Phân tích liên kết toàn bộ bộ gen tiết lộ một con đường mới do protein miền kép TIR trung gian cho khả năng kháng bệnh trong cây cotton

Zhang X, Bernoux M, Bentham AR, Newman TE, Ve T, Casey LW, et al. Multiple functional self-association interfaces in plant TIR domains. Proc Natl Acad Sci USA. 2017;114(10):E2046–52. Martin R, Qi T, Zhang H, Liu F, King M, Toth C, et al. Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ. Science. 2020;370(6521):eabd9993. Le Roux C, Huet G, Jauneau A, Camborde L, Tremousaygue D, Kraut A, et al. A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity. Cell. 2015;161(5):1074–88. Dodds PN, Lawrence GJ, Catanzariti AM. Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes. Proc Natl Acad Sci USA. 2006;103(23):8888–93. Narusaka M, Shirasu K, Noutoshi Y, Kubo Y, Shiraishi T, Iwabuchi M, et al. RRS1 and RPS4 provide a dual Resistance-gene system against fungal and bacterial pathogens. Plant J. 2009;60(2):218–26. Jia H, Xue S, Lei L, Fan M, Peng S, Li T, et al. A semi-dominant NLR allele causes whole-seedling necrosis in wheat. Plant Physiol. 2021;186(1):483–96. Bronkhorst J, Kasteel M, van Veen S, Clough JM, Kots K, Buijs J, et al. A slicing mechanism facilitates host entry by plant-pathogenic Phytophthora. Nat Microbiol. 2021;6(8):1000–6. Zhu C, Liu JH, Zhao JH, Liu T, Chen YY, Wang CH, et al. A fungal effector suppresses the nuclear export of AGO1-miRNA complex to promote infection in plants. Proc Natl Acad Sci USA. 2022;119(12): e2114583119. Li PT, Rashid MHO, Chen TT, Lu QW, Ge Q, Gong WK, et al. Transcriptomic and biochemical analysis of upland cotton (Gossypium hirsutum) and a chromosome segment substitution line from G. hirsutum x G. barbadense in response to Verticillium dahliae infection. BMC Plant Biol. 2019;19(1):19. Shaban M, Miao Y, Ullah A, Khan AQ, Menghwar H, Khan AH, et al. Physiological and molecular mechanism of defense in cotton against Verticillium dahliae. Plant Physiol Biochem. 2018;125(1):193–204. Zhang Y, Jin Y, Gong Q, Li Z, Zhao L, Han X, et al. Mechanismal analysis of resistance to Verticillium dahliae in upland cotton conferred by overexpression of RPL18A-6 (Ribosomal Protein L18A-6). Ind Crops Prod. 2019;141(1):111742. Fradin EF, Zhang Z, Juarez Ayala JC, Castroverde CD, Nazar RN, Robb J, et al. Genetic dissection of Verticillium wilt resistance mediated by tomato Ve1. Plant Physiol. 2009;150(1):320–32. Bartoli C, Roux F. Genome-Wide Association Studies In Plant Pathosystems: Toward an ecological enomics approach. Front Plant Sci. 2017;8(1):763. Abdelraheem A, Elassbli H, Zhu Y, Kuraparthy V, Zhang J. A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton. Theor Appl Genet. 2020;133(2):563–77. Li T, Ma X, Li N, Lei Z, Zheng L. Genome-wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). Plant Biotechnol J. 2017;15(12):1520–1532. Zhang Y, Chen B, Sun Z, Liu Z, Cui Y, Ke H, et al. A large-scale genomic association analysis identifies a fragment in Dt11 chromosome conferring cotton Verticillium wilt resistance. Plant Biotechnol J. 2021;19(10):2126–38. Chen B, Zhang Y, Sun Z, Liu Z, Zhang D, Yang J, et al. 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(3):831–46. Seah S, Bariana H, Jahier J, Sivasithamparam K, Lagudah E. The introgressed segment carrying rust resistance genes Yr17, Lr37 and Sr38 in wheat can be assayed by a cloned disease resistance gene-like sequence. Theor Appl Genet. 2001;102(1):600–5. Yun SJ, Gyenis L, Bossolini E, Hayes PM, Matus I, Smith KP, et al. Validation of quantitative trait loci for multiple disease resistance in barley using advanced backcross lines developed with a wild barley. Crop Sci. 2006;46(3):1179–86. Zamir D, Ekstein-Michelson I, Zakay Y, Navot N, Czosnek H. Mapping and introgression of a tomato yellow leaf curl virus tolerance gene, TY-1. Theor Appl Genet. 1994;88(2):141–6. Ronald PC, Albano B, Tabien R, Abenes L, Wu KS, Mccouch S, et al. Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21. Mol Gen Genet. 