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

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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Monogenic deficiency in murine intestinal Cdc42 leads to mucosal inflammation that induces crypt dysplasia

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Genes & Diseases 2024年第1期11卷 413-429页

作者： Dongsheng Zhang Wenjuan Tang Haitao Niu William Tse Hai-Bin Ruan Helmut Dolznig Thomas Knosel Friedrich Karl-Heinz Madeleine Themanns Jiang Wang Mingquan Song Lee Denson Lukas Kenner Richard Moriggl Yi Zheng Xiaonan Han Division of Hematology and Oncology Division of Cancer BiologyDepartment of MedicineMetroHealth Medical Center(MHMC)Case Western Reserve University(CWRU)School of MedicineClevelandOH 44109USA Cancer Genomics and Epigenomics Program Case Comprehensive Cancer CenterCase Western Reserve University(CWRU)ClevelandOH 44106USA Division of Gastroenterology Hepatology and NutritionCincinnati Children’s Hospital Medical Center(CCHMC)CincinnatiOH 45229USA Children’s Hospital of Fudan University Shanghai 201102China School of Medicine Jinan UniversityGuangzhouGuangdong 510632China Laboratory animal Science(ILAS) Chinese Academy of Medical Science(CAMS)and Peking Union Medical College(PUMC)Beijing 100006China department of Integrative Biology and Physiology University of Minnesota Medical SchoolMinneapolisMI 55455USA Institute of Medical Genetics Medical University of ViennaVienna 1040Austria Institute of Pathology Ludwig-Maximilians-University MunichMunich 80539Germany Institute of Biochemistry II University Hospital JenaJena 07743Germany Laboratory animal Pathology University of Veterinary Medicine ViennaVienna 1210Austria department of Pathology University of CincinnatiCincinnatiOH 45221USA department of Gastroenterology The Affiliated Hospital of Qingdao UniversityQingdaoShandong 266005China department of Pathology Medical University of ViennaVienna 1040Austria Ludwig Boltzmann Institute for Cancer Research Vienna 1090Austria Medical University of Vienna Vienna 1040Austria Institute of animal breeding and Genetics University of Veterinary Medicine ViennaVienna 1210Austria Division of Experimental Hematology CCHMCCincinnatiOH 45229USA

CDC42 controls intestinal epithelial(IEC)stem cell(IESC)*** aberrant CDC42 initiates intestinal inflammation or neoplasia is *** utilized models of inflam-matory bowel diseases(IBD),colorectal cancer,aging,and IESC injury to determine the loss of intestinal Cdc42 upon inflammation and *** specimens were collected to determine the levels of CDC42 in IBD or colorectal ***42 floxed mice were crossed with Villin-Cre,Villin-CreERT2 and/or Lgr5-eGFP-IRES-CreERT2,or Bmi1-CreERT2 mice to generate Cdc42 deficient ***,colitis,aging,and intestinal organoid were used to evaluate CDC42 upon mucosal inflammation,IESC/progenitor regenerative capacity,and IEC *** studies revealed that increased CDC42 in colorectal cancer correlated with lower survival;in contrast,lower levels of CDC42 were found in the inflamed IBD *** Cdc42 depletion significantly reduced Lgr5+IEsCs,increased progenitors'hyperplasia,and induced mucosal inflammation,which led to crypt *** Cdc42 depletion markedly enhanced irra-diation-or chemical-induced *** or inhibition of Cdc42 reduced colonic Lgr5+IESC *** conclusion,depletion of Cdc42 reduces the IESC regeneration and IEC repair,leading to prolonged mucosal *** monogenic loss of Cdc42 in-duces mucosal inflammation,which could result in intestinal neoplasia in the context of aging.

