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Combining QTL Mapping and Multi-Omics Identify Candidate Genes for Nutritional Quality Traits during Grain Filling Stage in Maize

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Phyton-International Journal of Experimental Botany 2024年第7期93卷 1441-1453页

作者： Pengcheng Li Tianze Zhu Yunyun Wang Shuangyi Yin Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Zefeng Yang Chenwu Xu Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhou225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou225009China

The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and ***,the genetic basis underlying these nutritional quality traits during grainﬁlling remains poorly *** this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages *** the traits exhibited considerable phenotypic *** the grain-ﬁlling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with signiﬁcant changes observed between 30 and 40 days after *** trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,*** QTLs were consistently detectable across different time *** integrating QTL analysis,glo-bal gene expression proﬁling,and comparative genomics,we identiﬁed 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,*** gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,MADS-box,bZIP,and MYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein *** study offers signiﬁcant insights into the genetic architecture of maize kernel nutritional quality and identiﬁes promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.

关键词： Maize protein oil starch QTL mapping candidate genes

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Enhancing sheepgrass through genomic exploration and targeted editing

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Science China(Life Sciences) 2024年第3期67卷 629-630页

作者： Miao Sun Sanwen Huang Yao Zhou Key Laboratory of plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China State Key Laboratory of Tropical Crop breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China State Key Laboratory of Tropical Crop breeding Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

The growth of grass industry is essential for meeting human needs for proteins and sustaining grassland ecosystems(Bengtsson et al., 2019). Leymus chinensis, also known as sheepgrass, is a perennial Triticeae forage r... 详细信息

关键词： grassland sheep ecosystems

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Auxin-brassinosteroid crosstalk:Regulating rice plant architecture and grain shape

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The Crop Journal 2024年第4期12卷 953-963页

作者： Meidi Wu Jing Zhou Qian Li Dunfan Quan Qingwen Wang Yong Gao Jiangsu Key Laboratory of Crop genomics and Molecular breeding/Key Laboratory of plant Functional genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology Yangzhou UniversityYangzhou 225009JiangsuChina Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of EducationYangzhou UniversityYangzhou 225009JiangsuChina

Rice(Oryza sativa)plant architecture and grain shape,which determine grain quality and yield,are modulatedby auxin and brassinosteroid via regulation of cell elongation and *** review the signaltransduction of these h... 详细信息

关键词： Auxin Brassinosteroid Auxin-brassinosteroid crosstalk plant architecture Grain shape

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WTV2.0:A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode

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Molecular plant 2024年第6期17卷 972-985页

作者： Honglun Yuan Yiding Jiangfang Zhenhuan Liu Rongxiu Su Qiao Li Chuanying Fang Sishu Huang Xianqing Liu Alisdair R.Fernie Jie Luo School of breeding and Multiplication(Sanya institute of breeding and Multiplication)and College of Tropical Agriculture and Forestry Hainan UniversitySanya Hainan 572025China Yazhouwan National Laboratory(YNL) Sanya Hainan 572025China Department of Molecular Physiology Max-Planck-Institute of Molecular Plant PhysiologyAm Mühlenberg 1Potsdam-Golm 14476Germany

Volatilomics is essential for understanding the biological functions and fragrance contributions of plant ***,the annotation coverage achieved using current untargeted and widely targeted volatomics(WTV)methods has been limited by low sensitivity and/or low acquisition ***,we introduce WTV 2.0,which enabled the construction of a high-coverage library containing 2111 plant volatiles,and report the development of a comprehensive selective ion monitoring(cSIM)acquisition method,including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method,that can acquire the smallest but sufficient number of ions for most plant volatiles,as well as the automatic qualitative and semi-quantitative analysis of cSIM ***,the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library,utilizing the obtained cSIM *** showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method,doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit,and led to the discovery of menthofuran as a novel flavor compound in passion *** 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.

关键词： volatilomics widely targeted methods GC-MS selective ion monitoring plant volatiles

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Low temperature-mediated repression and far-red light-mediated induction determine morning FLOWERING LOCUS T expression levels

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Journal of Integrative plant Biology 2024年第1期66卷 103-120页

作者： Hayeon Kim Hye Won Kang Dae Yeon Hwang Nayoung Lee Akane Kubota Takato Imaizumi Young Hun Song Department of Agricultural Biotechnology Seoul National UniversitySeoul 08826Korea Department of Biology Ajou UniversitySuwon 16499Korea plant genomics and breeding institute Seoul National UniversitySeoul 08826Korea Graduate School of Science and Technology Nara Institute of Science and TechnologyIkomaNara 630‐0192Japan Department of Biology University of WashingtonSeattleWA 98195USA institute of Agricultural Life Sciences Seoul National UniversitySeoul 08826Korea

