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CRISPR/CasRx-mediated resistance to Soybean mosaic virus in soybean

The crop Journal 2024年第4期12卷 1093-1101页

作者： Le Gao Lijun Xie Yanmin Xiao Xinge Cheng Ruosi Pu Ziheng Zhang Yu Liu Shaopei Gao Zilong Zhang Haoran Qu Haijian Zhi Kai Li MARA Key Laboratory of Biology and genetics Improvement of Soybean Zhongshan Biological Breeding Laboratory(ZSBBL)National Innovation Platform for Soybean Breeding and Industry-Education IntegrationState Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjing 210095JiangsuChina Department of Horticulture Beijing Vocational College of AgricultureBeijing 102442China College of Agronomy&Biotechnology China Agricultural UniversityBeijing 100193China College of Bioscience and Biotechnology Shenyang Agricultural UniversityShenyang 110866LiaoningChina

Soybean mosaic virus(SMV),an RNA virus,is the most common and destructive pathogenic virus in soybean *** newly developed CRISPR/Cas immune system has provided a novel strategy for improving plant resistance to viruses;hence,this study aimed to engineer SMV resistance in soybean using this ***,multiple sgRNAs were designed to target positive-and/or negative-sense strands of the SMV HC-Pro ***,the corresponding CRISPR/CasRx vectors were constructed and transformed into *** inoculation with SMV,39.02%,35.77%,and 18.70%of T_(1)plants were confirmed to be highly resistant(HR),resistant(R),and mildly resistant(MR)to SMV,respectively,whereas only 6.50%were identified as susceptible(S).Additionally,qRT-PCR and DAS-ELISA showed that,both at 15 and 30 d post-inoculation(dpi),SMV accumulation significantly decreased or was even undetectable in HR and R plants,followed by MR and S ***,the expression level of the CasRx gene varied in almost all T_(1)plants with different resistance level,both at 15 and 30 ***,when SMV resistance was evaluated in the T_(2)generation,the results were similar to those recorded for the T_(1)*** findings provide new insights into the application of the CRISPR/CasRx system for soybean improvement and offer a promising alternative strategy for breeding for resistance to biotic stress that will contribute to the development of SMV-immune soybean germplasm to accelerate progress towards greater soybean crop productivity.

关键词： Soybean RNA virus Soybean mosaic virus Resistance CRISPR/CasRx

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Computational tools for plant genomics and breeding

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Science China(Life Sciences) 2024年第8期67卷 1579-1590页

作者： Hai Wang Mengjiao Chen Xin Wei Rui Xia Dong Pei Xuehui Huang Bin Han State Key Laboratory of Maize Bio-breeding Frontiers Science Center for Molecular Design BreedingJoint International Research Laboratory of Crop Molecular BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Sanya Institute of China Agricultural University Sanya 572025China Hainan Yazhou Bay Seed Laboratory Sanya 572025China State Key Laboratory of Tree genetics and breeding Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091China Shanghai Key Laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China College of Horticulture South China Agricultural UniversityGuangzhou 510640China National Center for Gene research CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200233China

Plant genomics and crop breeding are at the intersection of biotechnology and information *** by a combination of highthroughput sequencing,molecular biology and data science,great advances have been made in omics technologies at every step along the central dogma,especially in genome assembling,genome annotation,epigenomic profiling,and transcriptome *** advances further revolutionized three directions of *** is genetic dissection of complex traits in crops,along with genomic prediction and *** second is comparative genomics and evolution,which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant *** third direction is the development of deep learning approaches for the rational design of biological sequences,especially proteins,for synthetic *** three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.

关键词： bioinformatics plant genomics breeding by design

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Mining elite loci and candidate genes for root morphology-related traits at the seedling stage by genome-wide association studies in upland cotton(Gossypium hirsutum L.)

