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Detection of candidate genes and development of KASP markers for Verticillium wilt resistance by combining genome-wide association study, QTL-seq and transcriptome sequencing in cotton

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Combining GWAS, QTL-seq and transcriptome sequencing detected basal defense-related genes showing gDNA sequence variation and expression difference in diverse cotton lines, which might be the molecular mechanisms of VW resistance in G. hirsutum.

Abstract

Verticillium wilt (VW), which is caused by the soil-borne fungus Verticillium dahliae, is a major disease in cotton (Gossypim hirsutum) worldwide. To facilitate the understanding of the genetic basis for VW resistance in cotton, a genome-wide association study (GWAS), QTL-seq and transcriptome sequencing were performed. The GWAS of VW resistance in a panel of 120 core elite cotton accessions using the Cotton 63K Illumina Infinium SNP array identified 5 QTL from 18 significant SNPs meeting the 5% false discovery rate threshold on 5 chromosomes. All QTL identified through GWAS were found to be overlapped with previously reported QTL. By combining GWAS, QTL-seq and transcriptome sequencing, we identified eight candidate genes showing both gDNA sequence variation and expression difference between resistant and susceptible lines, most related to transcription factors (TFs), flavonoid biosynthesis and those involving in the plant basal defense and broad-spectrum disease resistance. Ten KASP markers were successfully validated in diverse cotton lines and could be deployed in marker-assisted breeding to enhance VW resistance. These results supported our inference that the gDNA sequence variation or expression difference of those genes involving in the basal defense in diverse cotton lines might be the molecular mechanisms of VW resistance in G. hirsutum.

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References

  • Abdelraheem A, Liu F, Song M, Zhang JF (2017) A meta-analysis of quantitative trait loci for abiotic and biotic stress resistance in tetraploid cotton. Mol Genet Genom 292:1221–1235

    Article  CAS  Google Scholar 

  • Abdelraheem A, Elassbli H, Zhu Y, Vasu K, Hinze L, Stelly D, Wedegaertner T, Zhang J (2020) 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 133:563–577

    Article  CAS  PubMed  Google Scholar 

  • Abdullaev AA, Salakhutdinov IB, Egamberdiev SS, Khurshut EE, Rizaeva SM, Ulloa M, Abdurakhmonov IY (2017) Genetic diversity, linkage disequilibrium, and association mapping analyses of Gossypium barbadense L germplasm. PLoS One 12(11):e0188125

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Abdurakhmonov IY, Kohel RJ, Yu JZ, Pepper AE, Abdullaev AA et al (2008) Molecular diversity and association mapping of fiber quality traits in exotic 30 G. hirsutum L. germplasm. Genomics 92:478–487

    Article  CAS  PubMed  Google Scholar 

  • Abdurakhmonov IY, Saha S, Jenkins JN, Buriev ZT, Shermatov SE et al (2009) Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica 136:401–417

    Article  PubMed  Google Scholar 

  • Benjamini Y, Yekutieli D (2005) Quantitative trait loci analysis using the false discovery rate. Genetics 171:783–790

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y et al (2007) TASSEL:software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  PubMed  Google Scholar 

  • Cheng Q, Dong L, Gao T, Liu T, Li N, Wang L, Chang X, Wu J, Xu P, Zhang S (2018) The bHLH transcription factor GmPIB1 facilitates resistance to Phytophthora sojae in Glycine max. J Exp Bot 69(10):2527–2541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fang H, Zhou H, Sanogo S, Flynn R, Percy RG, Hughs SE, Ulloa M, Jones DC, Zhang J (2013) Quantitative trait locus mapping for Verticillium wilt resistance in a backcross inbred line population of cotton (Gossypium hirsutum ×Gossypium barbadense) based on RGA-AFLP analysis. Euphytica 194:79–91

    Article  CAS  Google Scholar 

  • Fang H, Zhou H, Sanogo S, Lipka AE, Fang DD, Percy RG, Hughs SE, Jones DC, Gore MA, Zhang JF (2014) Quantitative trait locus analysis of Verticillium wilt resistance in an introgressed recombinant inbred population of Upland cotton. Mol Breed 33:709–720

    Article  Google Scholar 

  • Gao W, Long L, Zhu LF, Xu L, Gao WH, Sun LQ, Liu LL (2013) Zhang XL (2013) Proteomic and virus-induced gene silencing (VIGS) analyses reveal that gossypol, brassinosteroids, and jasmonic acid contribute to the resistance of cotton to Verticillium dahliae. Mol Cell Proteom 12(12):3690–3703

    Article  CAS  Google Scholar 

  • Gong Q, Yang ZE, Chen EY, Sun GF, He SP, Butt HI, Zhang CJ et al (2018) A phi-class glutathione s-transferase gene for verticillium wilt resistance in gossypium arboreum identified in a genome-wide association study. Plant Cell Physiol 59(2):275–289