In order to flower in the appropriate season,plants monitor light and temperature changes and alter downstream pathways that regulate florigen genes such as Arabidopsis(Arabidopsis thaliana)FLOWERING LOCUS T(FT).In Arabidopsis,FT messenger RNA levels peak in the morning and evening under natural long-day conditions(LDs).However,the regulatory mechanisms governing morning FT induction remain poorly *** morning FT peak is absent in typical laboratory LDs characterized by high red:far-red light(R:FR)ratios and constant ***,we demonstrate that ZEITLUPE(ZTL)interacts with the FT repressors TARGET OF EATs(TOEs),thereby repressing morning FT expression in natural *** LDs with simulated sunlight(R:FR=1.0)and daily temperature cycles,which are natural LD-mimicking environmental conditions,FT transcript levels in the ztl mutant were high specifically in the morning,a pattern that was mirrored in the toe1 toe2 double *** night-to-morning temperatures increased the inhibitory effect of ZTL on morning FT expression by increasing ZTL protein levels early in the ***-red light counteracted ZTL activity by decreasing its abundance(possibly via phytochrome A(phyA))while increasing GIGANTEA(GI)levels and negatively affecting the formation of the ZTL-GI complex in the ***,the phyA-mediated high-irradiance response and GI play pivotal roles in morning FT *** findings suggest that the delicate balance between low temperature-mediated ZTL activity and the far-red light-mediated functions of phyA and GI offers plants flexibility in fine-tuning their flowering time by controlling FT expression in the morning.

关键词： far-red light FLOWERING LOCUS T flowering time GIGANTEA low night-to-morning temperature natural long days phytochrome A red to far-red ratio ZEITLUPE

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Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs

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Journal of Integrative Agriculture 2024年第1期23卷 217-227页

作者： Mu Zeng Binhu Wang Lei Liu Yalan Yang Zhonglin Tang Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise breeding/Key Laboratory of Animal Molecular Design and Precise breeding of Guangdong Higher Education institutes School of Life Science and EngineeringFoshan UniversityFoshan 528231China Kunpeng institute of Modern Agriculture at Foshan Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesFoshan 528200China Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture/Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China

Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory *** the major indicators of growth performance,the backfat thickness(BFT),loin eye area(LEA),and days to 100 kg(D100)traits are commonly used to the genetics improvement in ***,the available genetic markers for these traits are *** uncover novel loci and candidate genes associated with growth performance,we collected the phenotypic information of BFT,LEA,and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K *** performed a genome-wide association study(GWAS)using 4 statistical models,including mixed linear models(MLM),fixed and random model circulating probability unification(FarmCPU),settlement of MLM under progressively exclusive relationships(SUPER),Bayesian-information and linkage-disequilibrium Iteratively nested keyway(Blink),and identified 5,3,and 6 high-confidence single nucleotide polymorphisms(SNPs)associated with BFT,LEA,and D100,*** annotation and quantitative trait locus(QTL)mapping analysis suggested that6 genes(SKAP2,SATB1,PDE7B,PPP1R16B,WNT3,and WNT9B)were potentially associated with growth performance in *** analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2(SKAP2)was higher in prenatal muscles than in postnatal muscles,and the expression of Phosphodiesterase 7B(PDE7B)continuously increased during the prenatal stages and gradually decreased after birth,implying their potential roles in prenatal skeletal muscle ***,this study provides new candidate loci and genes for the genetic improvement of pigs.

关键词： GWAS pig growth trait QTL mapping skeletal muscle

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Recognition of the inducible,secretory small protein OsSSP1 by the membrane receptor OsSSR1 and the co-receptor OsBAK1 confers rice resistance to the blast fungus

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Molecular plant 2024年第5期17卷 807-823页

作者： Tianfeng Zhao Shijie Ma Ziying Kong Haimiao Zhang Yi Wang Junzhe Wang Jiazong Liu Wanzhen Feng Tong Liu Chunyan Liu Suochen Liang Shilin Lu Xinyu Li Haipeng Zhao Chongchong Lu Muhammad Zunair Latif Ziyi Yin Yang Li Xinhua Ding State Key Laboratory of Crop Biology Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaian 271018ShandongChina College of breeding and Multiplication(Sanya institute of breeding and Multiplication) Hainan UniversitySanya 572024HainanChina

The plant apoplast,which serves as the frontline battleground for long-term host–pathogen interactions,harbors a wealth of disease resistance ***,the identification of the disease resistance proteins in the apoplast is relatively *** this study,we identified and characterized the rice secretory protein OsSSP1(Oryza sativa secretory small protein 1).OsSSP1 can be secreted into the plant apoplast,and either in vitro treatment of recombinant OsSSP1 or overexpression of OsSSP1 in rice could trigger plant immune *** expression of OsSSP1 is suppressed significantly during Magnaporthe oryzae infection in the susceptible rice variety Taibei 309,and OsSSP1-overexpressing lines all show strong resistance to *** the knockout and overexpression results,we found that OsSSP1 positively regulates plant immunity in response to fungal ***,the recognition and immune response triggered by OsSSP1 depend on an uncharacterized transmembrane OsSSR1(secretory small protein receptor 1)and the key co-receptor OsBAK1,since most of the induced immune response and resistance are lost in the absence of OsSSR1 or ***,the OsSSP1 protein is relatively stable and can still induce plant resistance after 1 week of storage in the open environment,and exogenous OsSSP1 treatment for a 2-week period did not affect rice ***,our study reveals that OsSSP1 can be secreted into the apoplast and percepted by OsSSR1 and OsBAK1 during fungal infection,thereby triggering the immune response to enhance plant resistance to *** findings provide novel resources and potential strategies for crop breeding and disease control.