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Journal of Integrative Agriculture 2024年第10期23卷 3406-3418页

作者： Huaxiang Wu Xiaohui Song Muhammad Waqas-Amjid Chuan Chen Dayong Zhang Wangzhen Guo State Key Laboratory of crop genetics&Germplasm Enhancement and Utilization/Engineering research Center of Cotton Germplasm Enhancement and Application Ministry of Education/Nanjing Agricultural UniversityNanjing 210095China

Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental *** this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and ***,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the CottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for *** them,eight QTLs were repeatedly detected in two or more *** these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the ***,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture ***,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.

关键词： cotton root-morphology traits quantitative trait loci candidate genes GWAS

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Coupling of reduced inorganic fertilizer with plant-based organic fertilizer as a promising fertilizer management strategy for colored rice in tropical regions

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Journal of Integrative Agriculture 2024年第1期23卷 93-107页

作者： Tingcheng Zhao Aibin He Mohammad Nauman Khan Qi Yin Shaokun Song Lixiao Nie research Center for Physiology and Ecology and Green Cultivation of Tropical crops School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication)Hainan UniversitySanya 572000China

Colored rice is a type of high-quality,high-added-value rice that has attracted increasing attention in recent *** use of large amounts of inorganic nitrogen fertilizer in rice fields results in low fertilizer use efficiency and high environmental *** fertilizer is a promising way to improve soil quality and sustain high ***,most studies focus on the effect of animal-based organic *** effects of different ratios of plantbased organic fertilizer and inorganic fertilizer on the grain yield and quality of colored rice have rarely been ***,a two-year field experiment was conducted in 2020 and 2021 to study the effects of replacing inorganic N fertilizers with plant-based organic fertilizers on the yield,nitrogen use efficiency(NUE),and anthocyanin content of two colored rice varieties in a tropical region in *** experimental treatments included no nitrogen fertilization(T1),100% inorganic nitrogen fertilizer(T2),30%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T3),60%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T4),and 100% plantbased organic fertilizer(T5).The total nitrogen provided to all the treatments except T1 was the same at 120 kg *** results showed that the T3 treatment enhanced the grain yield and anthocyanin content of colored rice by increasing nitrogen use efficiency compared with *** average,grain yields were increased by 9 and 8%,while the anthocyanin content increased by 16 and 10% in the two colored rice varieties under T3 across the two years,respectively,as compared with *** study of the residual effect of partial substitution of inorganic fertilizers showed that the substitution of inorganic fertilizer with plant-based organic fertilizer improved the soil physiochemical properties,and thus increased the rice grain yield,in the subsequent *** highest grain yield of the subsequent rice crop was observe

关键词： colored rice organic fertilizer soil quality grain yield anthocyanin

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The RUBY reporter for visual selection in soybean genome editing

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aBIOTECH 2024年第2期5卷 209-213页

作者： Li Chen Yupeng Cai Xiaoqian Liu Weiwei Yao Shuiqing Wu Wensheng Hou State Key Laboratory of crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Ministry of Agriculture Key Laboratory of Soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Current systems to screen for transgenic soybeans(Glycine max)involve laborious molecular assays or the expression of fluorescent markers that are difficult to see in soybean ***,a visual system for early screening of transgenic plants would increase the efficiency of crop improvement by genome *** RUBY reporter system,which consists of three genes encoding betalain biosynthetic enzymes,leading to the accumulation of purple pigment in transgenic tissue,has been employed in some plants and dikaryon ***,we assessed the RUBY reporter for visual verification during soybean *** show that RUBY can be expressed in soybean,allowing for visual confirmation of transgenic events without the need for specialized *** with visible accumulation of purple pigment in any tissue were successfully transformed,confirming the accuracy of the RUBY system as a visual *** also assessed the genetic stability of the transgene across generations,which can be performed very early,using the cotyledons of the ***-free seedlings have a distinct green color,facilitating the selection of genome-edited but transgene-free soybean seedlings for *** the RUBY system,we quickly identified a transgene-free Gmwaxy mutant in the T1 *** system thus provides an efficient and convenient tool for soybean genome editing.

