinjiang Bingtuan Agricultural CollegeShihezi UniversityShiheziXinjiang 832003China Cotton Institute Xinjiang Academy of Agriculture and Reclamation ScienceShiheziXinjiang 832000China Agricultural Science Research Institute of the 5 Division of Xinjiang Production and Construction CorpsShuangheXinjiang 833408China Modern Agricultural College Kashi UniversityKashiXinjiang 844000China National key laboratory of crop Genetic Improvement College of Plant Sciences&TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China National key laboratory of Cotton Bio‑Breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan 455000China

Correction:J Cotton Res 7,20(2024)https://***/10.1186/s42397-024-00180-3 Following publication of the original article(Shui et al.2024),the author found 5 errors in the published *** of the author’s name has been corrected from Gou Chunping to Guo *** reference(Zhao SQ.2016)in Table 2 has been updated to:Zhao *** on the major gene and multigene mixed inheritance and QTL mapping for early maturity traits in upland *** Acad Agric ***://***/10.3969/***.201600501.(in Chinese with English abstract).***’Results’part,’Phenotype analysis of 238 cotton boll abscission among cotton accessions’paragraph,the phenotype analysis of AR1 ranging from 19.27%–63.79%,which was wrongly written as 19.27%-63.97%.***‘2018KRL’is modified to‘2018KEL’in Table 1.

关键词： germplasm traits cotton

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Versatile plant genome engineering using anti-CRISPR-Cas12a systems

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Science China Life Sciences 2024年

作者： Yao He Shishi Liu Long Chen Dongkai Pu Zhaohui Zhong Tang Xu Qiurong Ren Chuan Dong Yawei Wang Danning Wang Xuelian Zheng Fengbiao Guo Tao Zhang Yiping Qi Yong Zhang Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization School of Life Sciences Southwest University Department of biotechnology School of Life Sciences and Technology Center for Informational Biology University of Electronic Science and Technology of China Sichuan Institute of Edible Fungi Sichuan Academy of Agricultural Sciences Jiangsu key laboratory of crop Genomics and Molecular Breeding/Zhongshan Biological Breeding laboratory/key laboratory of Plant Functional Genomics of the Ministry of Education College of AgricultureYangzhou University Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops/Jiangsu key laboratory of crop Genetics and Physiology Yangzhou University Department of Respiratory and Critical Care Medicine Zhongnan Hospital of Wuhan University key laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and School of Pharmaceutical Sciences Wuhan University Department of Plant Science and Landscape Architecture University of Maryland College Park 20742 Institute for Bioscience and biotechnology Research University of Maryland

CRISPR-Cas12a genome engineering systems have been widely used in plant research and crop breeding. To date, the performance and use of anti-CRISPR-Cas12a systems have not been fully established in plants. Here, we conduct in silico analysis to identify putative anti-CRISPR systems for Cas12a. These putative anti-CRISPR proteins, along with known anti-CRISPR proteins, are assessed for their ability to inhibit Cas12a cleavage activity in vivo and in planta. Among all anti-CRISPR proteins tested, AcrVA1 shows robust inhibition of Mb2Cas12a and LbCas12a in E. coli. Further tests show that AcrVA1 inhibits LbCas12a mediated genome editing in rice protoplasts and stable transgenic lines. Impressively, co-expression of AcrVA1 mitigates off-target effects by CRISPR-LbCas12a, as revealed by whole genome sequencing. In addition, transgenic plants expressing AcrVA1 exhibit different levels of inhibition to LbCas12a mediated genome editing, representing a novel way of fine-tuning genome editing efficiency. By controlling temporal and spatial expression of AcrVA1, we show that inducible and tissue specific genome editing can be achieved in plants. Furthermore, we demonstrate that AcrVA1 also inhibits LbCas12a-based CRISPR activation(CRISPRa) and based on this principle we build logic gates to turn on and off target genes in plant cells. Together, we have established an efficient anti-CRISPR-Cas12a system in plants and demonstrate its versatile applications in mitigating off-target effects, finetuning genome editing efficiency, achieving spatial-temporal control of genome editing, and generating synthetic logic gates for controlling target gene expression in plant cells.