关键词： Cell divisioncycle 42(CDC42) Colitis Colorectal cancer(CRC) Inflammatory bowel diseases(IBD) Intestinal epithelial cell(IEC) Intestinal epithelial stem cell(IESC) Irradiation

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The liver transcriptome of two full-sibling Songliao black pigs with extreme differences in backfat thickness

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Journal of animal Science and Biotechnology 2015年第1期6卷 13-21页

作者： Kai Xing Feng Zhu Liwei Zhai Huijie Liu Zhijun Wang Zhuocheng Hou Chuduan Wang National Engineering Laboratory for animal breeding and MOA Key Laboratory of animal Genetics and breeding Department of Animal Genetics and BreedingChina Agricultural University Tianjin Ninghe Primary Pig breeding Farm

Background： Fatness traits in animals are important for their growth, meat quality, reproductive performance, and immunity. The liver is the principal organ of the regulation of lipid metabolism, and this study used massive parallelized high-throughput sequencing technologies to determine the porcine liver tissue transcriptome architecture of two full-sibling Songliao black pigs harboring extremely different phenotypes of backfat thickness. Results： The total number of reads produced for each sample was in the region of 53 million, and 8,226 novel transcripts were detected. Approximately 92 genes were differentially regulated in the liver tissue, while 31 spliced transcripts and 33 primary transcripts showed significantly differential expression between pigs with higher and lower backfat thickness. Genes that were differentially expressed were involved in the metabolism of various substances, smal molecule biochemistry, and molecular transport. Conclusions： Genes involved in the regulation of iipids could play an important role in lipid and fatty acid metabolism in the liver. These results could help us understand how liver metabolism affects the backfat thickness of pigs.

关键词： Backfat thickness Liver Pig RNA-Seq

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Genome-wide identification and expression profiling of photosystem II(PsbX)gene family in upland cotton(Gossypium hirsutum L.)

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Journal of Cotton Research 2024年第1期7卷 1-14页

作者： RAZA Irum PARVEEN Abida AHMAD Adeel HU Daowu PAN Zhaoe ALI Imran DU Xiongming Institute of Cotton Research Chinese Academy of Agricultural SciencesNational Key Laboratory of Cotton Bio-Breeding and Integrated UtilizationAnyangHenan 455000China department of Biotechnology and Genetic Engineering Kohat University of Science and TechnologyKohatPakistan department of Botany Kohat University of Science and TechnologyKohatPakistan.

Background Photosystem II(PSII)constitutes an intricate assembly of protein pigments,featuring extrinsic and intrinsic polypeptides within the photosynthetic *** low-molecular-weight transmembrane protein PsbX has been identified in PSII,which is associated with the oxygen-evolving *** expression of PsbX gene protein is regulated by ***’s central role involves the regulation of PSII,facilitating the binding of quinone molecules to the Qb(PsbA)site,and it additionally plays a crucial role in optimizing the efficiency of *** these insights,a comprehensive understanding of the PsbX gene’s functions has remained *** In this study,we identified ten PsbX genes in Gossypium hirsutum *** phylogenetic analysis results showed that 40 genes from nine species were classified into one *** resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium ***,the ortholo-gous/paralogous,Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence,which resulted in the whole genome and segmental *** expression patterns of GhPsbX genes exhibited variations across specific tissues,as indicated by the ***,the expression of GhPsbX genes could potentially be regulated in response to salt,intense light,and drought ***,GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic *** We examined the structure and function of PsbX gene family very first by using comparative genom-ics and systems biology approaches in *** seems that PsbX gene family plays a vital role during the growth and development of cotton under stress ***,the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plan

关键词： Photosystem Phylogenetic Synteny RNA seq Gene expression Orthologous

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Genetics of biochemical attributes regulating morpho-physiology of upland cotton under high temperature conditions

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Journal of Cotton Research 2024年第1期7卷 29-44页