关键词： Soybean RUBY Visual reporter Genome editing Biotechnology

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Engineering high amylose and resistant starch in maize by CRISPR/Cas9-mediated editing of starch branching enzymes

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The crop Journal 2024年第4期12卷 1252-1258页

作者： Mingzheng Ma Shanqiu Sun Jinjie Zhu Xiantao Qi Gaoke Li Jianguang Hu Chuanxiao Xie Changlin Liu State Key Laboratory of crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Hainan Yazhou Bay Seed Lab Sanya 572024HainanChina Anhui Agricultural University Hefei 230036AnhuiChina crops research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

To improve the amylose content(AC)and resistant starch content(RSC)of maize kernel starch,we employed the CRISPR/Cas9 system to create mutants of starch branching enzyme I(SBEI)and starch branching enzyme IIb(SBEIIb).A frameshift mutation in SBEI(E1,a nucleotide insertion in exon 6)led to plants with higher RSC(1.07%),lower hundred-kernel weight(HKW,24.71±0.14 g),and lower plant height(PH,218.50±9.42 cm)compared to the wild type(WT).Like the WT,E1 kernel starch had irregular,polygonal shapes with sharp edges.A frameshift mutation in SBEIIb(E2,a four-nucleotide deletion in exon 8)led to higher AC(53.48%)and higher RSC(26.93%)than that for the WT.E2 kernel starch was significantly different from the WT regarding granule morphology,chain length distribution pattern,X-ray diffraction pattern,and thermal characteristics;the starch granules were more irregular in shape and comprised typical B-type *** SBEI and SBEIIb(E12)had a synergistic effect on RSC,HKW,PH,starch properties,and starch biosynthesis-associated gene ***,SS1,SSIIa,SSIIIa,and SSIIIb were upregulated in E12 endosperm compared to WT *** study lays the foundation for rapidly improving the starch properties of elite maize lines.

关键词： Maize Gene editing Starch branching enzyme I Starch branching enzyme IIb

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A complete reference genome assembly for foxtail millet and Setaria-db, a comprehensive database for Setaria

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Molecular Plant 2024年第2期17卷 219-222页

作者： Qiang He Chunchao Wang Qiang He Jun Zhang Hongkai Liang Zefu Lui Kun Xie Sha Tang Yuhan Zhou Bin Liu Hui Zhi Guanqing Jia Ganggang Guo Huilong Du Xianmin Diao State Key Laboratory of crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China School of Life Sciences Institute of Life Sciences and Green DevelopmentHebei UniversityBaoding 071000China State Key Laboratory of Rice Biology&breeding Zhejang Provincial Key Laboratory of Crop GermplasmThe Advanced Seed InstituteZhejiang UniversityHangzhouChina

Dear Editor,,Foxtail millet(Setaria italica)and its wild ancestor green foxtail(***),are two C4 genetic model plants known for their desirable traits,such as small size,short life cycle,ease of transformation,and a compact genome size(~420 Mb)(He et al.,2023).Foxtail millet stands out as the only cultivated species within the Setaria *** a foundational crop for ancient east Asian agriculture civilization,it possesses remarkable drought and soil-nutrient deficiency tolerance.

关键词： comprehensive soil cultivated

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Genes controlling grain chalkiness in rice

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The crop Journal 2024年第4期12卷 979-991页

作者： Luo Chen Xiumei Li Minhua Zheng Rui Hu Jingfang Dong Lingyan Zhou Wuge Liu Dilin Liu Wu Yang Rice research Institute Guangdong Academy of Agricultural SciencesGuangdong Key Laboratory of New Technology in Rice BreedingGuangdong Rice Engineering LaboratoryKey Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province)Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina College of Agriculture and Biology Zhongkai University of Agriculture and EngineeringGuangzhou 510225GuangdongChina Guangdong Provincial Key Laboratory for crop Germplasm Resources Preservation and Utilization Agro-biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

