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genome-wide identification and analysis of the regulation wheat DnaJ family genes following wheat yellow mosaic virus infection

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Journal of Integrative Agriculture 2022年第1期21卷 153-169页

作者： LIU Ting-ting XU Miao-ze GAO Shi-qi ZHANG Yang HU Yang JIN Peng CAI Lin-na CHENG Ye CHEN Jian-ping YANG Jian ZHONG Kai-li State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province Institute of Plant VirologyNingbo UniversityNingbo 315211P.R.China Institutes of Biomedical Sciences Fudan UniversityShanghai 200032P.R.China Institute of Forest Health Zhejiang Academy of ForestryHangzhou 310021P.R.China

The co-chaperone DnaJ plays an important role in protein folding and regulation of various physiological activities, and participates in several pathological processes. DnaJ has been extensively studied in many species including humans,drosophila, mushrooms, tomatoes, and Arabidopsis. However, few studies have examined the role of DnaJ in wheat(Triticum aestivum), and the interaction mechanism between TaDnaJs and plant viruses. Here, we identified 236 TaDnaJs and performed a comprehensive genome-wide analysis of conserved domains, gene structure and protein motifs, chromosomal positions and duplication relationships, and cis-acting elements. We grouped these Ta Dna Js according to their domains, and randomly selected six genes from the groups for tissue-specific analysis, and expression profiles analysis under hormone stress, and 17 genes for plant virus infection stress. In qRT-PCR, we found that among the 17 TaDnaJ genes tested, 16 genes were up-regulated after wheat yellow mosaic virus(WYMV) infection, indicating that the TaDnaJ family is involved in plant defense response. Subsequent yeast two-hybrid assays verified the WYMV NIa, NIb and 7 KD proteins interacted with TaDJC(TraesCS7 A02 G506000), which had the most significant changes in gene expression levels after WYMV infection.Insights into the molecular mechanisms of Ta Dna J-mediated stress tolerance and sensitivity could inform different strategies designed to improve crop resistance to abiotic and biotic stress. This study provides a basis for future investigation of the TaDnaJ family and plant defense mechanisms.

关键词： TaDnaJ WYMV wheat genome-wide expression hormone biotic stress HSP40

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genome-wide identification and transcriptional profiling analysis of PIN/PILS auxin transporter gene families in Panax ginseng

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Chinese Herbal Medicines 2022年第1期14卷 48-57页

作者： Shuiming Xiao Yang Chu Yanjun Chen Qinghe Zhao Baosheng Liao Jingjing Zhang Yuan Gao Jiang Xu Shilin Chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China College of Pharmacy Hubei University of Chinese MedicineWuhan 430065China Institute of Medicinal Plant Development Chinese Academy of Medical SciencesBeijing 100193China

Objective:Plant hormones act as chemical messengers in the regulation of plant development and metabolism.The production of ginsenosides in Panax hybrid is promoted by auxins that are transported and accumulated by PIN-FORMED(PIN)and PIN-LIKES(PILS)auxin transporters.However,genome-wide studies of PIN/PILS of ginseng are still scarce.In current study,identification and transcriptional profiling of PIN/PILS gene families,as well as their potential relationship with ginsenoside biosynthesis in Panax ginseng were investigated.Methods:PIN/PILS genes in P.ginseng was identified via in silico genome-wide analysis,followed by phylogenetic relationships,gene structure,and protein profiles investigation.Moreover,previously reported RNA-sequence data from various tissues and roots after infection were utilized for PIN/PILS genes expression pattern analysis.The Pearson’s correlation analysis of specific PIN/PILS genes expression level and main ginsenoside contents were taken to reveal the potential relationship between auxin transports and ginsenoside biosynthesis in P.ginseng.Results:A genome-wide search of P.ginseng genome for homologous auxin transporter genes identified a total of 17 PIN and 11 PILS genes.Sequence alignment,putative motif organization,and sub-cellular localization indicated redundant and complementary biological functions of these PIN/PILS genes.Most PIN/PILS genes were differentially expressed in a tissue-specific manner,and showed significant correlations with ginsenoside content correspondingly.Eight auxin transporter genes,including both PIN and PILS subfamily members,were positively correlated with ginsenoside content(cor>0.60;P-value<0.05).The expression levels of eleven auxin transporter genes were increased dramatically in the early stage(0–0.5 DPI)after Cylindrocarpon destructans infection,accompanied with various overall expression patterns,implying the dynamic auxin transport in response to biotic stress.Conclusion:Based on the results,we speculate that the accumulation or depletion in tempor