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A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and droughttolerance mechanisms

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Plant Communications 2024年第7期5卷 157-177页

作者： Lei Feng Fei Teng Na Li Jia-Cheng Zhang Bian-Jiang Zhang Sau-Na Tsai Xiu-Le Yue Li-Fei Gu Guang-Hua Meng Tian-Quan Deng Suk-Wah Tong Chun-Ming Wang Yan Li Wei Shi Yong-Lun Zeng Yue-Ming Jiang Weichang Yu Sai-Ming Ngai Li-Zhe An Hon-Ming Lam Jun-Xian He School of Life Sciences and State key laboratory of Agrobiotechnology The Chinese University of Hong KongSha TinNew TerritoriesHong KongChina Guangdong Provincial key laboratory of biotechnology for Plant Development School of Life SciencesSouth China Normal UniversityGuangzhou 510631China BGI-Shenzhen Tech Co. Ltd.Beishan Industrial ZoneYantian DistrictShenzhen 518083China School of Life Sciences and Ministry of Education key laboratory of Cell Activities and Stress Adaptations Lanzhou UniversityLanzhou 730030China State key laboratory of Subtropical Silviculture Zhejiang Agriculture and Forestry UniversityHangzhou 311300China State key laboratory of Plant Diversity and Specialty crops South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China Guangdong Provincial key laboratory of Applied Botany&key laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China College of Life Sciences and Oceanography Shenzhen UniversityShenzhen 518060China State key laboratory of Efficient Production of Forest Resources Beijing Forestry UniversityBeijing 100083China

Plants that grow in extreme environments represent unique sources of stress-resistance genes and *** mongolicus(Leguminosae)is a xerophytic evergreen broadleaf shrub native to semi-arid and desert regions;however,its drought-tolerance mechanisms remain poorly ***,we report the assembly of a reference-grade genome for ***,describe its evolutionary history within the legume family,and examine its drought-tolerance *** assembled genome is 843.07 Mb in length,with 98.7%of the sequences successfully anchored to the nine chromosomes of *** genome is predicted to contain 47611 protein-coding genes,and 70.71%of the genome is composed of repetitive sequences;these are dominated by transposable elements,particularly longterminal-repeat *** analyses revealed two whole-genome duplication(WGD)events at 130 and 58 million years ago(mya)that are shared by the genus Ammopiptanthus and other legumes,but no species-specific WGDs were found within this *** genome reconstruction revealed that the *** genome has undergone fewer rearrangements than other genomes in the legume family,confirming its status as a"relict plant".Transcriptomic analyses demonstrated that genes involved in cuticular wax biosynthesis and transport are highly expressed,both under normal conditions and in response to polyethylene glycol-induced *** induction of genes related to ethylene biosynthesis and signaling was also observed in leaves under dehydration stress,suggesting that enhanced ethylene response and formation of thick waxy cuticles are two major mechanisms of drought tolerance in *** expression of AmERF2,an ethylene response factor unique to ***,can markedly increase the drought tolerance of transgenic Arabidopsis thaliana plants,demonstrating the potential for application of *** genes in crop improvement.

关键词： Ammopiptanthus mongolicus genome sequencing genome evolution drought tolerance cuticular wax ethylene

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The chromosome-level genome of double-petal phenotype jasmine provides insights into the biosynthesis of floral scent

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Horticultural Plant Journal 2024年第1期10卷 259-272页

作者： Xiangyu Qi Huadi Wang Shuyun Liu Shuangshuang Chen Jing Feng Huijie Chen Ziyi Qin Quanming Chen Ikram Blilou Yanming Deng Jiangsu key laboratory for Horticultural crop Genetic Improvement Institute of Leisure AgricultureJiangsu Academy of Agricultural SciencesNanjingJiangsu 210014China School of Life Sciences Jiangsu UniversityZhenjiangJiangsu 212013China College of Horticulture Nanjing Agricultural UniversityNanjingJiangsu 210014China Shanghai Personal biotechnology Company Limited Shanghai 200231China Biological and Environmental Sciences and Engineering King Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia

Jasmine(Jasminum sambac Aiton)is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and ***,the genetic basis of its floral scent is largely *** this study,using PacBio,Illumina,10×Genomics and highthroughput chromosome conformation capture(Hi-C)sequencing technologies,a high-quality chromosome-level reference genome for *** was obtained,exploiting a double-petal phenotype cultivar‘Shuangbanmoli’(JSSB).The results showed that the final assembled genome of JSSB is 580.33 Mb in size(contig N50=1.05 Mb;scaffold N50=45.07 Mb)with a total of 39618 predicted protein-coding *** analyses revealed that the JSSB genome has undergone an ancient whole-genome duplication(WGD)event at 91.68 million years ago(Mya).It was estimated that *** diverged from the lineage leading to Olea europaea and Osmanthus fragrans about 28.8 *** the basis of a combination of genomic,transcriptomic and metabolomic analyses,a range of floral scent volatiles and genes were identified involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis *** results provide new insights into the molecular mechanism of its fragrance biosynthesis in jasmine.