关键词： rice plant apoplast OsssP1 receptor plant resistance Magnaporthe oryzae

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Advances in DNA methylation and its role in cytoplasmic male sterility in higher plants

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Journal of Integrative Agriculture 2024年第1期23卷 1-19页

作者： Atiqur Rahman Hasan Sofiur Rahman Shakil Uddin Naima Sultana Shirin Akhter Ujjal Kumar Nath Shamsun Nahar Begum Mazadul Islam Afroz Naznin Nurul Amin Sharif Ahmed Akbar Hossain Department of Genetics and plant breeding Bangladesh Agricultural UniversityMymensingh 2202Bangladesh plant breeding Division Bangladesh Institute of Nuclear AgricultureMymensingh 2202Bangladesh Tuber Crop Research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Horticulture Research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Biotechnology Division Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh International Rice Research institute Bangladesh OfficeDhaka 1213Bangladesh Division of Soil Science Bangladesh Wheat and Maize Research InstituteDinajpur 5200Bangladesh

The impact of epigenetic modifications like DNA methylation on plant phenotypes has expanded the possibilities for crop *** methylation plays a part in the regulation of both the chromatin structure and gene expression,and the enzyme involved,DNA methyltransferase,executes the methylation process within the plant *** regulating crucial biological pathways,epigenetic changes actively contribute to the creation of the ***,epigenome editing may assist in overcoming some of the drawbacks of genome editing,which can have minor off-target consequences and merely facilitate the loss of a gene’s *** drawbacks include gene knockout,which can have such off-target *** review provides examples of several molecular characteristics of DNA methylation,as well as some plant physiological processes that are impacted by these epigenetic changes in the *** also discuss how DNA alterations might be used to improve crops and meet the demands of sustainable and environmentally-friendly farming.

关键词： DNA methylation epigenetics CMS male sterility chromatin architecture gene expression higher plants

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Versatile and efficient mammalian genome editing with Type I-C CRISPR System of Desulfovibrio vulgaris

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Science China Life Sciences 2024年

作者： Pan Li Dingcai Dong Fei Gao Yuyang Xie Honglin Huang Siwei Sun Zhao Ma Cheng He Jinsheng Lai Xuguang Du Sen Wu State Key Laboratory of Animal Biotech breeding College of Biological SciencesNational Engineering Laboratory for Animal BreedingFrontiers Science Center for Molecular Design BreedingChina Agricultural University College of Veterinary Medicine China Agricultural University Sanya institute of China Agricultural University State Key Laboratory of Maize Bio-breeding National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural University Frontiers Science Center for Molecular Design breeding China Agricultural University Center for Crop Functional genomics and Molecular breeding China Agricultural University

CRISPR-Cas tools for mammalian genome editing typically rely on single Cas9 or Cas12a *** type I CRISPR systems in Class I may offer greater specificity and versatility,they are not well-developed for genome ***,we present an alternative type I-C CRISPR system from Desulfovibrio vulgaris (Dvu) for efficient and precise genome editing in mammalian cells and *** optimized the Dvu type I-C editing complex to generate precise deletions at multiple loci in various cell lines and pig primary fibroblast cells using a paired PAM-in crRNA *** edited pig cells can serve as donors for generating transgenic cloned *** Dvu type I-C editor also enabled precise large fragment replacements with homology-directed ***,we adapted the Dvu-Cascade effector for cytosine and adenine base editing,developing Dvu-CBE and Dvu-ABE *** systems efficiently induced C-to-T and A-to-G substitutions in human genes without double-strand ***-target analysis confirmed the high specificity of the Dvu type I-C *** findings demonstrate the Dvu type I-C editor′s potential for diverse mammalian genome editing applications,including deletions,fragment replacement,and base editing,with high efficiency and specificity for biomedicine and agriculture.

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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang Guusje Bonnema Xiaowu Wang Aalt Dirk Jan van Dijk State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Sino-Dutch Joint Lab of Vegetable genomics Beijing 100081China Bioinformatics Group Wageningen University and Research6708 PB Wageningenthe Netherlands plant breeding Wageningen University and Research6708 PB Wageningenthe Netherlands Biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam1090 GE Amsterdamthe Netherlands

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains *** uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground *** expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription *** to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial *** on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial *** explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell *** results demonstrated the utility of our computational approach for predicting candidate genes in crop *** findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

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