关键词： auxin genome-wide ginsenoside PILS PIN transcriptome

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genome-wide identification and analysis of cytokinin dehydrogenase/oxidase(CKX) family genes in Brassica oleracea L.reveals their involvement in response to Plasmodiophora brassicae infections

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Horticultural Plant Journal 2022年第1期8卷 68-80页

作者： Mingzhao Zhu Yong Wang Shujin Lu Limei Yang Mu Zhuang Yangyong Zhang Honghao Lv Zhiyuan Fang Xilin Hou State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops Ministry of AgricultureInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Cytokinins are a class of phytohormones that promote cell division and differentiation and are thought to affect plant immunity to multiple pathogens.However,a comprehensive analysis of cytokinin dehydrogenase/oxidase(CKX)family genes in cabbage has not been reported.In this study,a total of 36 CKX genes were identified using a genome-wide search method.Phylogenetic analysis classified these genes into three groups.They were distributed unevenly across nine chromosomes in B.oleracea,and 15 of them did not contain any introns.The results of colinearity analysis showed that 36 CKX gene in Arabidopsis was present in several copies in the Brassica oleracea genome.An analysis of cisacting elements indicated that all genes possessed at least one stress or hormone responsive cis-acting element.A heatmap of CKX gene expression showed the patterns of expression of these genes in various tissues and organs.Three genes(Bol028363,Bol031036 and Bol018140)were relatively highly expressed in all of the investigated tissues under normal conditions,showing the expression profile of housekeeping genes.Generally,the expression patterns of CKX genes in Jingfeng 1 and Xiangan 336 were quite different under the same treatment.Notably,three genes(Bol020547,Bol028392 and Bol045724)were significantly down-regulated and up-regulated in the susceptible and resistant material,respectively,after inoculation,which may indicate their crucial roles in resistance to clubroot disease.The results provide insights for better understanding the roles of CKX genes in the B.oleracea–P.brassicae interaction.

关键词： Brassica oleracea genome-wide Cytokinin dehydrogenase/oxidase(CKX)genes Clubroot

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genome-wide characterization of graft-transmissible mRNA-coding P450 genes of cucumber(Cucumis sativus L.)

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Horticultural Plant Journal 2023年第2期9卷 250-260页

作者： Tao Wang Xiaohong Lu Chenggang Xiang Xiaojun Li Wenqian Liu QingWang Zixi Liu Lihong Gao Wenna Zhang Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops China Agricultural UniversityBeijing100193 China College of Life Science and Technology HongHe UniversityMengziYunnan661199 China

P450(cytochrome P450)is a supergene family,which is involved in various metabolic pathways in plants.Based on previous study,we found some of cucumber P450 mRNAs were systemic mobile in cucumber/pumpkin grafts.However,the reason that why P450 mRNAs were endorsed as signaling,and what specific motif(s)did they harbored is not clear yet.Here,we first identified 221 CsaP450 genes in cucumber genomewide level.Combining with graft-transmissiblemRNAs datasets in cucumber,we elucidated 15mobile-CsaP450-coding genes,of which 5 and 10 belonged to A-type and non-A type respectively.Compared with Arabidopsis and pumpkin(Cucubit moschata)graft-induced-transmissible P450 mRNAs,a phylogenetic treewas constructed and divided into eight clans by usingmultiple-sequence alignment.Gene ontology(GO)enrichment and Kyoto Encyclopedia of Genes and genomes(KEGG)annotations indicated that the expression patterns of the mobile-mRNA-coding CsaP450 genes in different tissues of cucumber was specifically enriched in oxidoreductase activity and secondary metabolic pathways.The structures and motifs of these 15 mobile-mRNA-coding CsaP450 genes and their types of regulatory elements told that the proportion of CU-rich motifs was higher than nonmobile-mRNA-coding CsaP450 genes.The integrated analysis of mobility direction and mRNA abundance of 15 mobilemRNA-coding CsaP450 genes allowed to conclude that there was rarely relationship between them.The study provided a new insight into the relationship between the motifs and functional characterization of mobile-mRNA-coding P450 genes of cucumber in genome-wide levels.

