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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 *** 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 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%(Pwide 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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genome-wide association study of vitamin E in sweet corn kernels

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The Crop Journal 2020年第2期8卷 341-350页

作者： Yingni Xiao Yongtao Yu Gaoke Li Lihua Xie Xinbo Guo Jiansheng Li Yuliang Li Jianguang Hu Crop Research Institute Guangdong Academy of Agricultural SciencesKey Laboratory of Crops Genetics and Improvement of Guangdong ProvinceGuangzhou 510640GuangdongChina School of Food Science and Engineering South China University of TechnologyGuangzhou 510641GuangdongChina National Maize Improvement Center of China Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Vitamin E,consisting of tocopherols and tocotrienols,serves as a lipid-soluble antioxidant in sweet corn kernels,providing nutrients to both plants and *** the key genes involved in the vitamin E biosynthesis pathway have been identified in plants,the genetic architecture of vitamin E content in sweet corn kernels remains largely *** the present study,an association panel of 204 inbred lines of sweet corn was *** compounds of vitamin E were quantified in sweet corn kernels at 28 days after pollination.A total of 119 loci for vitamin E were identified using a genome-wide association study based on genotyping by sequencing,and a genetic network of vitamin E was *** genes identified were involved mainly in RNA regulation and protein *** known gene ZmVTE4,encodingγ-tocopherol methyltransferase,was significantly associated with four traits(α-tocopherol,α-tocotrienol,theα/γ-tocopherol ratio,and theα/γ-tocotrienol ratio).The effects of two causative markers on ZmVTE4 were validated by haplotype ***,two elite cultivars(Yuetian 9 and Yuetian 22)with a 4.5-fold increase in the sum ofα-andγ-tocopherols were developed by marker-assisted selection,demonstrating the successful biofortification of sweet *** genes(DAHPS,ADT2,and cmu2)involved in chorismate and tyrosine synthesis were significantly associated with theα/γ-tocotrienol *** results shed light on the genetic architecture of vitamin E and may accelerate the nutritional improvement of sweet corn.

关键词： Sweet corn GBS genome-wide association study Vitamin E Marker-assisted selection

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genome-wide association study for starch content and constitution in sorghum(Sorghum bicolor(L.) Moench)

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Journal of Integrative Agriculture 2019年第11期18卷 2446-2456页

作者： CHEN Bing-ru WANG Chun-yu WANG Ping ZHU Zhen-xing XU Ning SHI Gui-shan YU Miao WANG Nai LI Ji-hong HOU Jia-ming LI Shu-jie ZHOU Yu-fei GAO Shi-jie LU Xiao-chun HUANG Rui-dong College of Agronomy Shenyang Agricultural UniversityShenyang 110866P.R.China Molecular Improvement of Agricultural Crops Lab Liaoning Academy of Agricultural SciencesShenyang 110161P.R.China Institute of Crop Germplasm Resources Jilin Academy of Agricultural SciencesGongzhuling 136100P.R.China

Starch is the most important component in endosperm of sorghum ***,two types of starch are present:amylose(AM)and amylopectin(AP).The levels of AM and AP contents play a significant role in the appearance,structure,and quality of sorghum grains and in marketing *** the present study,a panel of 634 sorghum(Sorghum bicolor(L.)Moench)accessions were evaluated for starch,AM,and AP contents of grain,which included a mini core collection of 242 accessions from the International Crops Research Institute for the Semi-Arid Tropics(ICRISAT)in India,and 252 landraces and 140 cultivars from *** average starch content was 67.64%and the average AM and AP contents were 20.19 and 79.81%,*** developed a total of 260000 high-confidence single nucleotide polymorphism(SNP)markers in the panel of 634 accessions of *** using specific locus amplified fragment sequencing(SLAF-seq).We performed genome-wide association studies(GWAS)of starch,AM,and AM/AP of grain and SNP markers based on a mixed linear model(MLM).In total,70 significant association signals were detected for starch,AM,and AM/AP ratio of grain with P<4.452×10^-7,of which 10 SNPs were identified with significant starch,51 SNPs were associated with AM,and nine SNPs were associated with the AM/AP *** Gene Ontology(GO)analysis identified 12 candidate genes at five QTLs associated with starch metabolism within the 200-kb intervals,located on chromosomes 1,5,6,and *** these genes,Sobic.006G036500.1 encodes peptidyl-prolyl cis-trans-isomerase CYP38 responsible for hexose monophosphate shunt(HMS)and Sobic.009G071800 encodes 6-phospho-fructokinase(PFK),which is involved in the embden-meyerhof pathway(EMP).Kompetitive allele specific PCR(KASP)markers were developed to validate the GWAS *** C allele is correlated with a high starch content,while the T allele is linked with a low level of starch content,and provides reliable haplotypes for MAS in sorghum quality improvement.