作者： MAJEED Sajid CHAUDHARY Muhammad Tanees MUBARIK Muhammad Salman RANA Iqrar Ahmad SHABAN Muhammad TAN Daniel KY JIA Yinhua DU Xiongming HINZE Lori AZHAR Muhammad Tehseen Federal Seed Certification and Registration department Ministry of National Food Security and ResearchIslamabad 44090Pakistan Horticultural Research Institute National Agricultural Research CentreIslamabad 44000Pakistan department of Biotechnology University of NarowalNarowal 51600Pakistan Centre of Agricultural Biochemistry and Biotechnology University of AgricultureFaisalabad 38400Pakistan department of Plant breeding and Genetics University of Agriculture FaisalabadSub-Campus BurewalaVehariPakistan Faculty of Science School of Life and Environ-mental SciencesPlant Breeding InstituteSydney Institute of AgricultureThe University of SydneySydneyNSW 2006Australia State Key Laboratory of Cotton Biology Institute of Cotton Research of Chinese Academy of Agri-cultural ScienceAnyang 455000China Agricultural Research Service USDASouthern Plains Agricultural Research CentreCollege StationTX 77845USA department of Plant breeding and Genetics University of AgricultureFaisal-abad 38400Pakistan School of Agriculture Sciences Zhengzhou UniversityZhengzhou 450000China.

Background Cotton is a strategically important fibre crop for global textile *** profoundly impacts several countries’industrial and agricultural *** cotton production is continuously threatened by the unpre-dictable changes in climate,specifically high *** heat-tolerant,high-yielding cotton cultivars with wide adaptability to be grown in the regions with rising temperatures is one of the primary objectives of modern cotton breeding ***,the main objective of the current study is to figure out the effective breed-ing approach to imparting heat tolerance as well as the judicious utilization of commercially significant and stress-tolerant attributes in cotton ***,the two most notable heat-susceptible(FH-115 and NIAB Kiran)and tolerant(IUB-13 and GH-Mubarak)cotton cultivars were spotted to develop filial and backcross populations to accom-plish the preceding study *** heat tolerant cultivars were screened on the basis of various morphological(seed cotton yield per plant,ginning turnout percentage),physiological(pollen viability,cell membrane thermostabil-ity)and biochemical(peroxidase activity,proline content,hydrogen peroxide content)*** The results clearly exhibited that heat stress consequently had a detrimental impact on every studied plant trait,as revealed by the ability of crossing and their backcross populations to tolerate high ***,when considering overall yield,biochemical,and physiological traits,the IUB-13×FH-115 cross went over particularly well at both normal and high temperature ***,overall seed cotton yield per plant exhibited a posi-tive correlation with both pollen viability and antioxidant levels(POD activity and proline content).Conclusions Selection from segregation population and criteria involving pollen viability and antioxidant levels concluded to be an effective strategy for the screening of heat-tolerant cotton g

关键词： Accessions Biochemical breeding Cotton Generation mean analysis Heat stress

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Implementation of the Acclimatization Process for Ginger Plantlets (Zingiber officinale Roscoe)

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Open Journal of Applied Sciences 2024年第8期14卷 2236-2248页

作者： Florentin Danton Kango Gilles Habib Todjro Cacaï Serge Sètondji Houédjissin Jerome Anani Hounguè Jaures Riwan Uriel Kouke David Dègbé Allotchémè Corneille Ahanhanzo Central Laboratory of Plant Biotechnology and Plant breeding Department of Genetic and Biotechnology Faculty of Science and Technology University of Abomey-Calavi Cotonou Benin

Ginger (Zingiber officinale Roscoe) is an important culinary and medicinal spice but is rarely cultivated due to the unavailability of seeds. Given the difficulties in adapting to plantlets produced in natural environments, it is important to analyze the survival conditions of ginger plantlets. For this reason, we varied the incubation temperature and humidity as well as the substrate during the weaning phase. Then, we varied the nutrients contained in the watering solution during the hardening phase. The statistical analysis showed that physical factors and substrates significantly influenced (p < 0.0001) plantlet survival. Nutrient solutions significantly influenced the phylogenesis, rhizogenesis, and height growth of the plantlets. The suitable physical factors for good development of plantlets are a temperature of 26.54˚C and a humidity of 96.16%. The 1C2T2TC substrate (1 Compost + 2 Soil + 2 Coconut Peat) had a significant survival rate of approximately 92.5%. During hardening, the Plantzym solution promoted good growth in terms of plantlet height (0.6 cm) and good development of roots (30 roots) and leaves (03 leaves). This work will make it possible to develop a technical seed production sheet for better development of ginger cultivation in Benin.