1992;236(1):113. Welgemoed T, Pierneef R, Sterck L, Van de Peer Y, Swart V, Scheepers KD, et al. De novo assembly of transcriptomes from a B73 maize line introgressed with a QTL for resistance to gray leaf spot disease reveals a candidate allele of a lectin receptor-like kinase. Front Plant Sci. 2020;11(1):191. Yu J, Hui Y, Chen J, Yu H, Gao X, Zhang Z, et al. Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage. Theor Appl Genet. 2021;134(10):3249–61. Shi Y, Zhang B, Liu A, Li W, Li J, Lu Q, et al. Quantitative trait loci analysis of Verticillium wilt resistance in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense. BMC Genomics. 2016;17(1):877. Zhao J, Liu J, Xu J, Zhao L, Wu Q, Xiao S. Quantitative trait locus mapping and candidate gene analysis for Verticillium wilt resistance using Gossypium barbadense chromosomal segment introgressed line. Front Plant Sci. 2018;9(1):682. He S, Sun G, Geng X, Gong W, Dai P, Jia Y, et al. The genomic basis of geographic differentiation and fiber improvement in cultivated cotton. Nat Genet. 2021;53(6):916–24. Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, et al. Variance component model to account for sample structure in genome-wide association studies. Nat Genet. 2010;42(4):348–354. Yang Z, Ge X, Yang Z, Qin W, Sun G, Wang Z, et al. Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nat Commun. 2019;10:2989. Said JI, Knapka JA, Song M, Zhang J. Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum x G. barbadense populations. Mol Genet Genomics. 2015;290(4):1615–1625. Romano G, Sacks E, Stetina S, Robinson A, Fang D, Gutierrez O, et al. Identification and genomic location of a reniform nematode (Rotylenchulus reniformis) resistance locus (Ren ari) introgressed from Gossypium aridum into upland cotton (G. hirsutum). Theor Appl Genet. 2009;120(1):139–150. Wang P, Dong N, Wang M, Sun G, Jia Y, Geng X, et al. Introgression from Gossypium hirsutum is a driver for population divergence and genetic diversity in Gossypium barbadense. Plant J. 2022;110(3):764–80. Du X, Huang G, He S, Yang Z, Sun G, Ma X, et al. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nat Genet. 2018;50(6):796–802. Chen Y, Wang Y, Zhao T, Yang J, Feng S, Nazeer W, et al. A New Synthetic Amphiploid (AADDAA) between Gossypium hirsutum and G. arboreum lays the foundation for transferring resistances to Verticillium and drought. PloS one. 2015;10(6):e0128981. Jones JD, Vance RE, Dangl JL. Intracellular innate immune surveillance devices in plants and animals. Science. 2016;354(6316):aaf6395. Zhang G, Zhao Z, Ma P, Qu Y, Sun G, Chen Q. Integrative transcriptomic and gene co-expression network analysis of host responses upon Verticillium dahliae infection in Gossypium hirsutum. Sci Rep. 2021;11(1):20586. Bernoux M, Ve T, Williams S, Warren C, Hatters D, Valkov E, et al. Structural and functional analysis of a plant resistance protein TIR domain reveals interfaces for self-association, signaling, and autoregulation. Cell Host Microbe. 2011;9(3):200–11. Schreiber KJ, Bentham A, Williams SJ, Kobe B, Staskawicz BJ. Multiple domain associations within the Arabidopsis immune receptor RPP1 regulate the activation of programmed cell death. PLoS Pathog. 2016;12(7): e1005769. Williams S, Sohn K, Wan L, Bernoux M, Sarris P, Segonzac C. Structural basis for assembly and function of a heterodimeric plant immune receptor. Science. 2014;344(6181):299–303. Yang Z, Zhang C, Yang X, Liu K, Wu Z, Zhang X, et al. PAG1, a cotton brassinosteroid catabolism gene, modulates fiber elongation. New Phytol. 2014;203(2):437–48. Noguchi T, Fujioka S, Choe S, Takatsuto S, Yoshida S, Yuan H, et al. Brassinosteroid-insensitive dwarf mutants of Arabidopsis accumulate brassinosteroids. Plant Physiol. 1999;121(3):743–52. Sponsel V, Schmidt F, Porter S, Nakayama M, Kohlstruk S, Estelle M. Characterization of new gibberellin-responsive semidwarf mutants of Arabidopsis. Plant Physiol. 