关键词： Cucumis sativus genome-wide Cytochrome P450 mRNA mobility Phylogeny CU-rich motif

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genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum

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Journal of Integrative Agriculture 2022年第11期21卷 3230-3244页

作者： LIU Lei WANG Heng-bo LI Yi-han CHEN Shu-qi WU Ming-xing DOU Mei-jie QI Yi-yin FANG Jing-ping ZHANG Ji-sen Center for Genomics and Biotechnology Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of GeneticsFujian Agriculture and Forestry UniversityFuzhouFujian 350002P.R.China State Key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources&Guangxi Key Lab for Sugarcane Biology Guangxi UniversityNanning 530004P.R.China College of Life Sciences Fujian Normal UniversityFuzhou 350007P.R.China

Sugarcane has a large,complex,polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection.The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes.However,these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane genomes.In this present study,744305and 361638 candidate SSRs were identified from the genomes of S.officinarum and S.spontaneum,respectively.We verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum,including S.spontaneum,S.officinarum,S.robustum,and modern sugarcane hybrid.The results showed that 660 SSR markers displayed interspecific polymorphisms among these accessions.Furthermore,100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions.A total of 320 alleles were generated using 100 polymorphic primers,with each marker ranging from two to seven alleles.The genetic diversity analysis revealed that these accessions were distributed in four main groups,including group I(14 S.spontaneum accessions),group II(two S.officinarum accessions),group III(18 modern sugarcane hybrid accessions),and group IV(five S.robustum accessions).Experimental verification supported the reliability of the SSR markers based on genome-wide predictions.The development of a large number of SSR markers based on wet experiments is valuable for genetic studies,including genetic linkage maps,comparative genome analysis,genome-wide association studies,and marker-assisted selection in Saccharum.

关键词： Saccharum genome-wide simple repeat sequences(SSR) microsatellite molecular markers

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A genome-wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids

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Molecular Plant 2008年第5期1卷 720-731页

作者： Hui-Yong Zhang Hang He Liang-Bi Chen Lei Li Man-Zhong Liang Xiang-Feng Wang Xi-Gang Liu Guang-Ming He Run-Sheng Chen Li-Geng Ma Xing Wang Deng National Institute of Biological Sciences Zhongguancun Life Science Park Beijing 102206 China Institute of Biophysics Chinese Academy of Sciences. 15 Oatun Road Beiiing 100101 China Department of Botany College of Life Sciences Hunan Normal University Changsha 410081 China Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology College of Life Sciences Peking University Beijing 100871 China Department of Molecular Cellular and Developmental Biology Yale University New Haven Connecticut 06520 USA

Heterosis, or hybrid vigor, refers to the phenomenon in which hybrid progeny of two inbred varieties exhibits enhanced growth or agronomic performance. Although a century-long history of research has generated several hypotheses regarding the genetic basis of heterosis, the molecular mechanisms underlying heterosis and heterotic gene expression remain elusive. Here, we report a genome-wide gene expression analysis of two heterotic crosses in rice, taking advantage of its fully sequenced genomes. Approximately 7-9% of the genes were differentially expressed in the seedling shoots from two sets of heterotic crosses, including many transcription factor genes, and exhibited multiple modes of gene action. Comparison of the putative promoter regions of the ortholog genes between inbred parents revealed extensive sequence variation, particularly small insertions/deletions （INDELs）, many of which result in the formation/disruption of putative cis-regulatory elements. Together, these results suggest that a combinatorial interplay between expression of transcription factors and polymorphic promoter cis-regulatory elements in the hybrids is one plausible molecular mechanism underlying heterotic gene action and thus heterosis in rice.