关键词： Jasminum sambac Aiton Oleaceae Genome evolution Floral scent Terpene synthase

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Small particles,big effects:How nanoparticles can enhance plant growth in favorable and harsh conditions

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Journal of Integrative Plant Biology 2024年第7期66卷 1274-1294页

作者： Jie Wang Honghong Wu Yichao Wang Wuwei Ye Xiangpei Kong Zujun Yin Zhengzhou Research Base State Key Laboratory of Cotton Bio‐breeding and Integrated UtilizationSchool of Agricultural SciencesZhengzhou UniversityZhengzhou 450001China State key laboratory of Cotton Bio‐breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000China National key laboratory of crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China School of Engineering Design and Built EnvironmentWestern Sydney UniversityPenrith NSW 2751Australia Western Agricultural Research Center Chinese Academy of Agricultural SciencesChangji 831100China The key laboratory of Plant Development and Environmental Adaptation Biology Ministry of EducationCollege of Life SciencesShandong UniversityQingdao 266237China

By 2050,the global population is projected to reach 9 billion,underscoring the imperative for innovative solutions to increase grain yield and enhance food *** has emerged as a powerful tool,providing unique solutions to this ***(NPs)can improve plant growth and nutrition under normal conditions through their high surface-to-volume ratio and unique physical and chemical ***,they can be used to monitor crop health status and augment plant resilience against abiotic stresses(such as salinity,drought,heavy metals,and extreme temperatures)that endanger global *** of NPs can enhance stress tolerance mechanisms in plants,minimizing potential yield losses and underscoring the potential of NPs to raise crop yield and *** review highlights the need for a comprehensive exploration of the environmental implications and safety of nanomaterials and provides valuable guidelines for researchers,policymakers,and agricultural *** thoughtful stewardship,nanotechnology holds immense promise in shaping environmentally sustainable agriculture amid escalating environmental challenges.

关键词： abiotic stress agricultural defense system nano-particles nanotechnology oxidative stress reactive oxygen species toxicity

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Transcription factors involved in tomato fruit quality improvement

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Food Quality and Safety 2024年第1期8卷 50-54页

作者：石艳娜戴正蓉陈昆松 College of Agriculture and biotechnology Zhejiang UniversityZijingang CampusHangzhouChina Zhejiang Provincial key laboratory of Horticultural Plant Integrative Biology Zhejiang UniversityZijingang CampusHangzhouChina State Agriculture Ministry laboratory of Horticultural Plant Growth Development and Quality ImprovementZhejiang UniversityZijingang CampusHangzhouChina

Fruit quality is both a consumer demand and an important goal for horticultural *** exploration of quality-related genes provides targets to create high-quality germplasm using biotechnology,of which transcription factors(TFs)exhibit dosage effects compared with structural ***,an important horticultural crop as well as model fruit,has been widely ***,we focused on TFs with potential utilization value that control appearance(***,pigment)and internal(***,texture,shelf life and health benefits)quality in ***,potential strategies to generate high-quality tomato fruit are discussed.

关键词： Fruit quality transcription factor tomato.

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Targeted G-to-T base editing for generation of novel herbicide-resistance gene alleles in rice

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Journal of Integrative Plant Biology 2024年第6期66卷 1048-1051页

作者： Yifu Tian Xinbo Li Jiyong Xie Zai Zheng Rundong Shen Xuesong Cao Mugui Wang Chao Dong Jian-Kang Zhu Ministry of Agriculture and Rural Affairs key laboratory of Gene Editing Technologies(Hainan) Institute of Crop Sciences and National Nanfan Research InstituteChinese Academy of Agricultural SciencesSanya 572024China Hainan Seed Industry laboratory Sanya 572024China Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesThe Chinese Academy of SciencesShanghai 201602China University of Chinese Academy of Sciences Beijing 100049China Institute of Advanced biotechnology and School of MedicineSouthern University of Science and TechnologyShenzhen 518055China

Deaminase-based cytosine base editors(CBEs)and adenine base editors(ABEs)induce C-to-T and A-to-G transitions,respectively,enabling single-nucleotide variants(SNVs)in plants for research and crop enhancement(Li et al.,2023a).The C-to-G base editors(CGBEs)and A-to-Y base editors(AYBEs),developed by incorporating glycosylases with CBEs and ABEs,expand the repertoire of base editing products,allowing C-to-T/G and A-to-T/G transversions in plants(Li et al.,2023b,2023c;Sretenovic et a.,2021).

