Block C, Reitsma K. Powdery mildew resistance in the U.S. national plant germplasm system cucumber collection. Hortscience. 2005;40:414–20.
Lebeda A, Mieslerová B. Taxonomy, distribution and biology of lettuce powdery mildew (Golovinomyces cichoracearum sensu stricto). Plant Pathol. 2011;60(3):400–15.
Keinath AP, Dubose VB. Controlling powdery mildew on cucurbit rootstock seedlings in the greenhouse with fungicides and biofungicides. Crop Prot. 2012;42:338–44.
Hafez YM, Attia KA, Kamel S, Alamery SF, Abdelaal K. Bacillus subtilis as a bio-agent combined with nano molecules can control powdery mildew disease through histochemical and physiobiochemical changes in cucumber plants. Physiol Mol Plant Pathol. 2020;11:101489.
Wang Y, Bo K, Gu X, Pan J, Li Y, Chen J, Wen C, Ren Z, Ren H, Chen X, Grumet R, Weng Y. Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature. Hortic Res. 2020;7:3.
Fukino N, Yoshioka Y, Sugiyama M, Sakata Y, Matsumoto S. Identification and validation of powdery mildew (Podosphaera xanthii)-resistant loci in recombinant inbred lines of cucumber (Cucumis sativus L.). Mol Breed. 2013;32:267–77.
He X, Li Y, Pandey S, Yandell BS, Pathak M, Weng Y. QTL mapping of powdery mildew resistance in WI2757 cucumber (Cucumis sativus L.). Theor Appl Genet. 2013;126:2149–61.
Zhang K, Wang X, Zhu W, Qin X, Xu J, Cheng C, Lou Q, Li J, Chen J. Complete resistance to powdery mildew and partial resistance to downy mildew in a Cucumis hystrix introgression line of cucumber were controlled by a co-localized locus. Theor Appl Genet. 2018;131:2229–43.
Berg JA, Appiano M, Santillán Martínez M, Hermans FW, Vriezen WH, Visser RG, Bai Y, Schouten HJ. A transposable element insertion in the susceptibility gene CsaMLO8 results in hypocotyl resistance to powdery mildew in cucumber. BMC Plant Biol. 2015;15:243.
Nie J, Wang Y, He H, Guo C, Zhu W, Pan J, Li D, Lian H, Pan J, Cai R. Loss-of-function mutations in CsMLO1 confer durable powdery mildew resistance in cucumber (Cucumis sativus L.). Front Plant Sci. 2015;6:1155.
Badri Anarjan M, Bae I, Lee S. Marker-assisted evaluation of two powdery mildew resistance candidate genes in Korean cucumber inbred lines. Agronomy. 2021;11:2191.
Lu H, Wang F, Wang Y, Lin R, Wang Z, Mao C. Molecular mechanisms and genetic improvement of low-phosphorus tolerance in rice. Plant Cell Environ. 2023;46(4):1104–19.
Wang F, Deng M, Xu J, Zhu X, Mao C. Molecular mechanisms of phosphate transport and signaling in higher plants. Semin Cell Dev Biol. 2018;74:114–22.
Dong Z, Li W, Liu J, Li L, Pan S, Liu S, Gao J, Liu L, Liu X, Wang GL, Dai L. The rice phosphate transporter protein OsPT8 regulates disease resistance and plant growth. Sci Rep. 2019;9:2–11.
Poirier Y, Thoma S, Somerville C, Schiefelbein J. Mutant of Arabidopsis deficient in xylem loading of phosphate. Plant Physiol. 1991;97:1087–93.
Arruda MP, Brown P, Brown-Guedira G, Krill AM, Thurber C, Merrill KR, Foresman BJ, Kolb FL. Genome-wide association mapping of fusarium head blight resistance in wheat using genotyping-by-sequencing. Plant Genome. 2016;9:1–14.
Li W, Zhu Z, Chern M, Yin J, Yang C, Ran L, Cheng M, He M, Wang K, Wang J, Zhou X, Zhu X, Chen Z, Wang J, Zhao W, Ma B, Qin P, Chen W, Wang Y, Liu J, Wang W, Wu X, Li P, Wang J, Zhu L, Li S, Chen X. A natural allele of a transcription factor in rice confers broad-spectrum blast resistance. Cell. 2017;170:114–126.e15.
Li N, Lin B, Wang H, Li X, Yang F, Ding X, Yan J, Chu Z. Natural variation in ZmFBL41 confers banded leaf and sheath blight resistance in maize. Nature Genet. 2019;51:1540–8.
Chen B, Zhang Y, Sun Z, Liu Z, Zhang D, Yang J, Wang G, Wu J, Ke H, Meng C, Wu L, Yan Y, Cui Y, Li Z, Wu L, Zhang G, Wang X, Ma Z. Tissue-specific expression of GhnsLTPs identified via GWAS sophisticatedly coordinates disease and insect resistance by regulating metabolic flux redirection in cotton. Plant J. 2021;107:831–46.
Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X, Huang Z, Li J, Zhang C, Wang T, Zhang Y, Wang A, Zhang Y, Lin K, Li C, Xiong G, Xue Y, Mazzucato A, Causse M, Fei Z, Giovannoni JJ, Chetelat RT, Zamir D, Städler T, Li J, Ye Z, Du Y, Huang S. Genomic analyses provide insights into the history of tomato breeding. Nature Genet. 2014;46:1220–6.
Han K, Lee HY, Ro NY, Hur OS, Lee JH, Kwon JK, Kang BC. QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum. Plant Biotechnol J. 2018;16:1546–58.
Liu S, Gao P, Zhu Q, Zhu Z, Liu H, Wang X, Weng Y, Gao M, Luan F. Resequencing of 297 melon accessions reveals the genomic history of improvement and loci related to fruit traits in melon. Plant Biotechnol J. 2020;18:2545–58.
Qi J, Liu X, Shen D, Miao H, Xie B, Li X, Zeng P, Wang S, Shang Y, Gu X, Du Y, Li Y, Lin T, Yuan J, Yang X, Chen J, Chen H, Xiong X, Huang K, Fei Z, Mao L, Tian L, Städler T, Renner SS, Kamoun S, Lucas WJ, Zhang Z, Huang S. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nature Genet. 2013;45:1510–5.
Wang X, Bao K, Reddy UK, Bai Y, Hammar SA, Jiao C, Wehner TC, Ramírez-Madera AO, Weng Y, Grumet R, Fei Z. The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development. Horti Res. 2018;5:64.
Lee HY, Kim JG, Kang BC. Assessment of the genetic diversity of the breeding lines and a genome wide association study of three horticultural traits using worldwide cucumber (Cucumis spp.) germplasm collection. Agronomy. 2020;10:1736.
Liu M, Liang Z, Aranda MA, Hong N, Liu L, Kang B, Gu Q. A cucumber green mottle mosaic virus vector for virus-induced gene silencing in cucurbit plants. Plant Methods. 2020;16:9.
Xu X, Liu M, Hu Q, Yan W, Pan J, Yan Y, Chen X. A CsEIL3-CsARN6.1 module promotes waterlogging-triggered adventitious root formation in cucumber by activating the expression of CsPrx5. Plant J. 2023;114(4):824–35.
Liu S, Huang H, Yi X, Zhang Y, Yang Q, Zhang C, Fan C, Zhou Y. Dissection of genetic architecture for glucosinolate accumulations in leaves and seeds of Brassica napus by genome-wide association study. Plant Biotechnol J. 2020;18:1472–84.
Innark P, Khanobdee C, Samipak S, Jantasuriyarat C. Evaluation of genetic diversity in cucumber (Cucumis sativus L.) germplasm using agro-economic traits and microsatellite markers. Sci Hortic. 2013;162:278–84.
Mohler V, Stadlmeier M. Dynamic qtl for adult plant resistance to powdery mildew in common wheat (Triticum aestivum L.). J Appl Genet. 2019;60:291–300.
Castro AJ, Chen X, Hayes PM, Knapp SJ, Vivar H. Coincident QTL which determine seedling and adult plant resistance to stripe rust in barley. Crop Sci. 2002;42:1701–8.
Matoulkova E, Michalova E, Vojtesek B, Hrstka R. The role of the 3’ untranslated region in post-transcriptional regulation of protein expression in mammalian cells. RNA Biol. 2012;9:563–76.
Mayr C. Regulation by 3’-untranslated regions. Annu Rev Genet. 2017;51:171–94.
Ortega JL, Moguel-Esponda S, Potenza C, Conklin CF, Quintana A, Sengupta-Gopalan C. The 3’ untranslated region of a soybean cytosolic glutamine synthetase (GS1) affects transcript stability and protein accumulation in transgenic alfalfa. Plant J. 2006;45:832–46.
Shin J, Yuan Z, Fordyce K, Sreeramoju P, Kent TS, Kim J, Wang V, Schneyer D, Weber TK. A del T poly T (8) mutation in the 3’ untranslated region (UTR) of the CDK2-AP1 gene is functionally significant causing decreased mRNA stability resulting in decreased CDK2-AP1 expression in human microsatellite unstable (MSI) colorectal cancer (CRC). Surgery. 2007;142:222–7.
Liu S, Wang D, Lin M, Sehgal SK, Dong L, Wu Y, Bai G. Artificial selection in breeding extensively enriched a functional allelic variation in taphs1 for pre-harvest sprouting resistance in wheat. Theor Appl Genet. 2020;134:339–50.