1997;115(3):1009–20. Dodds PN, Lawrence GJ, Catanzariti AM, Ayliffe MA, Ellis JG. The Melampsora lini AvrL567 avirulence genes are expressed in haustoria and their products are recognized inside plant cells. Plant Cell. 2004;16(3):755–68. Zhang Y, Wang X, Rong W, Yang J, Li Z, Wu L, et al. Histochemical analyses reveal that stronger intrinsic defenses in Gossypium barbadense than in G. hirsutum are associated with resistance to Verticillium dahliae. Mol Plant Microbe Interact. 2017;30(12):984–996. Li L, Ying J, Li E, Ma T, Li M, Gong L, et al. Arabidopsis CBP60b is a central transcriptional activator of immunity. Plant Physiol. 2021;186(3):1645–59. Thaler JS, Owen B, Higgins VJ. The role of the jasmonate response in plant susceptibility to diverse pathogens with a range of lifestyles. Plant Physiol. 2004;135(1):530–8. Nishimura MT, Anderson RG, Cherkis KA, Law TF, Liu QL, Machius M, et al. TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis. Proc Natl Acad Sci USA. 2017;114(10):E2053–62. Chen G, Zhang B, Ding J, Wang H, Deng C, Wang J, et al. Cloning southern corn rust resistant gene RppK and its cognate gene AvrRppK from Puccinia polysora. Nat Commun. 2022;13(1):4392. Yoshida K, Saitoh H, Fujisawa S, Kanzaki H, Matsumura H, Yoshida K, et al. Association genetics reveals three novel avirulence genes from the rice blast fungal pathogen Magnaporthe oryzae. Plant Cell. 2009;21(5):1573–91. Deng C, Leonard A, Cahill J, Lv M, Li Y, Thatcher S, et al. The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize. Mol Plant. 2022;15(5):904–12. Wang Z, Huang J, Nie L, Hu Y, Zhang N, Guo Q, et al. Molecular and functional analysis of a brown planthopper resistance protein with two nucleotide-binding site domains. J Exp Bot. 2021;72(7):2657–71. Ma S, Lapin D, Liu L, Sun Y, Song W, Zhang X, et al. Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Science. 2020;370(6521):eabe3069. Williams SJ. Structural basis for assembly and function of a heterodimeric plant immune receptor. Science. 2014;344(1):299–303. Wan L, Essuman K, Anderson RG, Sasaki Y, Monteiro F, Chung EH, et al. TIR domains of plant immune receptors are NAD+-cleaving enzymes that promote cell death. Science. 2019;365(6455):799–803. Krasileva KV, Dahlbeck D, Staskawicz BJ. Activation of an Arabidopsis resistance protein is specified by the in planta association of its leucine-rich repeat domain with the cognate oomycete effector. Plant Cell. 2010;22(7):2444–58. Deng Y, Zhai K, Xie Z, Yang D, Zhu X, Liu J, et al. Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance. Science. 2017;355(6328):962–5. He Z, Li L, Luan S. Immunophilins and parvulins. Superfamily of peptidyl prolyl isomerases in Arabidopsis. Plant Physiol. 2004;134(4):1248–1267. Qi T, Seong K, Thomazella DPT, Kim JR, Pham J, Seo E, et al. NRG1 functions downstream of EDS1 to regulate TIR-NLR-mediated plant immunity in Nicotiana benthamiana. Proc Natl Acad Sci USA. 2018;115(46):E10979–87. Fang L, Wang Q, Hu Y, Jia Y, Chen J, Liu B, et al. Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat Genet. 2017;49(7):1089–98. Li TG, Wang BL, Yin CM, Zhang DD, Wang D, Song J, et al. The Gossypium hirsutum TIR-NBS-LRR gene GhDSC1 mediates resistance against Verticillium wilt. Mol Plant Pathol. 2019;20(6):857–76. Saucet SB, Ma Y, Sarris PF, Furzer OJ, Sohn KH, Jones JD. Two linked pairs of Arabidopsis TNL resistance genes independently confer recognition of bacterial effector AvrRps4. Nat Commun. 2015;6(1):6338. Freddy M, Nishimura MT. Structural, Functional, and Genomic Diversity of Plant NLR Proteins: An Evolved Resource for Rational Engineering of Plant Immunity. Annu Rev Phytopathol. 2018;56(1):243–67. Dong OX, Ao K, Xu F, Johnson KCM, Wu Y, Li L, et al. Individual components of paired typical NLR immune receptors are regulated by distinct E3 ligases. Nat Plants. 2018;4(9):699–710. Yang Z, Gao C, Zhang Y, Yan Q, Hu W, Yang L, et al. Recent progression and future perspectives in cotton genomic breeding. J Integr Plant Biol. 2023;65(2):548–69. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10(6):845–58. Crisan CV, Chande AT, Williams K, Raghuram V, Rishishwar L, Steinbach G, et al. Analysis of Vibrio cholerae genomes identifies new type VI secretion system gene clusters. Genome Biol. 2019;20(1):163. Ma Z, He S, Wang X, Sun J, Zhang Y, Zhang G, et al. Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield. Nat Genet. 2018;50(6):803–13. Li MX, Yeung JM, Cherny SS, Sham PC. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum Genet. 2012;131(5):747–56. Turner SD. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. Journal of Open Source Software. 2014;3(25):731. Marsh J. Linkage disequilibrium statistics and block visualization. Methods Mol Biol. 2022;2443(1):483–96. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16): e164. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–50. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357–60. Veronese P, Narasimhan ML, Stevenson RA, Zhu JK, Weller SC, Subbarao KV, et al. Identification of a locus controlling Verticillium disease symptom response in Arabidopsis thaliana. Plant J. 2003;35(5):574–87. Heckman KL, Pease LR. Gene splicing and mutagenesis by PCR-driven overlap extension. Nat Protoc. 2007;2(4):924–32. Gong Q, Yang Z, Chen E, Sun G, He S, Butt HI, et al. A phi-class glutathione S-Transferase gene for Verticillium wilt resistance in Gossypium arboreum identified in a genome-wide association study. Plant Cell Physiol. 2018;59(2):275–89. Tang Y, Zhang Z, Lei Y, Hu G, Liu J, Hao M, et al. Cotton WATs modulate SA biosynthesis and local lignin deposition participating in plant resistance against Verticillium dahliae. Front Plant Sci. 2019;10(1):526. Clough SJ, Bent AF. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1998;16(6):735–43. Yang X, Lu Y, Zhao X, Jiang L, Xu S, Peng J, et al. Nicotiana benthamiana downregulation of nuclear protein H2B induces salicylic acid mediated defense against PVX infection in. Front Microbiol. 2019;10(1):1000. Liu L, Wang Z, Li J, Wang Y, Yuan J, Zhan J, et al. Verticillium dahliae secreted protein Vd424Y is required for full virulence, targets the nucleus of plant cells, and induces cell death. Mol Plant Pathol. 2021;22(9):1109–20. Earley KW, Haag JR, Pontes O, Opper K, Juehne T, Song K, et al. Gateway-compatible vectors for plant functional genomics and proteomics. Plant J. 2006;45(4):616–29. Schultink A, Qi T, Lee A, Steinbrenner AD, Staskawicz B. Roq1 mediates recognition of the Xanthomonas and Pseudomonas effector proteins XopQ and HopQ1. Plant J. 2017;92(5):787–95. Yang X, Lu Y, Wang F, Chen Y, Tian Y, Jiang L, et al. Involvement of the chloroplast gene ferredoxin 1 in multiple responses of Nicotiana benthamiana to Potato virus X infection. J Exp Bot. 2020;71(6):2142–56. Zhan J, Chu Y, Wang Y, Diao Y, Zhao Y, Liu L, et al. The miR164-GhCUC2-GhBRC1 module regulates plant architecture through abscisic acid in cotton. Plant Biotechnol J. 2021;19(9):1839–51. Alcantara A, Bosch J, Nazari F, Hoffmann G, Gallei M, Uhse S, et al. Systematic Y2H screening reveals extensive effector-complex formation. Front Plant Sci. 2019;10(1):1437. Ge X, Xu J, Yang Z, Yang X, Wang Y, Chen Y, et al. Efficient genotype-independent cotton genetic transformation and genome editing. J Integr Plant Biol. 2023;65(4):907–17. Zhang Y. mRNA-seq data of cotton root inoculated with Verticillium dahliae. PRJNA953671. Sequence Read Archive. 2023. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA953671/. Du X. Gossypium arboreum Raw sequence reads. PRJNA349094. Sequence Read Archive. 2016. https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA349094. Ma Z. Gossypium hirsutum Genome sequencing. PRJNA399050. Sequence Read Archive. 2017. https://www.ncbi.nlm.nih.gov/bioproject/399050. Yuan D. Genomic Sequence Resources of Allotetraploid Cotton. PRJNA414461. Sequence Read Archive. 2017. https://www.ncbi.nlm.nih.gov/bioproject/414461. Zhang Z, Chai M, Yang Z, Yang Z, Fan L. GRAND: An integrated genome, transcriptome resources, and Gene Network Database for Gossypium. Front Plant Sci. 2022;13(1): 773107.