关键词： base alleles CBE

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Knockout of miR396 genes increases seed size and yield in soybean

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Journal of Integrative Plant Biology 2024年第6期66卷 1148-1157页

作者： Hongtao Xie Fei Su Qingfeng Niu Leping Geng Xuesong Cao Minglei Song Jinsong Dong Zai Zheng Rui Guo Yang Zhang Yuanwei Deng Zhanbo Ji Kang Pang Jian‐Kang Zhu Jianhua Zhu School of Life Sciences Anhui Agricultural UniversityHefei 230036China Research Center for Biological Breeding Technology Research Institute of Frontier ScienceAnhui Agricultural UniversityHefei 230036China Bellagen biotechnology Co.Ltd Jinan 250000China Institute of crop Sciences/National Nanfan Research Institute Chinese Academy of Agricultural SciencesKey Laboratory of Gene Editing Technologies(Hainan)Ministry of Agriculture and Rural AffairsSanya 572025China Southern University of Science and TechnologyShenzhen 518055China Hainan Yazhou Bay Seed laboratory Sanya 572024China

Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal *** R396 genes have been shown to negatively regulate grain size in rice,but whether mi R396 family members may function in a similar manner in soybean is ***,we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean mi R396genes through genome editing with clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas)12SF01 in the elite soybean cultivar Zhonghuang 302(ZH302).Four triple mutants(mir396aci,mir396acd,mir396adf,and mir396cdf),two quadruple mutants(mir396-abcd and mir396acfi),and two quintuple mutants(mir396abcdf and mir396bcdfi)were *** found that plants of all the mir396 mutants produced larger seeds compared to ZH302 *** tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower *** contrast,mir396abcdf and mir396bcdfiplants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues,but they are suited for low latitude growth zones with increased yield without lodging *** together,our study demonstrated that loss-of-function of mi R396 genes leads to significantly enlarged seed size and increased yield in soybean,providing valuable germplasms for breeding high-yield soybean.

关键词： Cas12SF01 CRISPR/Cas miR396 seed size soybean yield

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Comparison of nitrification inhibitors for mitigating cadmium accumulation in pakchoi and their associated microbial mechanisms

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Journal of Zhejiang University-Science B(Biomedicine & biotechnology) 2024年第9期25卷 773-788页

作者： Wenxin DU Qingyang ZHU Xiangting JING Wejie HU Yao ZHUANG Yijie JIANG Chongwei JIN State key laboratory of Plant Environmental Resilience Zhejiang UniversityHangzhou 310058China

The use of nitrification inhibitors has been suggested as a strategy to decrease cadmium(Cd)accumulation in ***,the most efficient nitrification inhibitor for mitigating crop Cd accumulation remains to be elucidated,and whether and how changes in soil microbial structure are involved in this process also remains *** address these questions,this study applied three commercial nitrification inhibitors,namely,dicyandiamide(DCD),3,4-dimethylpyrazole phosphate(DMPP),and nitrapyrin(NP),to *** results showed that both DCD and DMPP(but not NP)could efficiently decrease Cd concentrations in pakchoi in urea-and ammonium-fertilized *** addition,among the three tested nitrification inhibitors,DMPP was the most efficient in decreasing the Cd concentration in *** nitrification inhibitors decreased pakchoi Cd concentrations by suppressing acidification-induced Cd availability and reshaping the soil microbial structure;the most effective nitrification inhibitor was *** oxidation generates the most protons during nitrification and is inhibited by nitrification *** in environmental factors and predatory bacterial abundance caused by the nitrification inhibitors changed the soil microbial structure and increased the potential participants in plant Cd *** summary,our study identified DMPP as the most efficient nitrification inhibitor for mitigating crop Cd contamination and observed that the soil microbial structural changes caused by the nitrification inhibitors contributed to decreasing Cd concentration in pakchoi.

关键词： Cadmium(Cd) Nitrification inhibitor Soil microbial structure Safe crop production

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