Yang YL, Guo L, Xu SA, Holland CA, Kitamura T, Hunter K, Cunningham JM. Receptors for polytropic and xenotropic mouse leukaemia viruses encoded by a single gene at Rmc1. Nature Genet. 1999;21:216–9.
Battini JL, Rasko JEJ, Miller AD. A human cell-surface receptor for xenotropic and polytropic murine leukemia viruses: possible role in G protein-coupled signal transduction. P Natl Acad Sci USA. 1999;96:1385–90.
Wege S, Poirier Y. Expression of the mammalian xenotropic polytropic virus receptor 1 (xpr1) in tobacco leaves leads to phosphate export. FEBS Lett. 2014;588:482–9.
Liu H, Dong S, Li M, Gu F, Yang G, Guo T, Chen Z, Wang J. The class III peroxidase gene OsPrx30, transcriptionally modulated by the AT-hook protein OsATH1, mediates rice bacterial blight-induced ROS accumulation. J Integr Plant Biol. 2021;63(2):393–408.
Li R, Zhang X, Zhao B, Song P, Zhang X, Wang B, Li Q. Wheat class III peroxidase TaPOD70 is a potential susceptibility factor negatively regulating wheat resistance to Blumeria graminis f. sp. tritici. Phytopathology. 2023;113(5):873–83.
Xu X, Liu X, Yan Y, Wang W, Gebretsadik K, Qi X, Xu Q, Chen X. Comparative proteomic analysis of cucumber powdery mildew resistance between a single-segment substitution line and its recurrent parent. Hortic Res. 2019;6:115.
Sun M, Jiang F, Cen B, Wen J, Zhou Y, Wu Z. Respiratory burst oxidase homologue-dependent H2O2 and chloroplast H2O2 are essential for the maintenance of acquired thermotolerance during recovery after acclimation. Plant Cell Environ. 2018;41(10):2373–89.
Ma B, Suo Y, Zhang J, Xing N, Gao Z, Lin X, Zheng L, Wang Y. Glutaredoxin like protein (RtGRL1) regulates H2O2 and Na+ accumulation by maintaining the glutathione pool during abiotic stress. Plant Physiol Biochem. 2021;159:135–47.
Koo SC, Moon BC, Kim JK, Kim CY, Sung SJ, Kim MC, Cho MJ, Cheong YH. OsBWMK1 mediates SA-dependent defense responses by activating the transcription factor OsWRKY33. Biochem Biophys Res Commun. 2009;387(2):365–70.
Murray M, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980;8:4321–6.
Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–890.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics. 2009;25:1754–60.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9.
Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–5.
Alexander D, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–64.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.
Zhang C, Dong S, Xu J, He W, Yang T. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics. 2019;35:1786–8.
Xu X, Yu T, Xu R, Shi Y, Lin X, Xu Q, Qi X, Weng Y, Chen X. Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes. Theor Appl Genet. 2016;129:507–16.
Bradbury P, Zhang Z, Kroon D, Casstevens T, Ramdoss Y, Buckler E. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23:2633–5.
Yang J, Lee S, Goddard M, Visscher P. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet. 2011;88:76–82.
Yang N, Lu Y, Yang X, Huang J, Zhou Y, Ali F, Wen W, Liu J, Li J, Yan J. Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS Genet. 2014;10:e1004573.
Turner S. Qqman: q-q and manhattan plots for GWAS data. J Open Source Softw. 2018;3:731.
Dong S, He W, Ji J, Zhang C, Guo Y, Yang T. Ldblockshow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. Brief Bioinform. 2020;30:bbaa227.
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnol. 2019;37(8):907–15.
Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
Xu X, Du Y, Li S, Tan M, Sohail H, Liu X, Qi X, Yang X, Chen X. A genome-wide association study reveals molecular mechanism underlying powdery mildew resistance in cucumber. Datasets. Genome Sequence Archive. 2021. https://ngdc.cncb.ac.cn/gsa/browse/CRA002417.
Xu X, Du Y, Li S, Tan M, Sohail H, Liu X, Qi X, Yang X, Chen X. A genome-wide association study reveals the genetic basis of powdery mildew resistance in cucumber. Datasets. Sequence Read Archive. 2023.
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA998480.
Xu X, Du Y, Li S, Tan M, Sohail H, Liu X, Qi X, Yang X, Chen X. A genome-wide association study reveals molecular mechanism underlying powdery mildew resistance in cucumber. Github. 2024.
https://github.com/xiaodongy86/PM_GWAS_Cucumber.
Xu X, Du Y, Li S, Tan M, Sohail H, Liu X, Qi X, Yang X, Chen X. A genome-wide association study reveals molecular mechanism underlying powdery mildew resistance in cucumber. Zenodo. 2024.
https://zenodo.org/records/13635209.
Add Comment