关键词： Acclimatization Zingiber officinale Weaning Nutrient Solutions Substrates

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The trxG protein ULT1 regulates Arabidopsis organ size by interacting with TCP14/15 to antagonize the LIM peptidase DA1 for H3K4me3 on target genes

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Plant Communications 2024年第4期5卷 255-274页

作者： Fan Xu Huixue Dong Weijun Guo Liang Le Yexing Jing Jennifer C.Fletcher Jiaqiang Sun Li Pu Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory of Crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China department of Plant and Microbial Biology University of CaliforniaBerkeleyBerkeleyCA 94720USA Plant Gene Expression Center United States Department of Agriculture-Agricultural Research ServiceAlbanyCA 94710USA These authors contributed equally to this article

Plant organ size is an important agronomic trait that makes a significant contribution to plant *** its central importance,the genetic and molecular mechanisms underlying organ size control remain to be fully ***,we report that the trithorax group protein ULTRAPETALA1(ULT1)interacts with the TEOSINTE BRANCHED1/CYCLOIDEA/PCF14/15(TCP14/15)transcription factors by antagonizing the LIN-11,ISL-1,and MEC-3(LIM)peptidase DA1,thereby regulating organ size in *** of ULT1 function significantly increases rosette leaf,petal,silique,and seed size,whereas overexpression of ULT1 results in reduced organ ***1 associates with TCP14 and TCP15 to co-regulate cell size by affecting cellular *** analysis revealed that ULT1 and TCP14/15 regulate common target genes involved in endoreduplication and leaf ***1 can be recruited by TCP14/15 to promote lysine 4 of histone H3 trimethylation at target genes,activating their expression to determinefinal cell ***,we found that ULT1 influences the interaction of DA1 and TCP14/15 and antagonizes the effect of DA1 on TCP14/15 ***,ourfindings reveal a novel epigenetic mechanism underlying the regulation of organ size in Arabidopsis.

关键词： ULT1 TCP DA1 organ size endoreduplication

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Identification and effective regulation of scarb1 gene involved in pigmentation change in autotetraploid Carassius auratus

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Zoological Research 2024年第2期45卷 381-397页

作者： Xi-Dan Xu Yue Zhou Chong-Qing Wang Xu Huang Kun Zhang Xiao-Wei Xu Li-Wen He Xin-Yue Zhang Xin-Zhu Fu Ming Ma Qin-Bo Qin Shao-Jun Liu State Key Laboratory of Developmental Biology of Freshwater Fish Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education MinistryCollege of Life SciencesHunan Normal UniversityChangshaHunan 410081China Nansha-South China Agricultural University Fishery Research Institute GuangzhouGuangdong 511458China Hunan Yuelu Mountain Science and Technology Co.Ltd.for Aquatic breeding ChangshaHunan 410081China College of Chemistry and Chemical Engineering Hunan Normal UniversityChangshaHunan 410081China