    Article  CAS  PubMed  Google Scholar 

  • González-Hernández AI, Fernández-Crespo E, Scalschi L, Hajirezaei MR, von Wirén N, García-Agustín P, Camañes G (2019) Ammonium mediated changes incarbon and nitrogen metabolisms induce resistance against Pseudomonas syringae in tomato plants. J Plant Physiol 239:28–37

    Article  PubMed  CAS  Google Scholar 

  • Grover CE, Zhu X, Grupp KK, Jareczek JJ, Gallagher JP, Szadkowski E, Seijo JG et al (2014) Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum Wittmack. Genet Resour Crop Ev 62:103–114

    Article  Google Scholar 

  • Hadfield A, Shammas C, Kryger G, Ringe D, Petsko GA, Ouyang J, Viola RE (2001) Active site analysis of the potential antimicrobial target aspartate semialdehyde dehydrogenas. Biochemistry 40(48):14475–14483

    Article  CAS  PubMed  Google Scholar 

  • Hatzig SV, Frisch M, Breuer F, Nesi N, Ducournau S, Wagner M-H, Leckband G, Abbadi A, Snowdon RJ (2015) Genome-wide association mapping unravels the genetic control of seed germination and vigor in Brassica napus. Front Plant Sci 6:221

    Article  PubMed  PubMed Central  Google Scholar 

  • Hernández-Vega JC, Cady B, Kayanja G, Mauriello A, Cervantes N, Gillespie A, Lavia L, Trujillo J, Alkio M, Colón-Carmona A (2017 Jan) (2017) Detoxification of polycyclic aromatic hydrocarbons (PAHs) in Arabidopsis thaliana involves a putative flavonol synthase. J Hazard Mater 5(321):268–280

    Article  CAS  Google Scholar 

  • Huang C, Nie X, Shen C, You C et al (2017) Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genomewide association study using high-density SNPs. Plant Biotechnol J 15:1374–1386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang F, Zhao J, Zhou L, Guo WZ, Zhang TZ (2009) Molecular mapping of Verticillium wilt resistance QTL clustered on chromosomes D7 and D9 in Upland cotton. Sci China Ser C-Life Sci 52:872–884

    Article  Google Scholar 

  • Kang HM, Sul JH, Service SK et al (2010) Variance component model to account for sample structure in genome wide association studies. Nat Genet 42:348–354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li TG, Ma XF, Li NY, Zhou L, Liu Z, Han HY, Gui YJ et al (2017) Genome-wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). Plant Biotechnol J 15:1520–1532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu S, Fan C, Li J, Cai G, Yang Q, Wu J, Yi X et al (2016) A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus. Theor Appl Genet 129:1203–1215

    Article  CAS  PubMed  Google Scholar 

  • Long L, Liu J, Gao Y, Xu FC, Zhao JR, Li B, Gao W (2019) Flavonoid accumulation in spontaneous cotton mutant results in red coloration and enhanced disease resistance. Plant Physiol Biochem 143:40–49

    Article  CAS  PubMed  Google Scholar 

  • Ning ZY, Zhao R, Chen H, Ai NJ, Zhang X, Zhao J et al (2013) Molecular tagging of a major quantitative trait locus for broad-spectrum resistance to Verticillium wilt in Upland cotton cultivar Prema. Crop Sci 53:2304–2312

    Article  CAS  Google Scholar 

  • Palanga KK, Jamshed M, Rashid MH, Gong JW, Li JW, Iqbal MS, Liu AY et al (2017) Quantitative trait locus mapping for verticillium wilt resistance in an upland cotton recombinant inbred line using snp-based high density genetic map. Front Plant Sci 8:382

    Article  PubMed  PubMed Central  Google Scholar 

  • Pastor V, Gamir J, Camañes G, Cerezo M, Sánchez-Bel P, Flors V (2014) Front Plant Sci 5:231

    PubMed  PubMed Central  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure usingmulti-locus genotype data. Genetics 155:945–959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schwarz B, Bauer P (2020) FIT, a regulatory hub for iron deficiency and stress signaling in roots, and FIT-dependent and -independent gene signatures. J Exp Bot 71(5):1694–1705

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14

    Article  CAS  Google Scholar 

  • Shi YZ, Zhang BC, Liu AY, Li WT, Li JW, Lu QW, Zhang Z et al (2016) Quantitative trait loci analysis of Verticillium wilt resistance in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense. BMC Genomics 17:877

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh K, Foley RC, Onate-Sanchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5:430–436

    Article  CAS  PubMed  Google Scholar 

  • Sun Q, Jiang H, Zhu X, Wang W, He X, Shi Y, Yuan Y, Du X, Cai Y (2013) Analysis of sea-island cotton and upland cotton in response to Verticillium dahliae infection by RNA sequencing. BMC Genom 14:852