关键词： genome-wide INDEL

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genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings

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Journal of Integrative Plant Biology 2019年第6期61卷 658-674页

作者： Xi Luo Bingcai Wang Shan Gao Fei Zhang William Terzaghi Mingqiu Dai National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China College of Plant Science Tarim UniversityAlaer 843300China Department of Biology Wilkes UniversityWilkes-BarrePennsylvania 18766USA

Excess salinity is a natural stress that causes crop yield losses worldwide. The genetic bases of maize salt tolerance remain largely unknown. Here we investigated the survival rates of 445 maize natural accessions after salt treatments. A skewed distribution of the salttolerant phenotypes was observed in this population.genome-wide association studies(GWAS) revealed 57 loci significantly associated with salt tolerance. Forty-nine candidate genes were detected from these loci. About10% of these genes were co-localized with loci from QTL mapping. Forty four percent of the candidate genes were involved in stress responses, ABA signaling,stomata division, DNA binding/transcription regulation and auxin signaling, suggesting that they are key genetic mechanisms of maize salt tolerance. Transgenic studies showed that two genes, the salt-tolerance-associatedgene 4(SAG4, GRMZM2 G077295) and SAG6(GRMZM2 G106056), which encode a protein transport protein and the double-strand break repair protein MRE11,respectively, had positive roles in plant salt tolerance,and their salt-tolerant haplotypes were revealed. The genes we identified in this study provide a list of candidate targets for further study of maize salt tolerance, and of genetic markers and materials that may be used for breeding salt-tolerance in maize.

关键词： genome-wide association dissects tolerance

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genome-wide analysis identified 17 new loci influencing intraocular pressure in Chinese population

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Science China(Life Sciences) 2019年第2期62卷 153-164页

作者： Lulin Huang Yuhong Chen Ying Lin Pancy O.S.Tam Yilian Cheng Yi Shi Bo Gong Fang Lu Jialiang Yang Haixin Wang Yi Yin Yong Cao Dan Jiang Ling Zhong Bai Xue Jing Wang Fang Hao Dean-Yao Lee Chi-Pui Pang Xinghuai Sun Zhenglin Yang The Key Laboratory for Human Disease Gene Study of Sichuan Province Sichuan Provincial People's Hospital School of MedicineUniversity of Electronic Science and Technology of China Institute of Chengdu Biology Sichuan Translational Medicine Hospital Chinese Academy of Sciences Department of Ophthalmology Visual Science Eye and ENT Hospital Shanghai Medical School Fudan University Department of Ophthalmology and Visual Sciences The Chinese University of Hong Kong Department of Ophthalmology Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital

Intraocular pressure(IOP) is a major risk factor for glaucoma. Genetic determinants of intraocular pressure can provide critical insights into the genetic architecture of glaucoma and, as a result, open new avenues for therapeutic intervention. We performed a genome-wide association study and replication analysis of 8,552 Chinese participants. In the genome-wide association study, we identified 51 loci that surpassed the significance of Pgenome-wide loci that surpassed the genome-wide significance of P<5×10^(-8), including 4 previously reported loci: rs145063132(7 p21.2, ETV1/DGKB), rs548030386(7 q31.2, ST7 near CAV1/CAV2), rs7047871(9 p24.2, GLIS3), and rs2472494(9 q31.1, ABCA1/SLC44 A1). Of the 17 newly identified loci, five were reported to have ocular related phenotypes: PTCH2(rs7525308 in 1 p34.1), LRIF1/DRAM2(rs1282146 in 1 p13.3), COLEC11(rs201143466 in 2 p25.3),SPTBN1(rs4514918 in 2 p16.2), and CRK(rs11078446 in 17 p13.3). The genetic loci identified in this study not only increase our understanding of the genes involved in intraocular pressure but also provide important genetic markers to improve future genetic screening and drug discovery for intraocular pressure disorders.