The autotetraploid Carassius auratus(4nRR,4n=200,RRRR)is derived from whole-genome duplication of Carassius auratus red var.(RCC,2n=100,RR).In the current study,we demonstrated that chromatophores and pigment changes directly caused the coloration and variation of 4nRR skin(red in RCC,brownish-yellow in4nRR).To further explore the molecular mechanisms underlying coloration formation and variation in 4nRR,we performed transcriptome profiling and molecular functional verification in RCC and *** revealed that scarb1,associated with carotenoid metabolism,underwent significant down-regulation in *** editing of this candidate pigment gene provided clear evidence of its significant role in RCC ***,we identified four divergent scarb1 homeologs in 4nRR:two original scarb1 homeologs from RCC and two duplicated ***,three of these homeologs possessed two highly conserved alleles,exhibiting biased and allelespecific expression in the ***,after precise editing of both the original and duplicated scarb1homeologs and/or alleles,4nRR individuals,whether singly or multiply mutated,displayed a transition from brownishyellow skin to a cyan-gray ***,the proportional areas of the cyan-gray regions displayed a gene-dose *** findings illustrate the subfunctionalization of duplicated scarb1,with all scarb1genes synergistically and equally contributing to the pigmentation of *** is the first report concerning the functional differentiation of duplicated homeologs in an autopolyploidfish,substantiallyenrichingour understanding of coloration formation and change within this group of organisms.

关键词： Autopolyploidization Coloration change scarb1 Functional differentiation Genetic changes

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Transcriptome responses to heat stress in hypothalamus of a meat-type chicken

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Journal of animal Science and Biotechnology 2015年第3期6卷 291-302页

作者： Hongyan Sun Runshen Jiang Shengyou Xu Zebin Zhang Guiyun Xu Jiangxia Zheng Lujiang Qu department of animal Genetics and breeding National Engineering Laboratory for Animal BreedingCollege of Animal Science and TechnologyChina Agricultural University College of animal Science and Technology Anhui Agricultural University

Background： Heat stress has resulted in great losses in poultry production. To address this issue, we systematically analyzed chicken hypothalamus transcriptome responses to thermal stress using a 44 k chicken Agilent microarray, Methods： Hypothalamus samples were collected from a control group reared at 25℃, a heat-stress group treated at 34℃ for 24 h, and a temperature-recovery group reared at 25℃ for 24 h following a heat-stress treatment. We compared the expression profiles between each pair of the three groups using microarray data. Results： A total of 1,967 probe sets were found to be differentially expressed in the three comparisons with P 〈 0.05 and a fold change （FC） higher than 1.5, and the genes were mainly involved in self-regulation and compensation required to maintain homeostasis. Consistent expression results were found for 11 selected genes by quantitative real-time PCR. Thirty-eight interesting differential expression genes were found from GO term annotation and those genes were related to meat quality, growth, and crucial enzymes. Using these genes for genetic network analysis, we obtained three genetic networks. Moreover, the transcripts of heat-shock protein, including Hsp 40 and Hsp 90, were significantly altered in response to thermal stress. Conclusions： This study provides a broader understanding of molecular mechanisms underlying stress response in chickens and discovery of novel genes that are regulated in a specific thermal-stress manner.

关键词： Chicken Heat shock protein Heat stress Hypothalamus Microarray Transcription

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Multi-genome evolutionary study of the ABC1 gene family and identification of the pleiotropic effects of OsABC1-13 in rice development

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The Crop Journal 2024年第4期12卷 1022-1030页

作者： Fuying Ma Mingyu Liu Peiwen Yan Shicong He Jian Hu Xinwei Zhang Fuan Niu Jinhao Cui Xinyu Yuan Xiaoyun Xin Liming Cao Jinshui Yang Ying Wang Xiaojin Luo State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology(Ministry of Education) School of Life SciencesFudan UniversityShanghai 200433China Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering Department of Ecology and Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200433China Institute of Crop breeding and Cultivation Shanghai Academy of Agricultural SciencesShanghai 200241China Ministry of Education Key Laboratory of Crop PhysiologyEcology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045JiangxiChina

In four rice genomes,85 ABC1-family genes were identified by comparative genomics,evolution,genetics,and ***,OsABC1-13,was shown by knockdown and knockout experiments to affect plant height,grain size,and photosynthet... 详细信息

关键词： Multi-genome analysis Activity of bc1 complex gene Photosynthesis Biomass Osabc1-13 Haplotype

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