With rising living standards,there is an increasing demand for high-quality *** quality is mainly defined by milling quality,appearance quality,cooking and eating quality,and nutrition *** them,chalkiness is a key trait for appearance quality,which adversely affects cooking and eating quality,head rice yield,and commercial ***,chalkiness is undesirable,and reducing chalkiness is a major goal in rice quality ***,chalkiness is a complex trait jointly influenced by genetic and environmental factors,making its genetic study and precision improvement a huge *** the rapid development of molecular techniques,much knowledge has been gained about the genes and molecular networks involved in chalkiness *** present review describes the major environmental factors affecting chalkiness and summarizes the quantitative trait loci(QTL)associated with *** than 150 genes related to chalkiness formation have been *** functions of the genes regulating chalkiness,primarily those involved in starch synthesis,storage protein synthesis,transcription regulation,organelle development,grain shape regulation,and hightemperature response,are ***,we identify the challenges associated with genetic improvement of chalkiness and suggest potential ***,the review offers insight into the molecular dynamics of chalkiness and provides a strong basis for the future breeding of high-quality rice varieties.

关键词： Rice Grain quality Chalkiness QTL identification Gene

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GmDFB1,an ARM-repeat superfamily protein,regulates floral organ identity through repressing siRNA-and miRNA-mediated gene silencing in soybean

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Journal of Integrative Plant Biology 2024年第8期66卷 1620-1638页

作者： Jie Li Wenxiao Zhang Qing Lu Jiaqi Sun Chuang Cheng Shiyu Huang Shuo Li Qiang Li Wei Zhang Chuanen Zhou Bin Liu Fengning Xiang The Key Laboratory of Plant Development and Environmental Adaptation Biology Ministry of EducationSchool of Life SciencesShandong UniversityQingdao 266237China State Key Laboratory of crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

The development of flowers in soybean(Glycine max)is essential for determining the yield potential of the *** silencing pathways are involved in modulating flower development,but their full elucidation is still ***,we conducted a forward genetic screen and identified an abnormal flower mutant,deformed floral bud1-1(Gmdfb1-1),in *** mapped and identified the causal gene,which encodes a member of the armadillo(ARM)-repeat *** small RNA sequencing(sRNA-seq),we found an abnormal accumulation of small interfering RNAs(si RNAs)and microRNA(miRNAs)in the Gmdfb1 *** further demonstrated that GmDFB1 interacts with the RNA exosome cofactor SUPER KILLER7(Gm SKI7).Additionally,GmDFB1 interacts with the PIWI domain of ARGONAUTE 1(GmAGO1)to inhibit the cleavage efficiency on the target genes of s *** enhanced gene silencing mediated by siRNA and miRNA in the Gmdfb1 mutants leads to the downregulation of their target genes associated with flower *** study revealed the crucial role of GmDFB1 in regulating floral organ identity in soybean probably by participating in two distinct gene silencing pathways.

关键词： ARM-repeat superfamily protein ARGONAUTE 1 SUPER KILLER 7 flower development gene silencing small RNAs soybean

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Transcription factor OsSPL10 interacts with OsJAmyb to regulate blast resistance in rice

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The crop Journal 2024年第1期12卷 301-307页

作者： Zaofa Zhong Lijing Zhong Xiang Zhu Yimin Jiang Yihong Zheng Tao Lan Haitao Cui College of Life Science Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Key Laboratory of genetics Breeding and Multiple Utilization of CropsMinistry of EducationCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Fujian Provincial Key Laboratory of crop breeding by Design Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina College of Plant Protection Shandong Agricultural UniversityTai’an 271018ShandongChina

Transcription factors(TFs)play essential roles in transcriptional reprogramming during activation of plant immune responses to ***10(SQUAMOSA promoter binding protein-like10)is an important TF regulating trichome development and salt tolerance in *** we report that knockout of OsSPL10 reduces whereas its overexpression enhances rice resistance to blast ***10 positively regulates chitin-induced immune responses including reactive oxygen species(ROS)burst and callose *** show that OsSPL10 physically associates with OsJAmyb,an important TF involved in jasmonic acid(JA)signaling,and positively regulates its protein *** then prove that OsJAmyb positively regulates resistance to *** results reveal a molecular module consisting of OsSPL10 and OsJAmyb that positively regulates blast resistance.

关键词： Immunity Jasmonate Oryza sativa OsSPL10 Transcription factor

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