关键词： sorghum genome-wide association mapping (GWAS) starch content amylose (AM) candidate genes KASP

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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 *** on previous study,we found some of cucumber P450 mRNAs were systemic mobile in cucumber/pumpkin ***,the reason that why P450 mRNAs were endorsed as signaling,and what specific motif(s)did they harbored is not clear ***,we first identified 221 CsaP450 genes in cucumber genomewide *** 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 *** with Arabidopsis and pumpkin(Cucubit moschata)graft-induced-transmissible P450 mRNAs,a phylogenetic treewas constructed and divided into eight clans by usingmultiple-sequence *** 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 *** 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 *** integrated analysis of mobility direction and mRNA abundance of 15 mobilemRNA-coding CsaP450 genes allowed to conclude that there was rarely relationship between *** 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 Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice

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Rice science 2019年第6期26卷 384-392页

作者： LV Yang WANG Yueying Noushin JAHAN HU Haitao CHEN Ping SHANG Lianguang LIN Haiyan DONG Guojun HU Jiang GAO Zhenyu QIAN Qian ZHANG Yu GUO Longbiao State Key Lab for Rice Biology China National Rice Research Institute Hangzhou 310006 China Tobacoo Research Institute Chinese Academy of Agricultural Sciences Qingdao 266101 China

Excavating single nucleotide polymorphisms (SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study (GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length (GL), grain width (GW), 1000-grain weight (TGW), and grain length/width (GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and qGL3 were found to regulate GL. On chromosome 6, TGW6 and GW6a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.

关键词： candidate gene grain shape genome-wide association study haplotype rice single nucleotide polymorphism

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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 Transcription Factor Gene Prediction and their Expressional Tissue-Specificities in Maize

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Journal of Integrative Plant Biology 2012年第9期54卷 616-630页

作者： Yi Jiang Biao Zeng Hainan Zhao Mei Zhang Shaojun Xie Jinsheng Lai State Key Laboratory of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Transcription factors （TFs） are important regulators of gene expression. To better understand TFencoding genes in maize （Zea mays L.）, a genome-wide TF prediction was performed using the updated B73 reference genome. A total of 2 298 TF genes were identified, which can be classified into 56 families. The largest family, known as the MYB superfamily, comprises 322 MYB and MYB-related TF genes. The expression patterns of 2014 （87.64%） TF genes were examined using RNA-seq data, which resulted in the identification of a subset of TFs that are specifically expressed in particular tissues （including root, shoot, leaf, ear, tassel and kernel）. Similarly, 98 kernel-specific TF genes were further analyzed, and it was observed that 29 of the kernel-specific genes were preferentially expressed in the early kernel developmental stage, while 69 of the genes were expressed in the late kernel developmental stage. Identification of these TFs, particularly the tissue-specific ones, provides important information for the understanding of development and transcriptional regulation of maize.

关键词： genome-wide maize tissue-specific transcription factor.

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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 *** user-friendly SSR markers have attracted considerable attention owing to their ideal genetic ***,these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane *** this present study,744305and 361638 candidate SSRs were identified from the genomes of *** and ***,*** verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum,including ***,***,***,and modern sugarcane *** results showed that 660 SSR markers displayed interspecific polymorphisms among these ***,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 *** genetic diversity analysis revealed that these accessions were distributed in four main groups,including group I(14 *** accessions),group II(two *** accessions),group III(18 modern sugarcane hybrid accessions),and group IV(five *** accessions).Experimental verification supported the reliability of the SSR markers based on genome-wide *** 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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genome-wide identification and analysis of cytokinin dehydrogenase/oxidase(CKX) family genes in Brassica oleracea *** 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 ***,a comprehensive analysis of cytokinin dehydrogenase/oxidase(CKX)family genes in cabbage has not been *** this study,a total of 36 CKX genes were identified using a genome-wide search *** analysis classified these genes into three *** were distributed unevenly across nine chromosomes in ***,and 15 of them did not contain any *** results of colinearity analysis showed that 36 CKX gene in Arabidopsis was present in several copies in the Brassica oleracea *** 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 *** genes(Bol028363,Bol031036 and Bol018140)were relatively highly expressed in all of the investigated tissues under normal conditions,showing the expression profile of housekeeping ***,the expression patterns of CKX genes in Jingfeng 1 and Xiangan 336 were quite different under the same ***,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 *** results provide insights for better understanding the roles of CKX genes in the ***–*** interaction.

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

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