关键词： intraocular pressure glaucoma genome-wide association study

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genome-wide analysis of odorant-binding proteins and chemosensory proteins in the sweet potato whitefly, Bemisia tabaci

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Insect Science 2019年第4期26卷 620-634页

作者： Yang Zeng Yu-Ting Yang Qing-Jun Wu Shao-Li Wang Wen Xie You-Jun Zhang Department of Plant Protection Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences Beijing China Department of Agriculture of Yangtze University Jingzhou Hubei Province China

Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) of insects are thought to play roles in olfactory recognition affecting host choice, copulation, reproduction and other behaviors. Previous descriptions of OBPs and CSPs in the whitefly Bemisia tabaci often provided no or incomplete genetic information. In this study, we present a genome-wide and transcriptome-wide investigation of the OBPs and CSPs in B. tabaci MEAMl (Middle East-Asia Minorl species). Eight OBP and 19 CSP genes were identified that covered all previous sequences. Phylogenetic analyses showed that the CSP genes had a lineage-specific expansion (BtabBCSP人 BtabBCSP3, BtabBCSPl3, BtabBCSPl 7, BtabBCSP18 and BtabBCSP 19). Expression profiling of OBPs and CSPs by transcriptome sequencing and quantitative real-time polymerase chain reaction (qPCR) revealed that expression patterns differed among developmental stages of B. tabaci MEAM 1. Five OBP genes and 11 CSP genes significantly differed between males and females;four of the 19 CSP genes were highly expressed in adults, while two were highly expressed in nymphs. The expression profiles of the OBP and CSP genes in different tissues of B. tabaci MEAM1 adults were analyzed by qPCR. Four OBP genes found in B. tabaci MEAM 1 were highly expressed in the head. Conversely, only two CSPs were enriched in the head, while the other six CSPs were specifically expressed in other tissues. Our results provide a foundation for future research on OBPs and CSPs in B. tabaci.

关键词： Bemisia tabaci CSPs expression patterns genome-wide identification OBPs phylogenetic

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genome-wide detection of additional fetal chromosomal abnormalities by cell-free DNA testing of 15,626 consecutive pregnant women

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Science China(Life Sciences) 2019年第2期62卷 215-224页

作者： Hong Yao Ya Gao Jia Zhao Rong Zhang Huixin Xu Huamei Hu Yanmei Luo Yuying Yuan Meili Fu Hongyun Zhang Hui Jiang Wei Wang Huanming Yang Jian Wang Zhiqing Liang Fang Chen Department of Gynecology & Obstetrics Southwest Hospital the Third Military Medical University BGI-Shenzhen China National GeneBank BGI-Shenzhen Birth Defect Screening Project Lab BGI-Shenzhen Clinical laboratories of BGI Health BGI-Shenzhen James D.Watson Institute of genome Sciences Laboratory of Genomics and Molecular Biomedicine Department of Biology University of Copenhagen

Cell-free DNA(cfDNA) testing for common fetal trisomies(T21, T18, T13) is highly effective. However, the usefulness of cfDNA testing in detecting other chromosomal abnormalities is unclear. We evaluated the performance of cfDNA testing for genome-wide abnormalities, and analyzed the incremental yield by reporting extra abnormalities. We performed genome-wide cfDNA testing in 15,626 consecutive pregnancies prospectively enrolled in this study. cfDNA testing results were reported and counseling was given depending on the presence of extra chromosomal abnormalities. cfDNA testing identified 190 cases(1.2%)of chromosomal abnormalities including 100 common trisomies and 90 additional abnormalities. By expanding the cfDNA reporting range to genome-wide abnormalities, the false positive rate increased to 0.39%(Pgenome-wide cfDNA testing significantly increased the diagnostic yield by detecting extra abnormalities, especially those without diagnostic indications. genome-wide cfDNA testing has fewer false positive and false negative results compared with biochemical screening.

关键词： cell-free DNA genome-wide chromosomal abnormalities sensitivity specificity PPV

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