    Article  CAS  Google Scholar 

  • Sun Z, Wang X, Liu Z, Gu Q, Zhang Y et al (2017) Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome wide association study using high-density SNPs. Plant Biotechnol J 15:1374–1386

    Article  CAS  Google Scholar 

  • Takagi H et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183

    Article  CAS  PubMed  Google Scholar 

  • Tan CT, Yu H, Yang Y, Xu X, Chen M et al (2017) Development and validation of KASP markers for the greenbug resistance gene Gb7 and the Hessian fly resistance gene H32 in wheat. Theor Appl Genet 130(9):1867–1884

    Article  CAS  PubMed  Google Scholar 

  • Wang FR, Liu RZ, Wang LM, Zhang CY, Liu GD et al (2007) Molecular marker of Verticillium resistance in upland cotton (Gossypium hirsutum L.) cultivar and their effects on assisted phenotypic selection. Cotton Sci 6:424–430

    Google Scholar 

  • Wang HM, Lin ZX, Zhang XL, Chen W, Guo XP, Nie YC, Li YH (2008) Mapping and quantitative trait loci analysis of Verticillium wilt resistance genes in cotton. J Integr Plant Biol 50:174–182

    Article  PubMed  Google Scholar 

  • Wang Z, Wang S, Wu M, Li Z, Liu P, Li F, Chen Q, Yang A, Yang J (2019) Evolutionary and functional analyses of the 2-oxoglutarate-dependent dioxygenase genes involved in the flavonoid biosynthesis pathway in tobacco. Planta 249(2):543–561

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Shang Y, Fan B, Yu JQ, Chen Z (2014) Arabidopsis LIP5, a positive regulator of multivesicular body biogenesis, is a critical target of pathogen-responsive MAPK cascade in plant basal defense. Front Plant Sci 30(5):231

    CAS  Google Scholar 

  • Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. Adv Agron 78:139–186

    Article  Google Scholar 

  • Xia Z, Wei Y, Sun K, Wu J, Wang Y, Wu K (2013) The maize AAA-type protein SKD1 confers enhanced salt and drought stress tolerance in transgenic tobacco by interacting with Lyst-interacting protein 5. PLoS One 8(7):69787

    Article  CAS  Google Scholar 

  • Xu L, Zhu L, Tu L, Liu L, Yuan D, Jin L, Long L, Zhang X et al (2011) Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium hahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. J Exp Bot 62:5607–5621

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang C, Guo WZ, Li GY, Gao F, Lin SS, Zhang TZ (2008) QTLs mapping for Verticillium wilt resistance at seedling and maturity stages in Gossypium barbadense L. Plant Sci 174:290–298

    Article  CAS  Google Scholar 

  • Zhang JF, Fang H, Zhou HP, Sanogo S, Ma ZY (2014a) Genetics, breeding, and marker-assisted selection for Verticillium wilt resistance in cotton. Crop Sci 54:1289–1303

    Article  Google Scholar 

  • Zhang JF, Yu JW, Pei WF, Li XL, Said J, Song MZ, Sanogo S (2015a) Genetic analysis of Verticillium wilt resistance in a backcross inbred line population and a meta-analysis of quantitative trait loci for disease resistance in cotton. BMC Genom 16:577

    Article  CAS  Google Scholar 

  • Zhang T, Jin Y, Zhao JH, Gao F, Zhou BJ, Fang YY, Guo HS (2016) Host-induced gene silencing of the target gene in fungal cells confers effective resistance to the cotton wilt disease pathogen Verticillium dahliae. Mol Plant 9:939–942

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Liu B, Li X, Ouyang Z, Huang L, Hong Y, Zhang H, Li D, Song F (2014b) The de novo biosynthesis of vitamin B6 is required for disease resistance against Botrytis cinerea in tomato. Mol Plant Microbe Interact 27(7):688–699

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Jin X, Ouyang Z, Li X, Liu B, Huang L, Hong Y, Zhang H, Song F, Li D (2015b) Vitamin B6 contributes to disease resistance against Pseudomonas syringae pv. tomato DC3000 and Botrytis cinerea in Arabidopsis thaliana. J Plant Physiol 175:21–25

    Article  CAS  PubMed  Google Scholar 

  • Zhang WW, Wang SZ, Liu K, Si N, Qi FJ et al (2012a) Comparative expression analysis in susceptible and resistant Gossypium hirsutum responding to Verticillium dahliae infection by cDNA-AFLP. Physiol Mol Plant Pathol 80:50–57

    Article  CAS  Google Scholar 

  • Zhang JF, Sanogo S, Flynn R, Baral JB, Bajaj S, Hughs SE, Percy RG (2012b) Germplasm evaluation and transfer of Verticillium wilt resistance from Pima (Gossypium barbadense) to Upland cotton (G. hirsutum). Euphytica 187:147–160

    Article  Google Scholar 

  • Zhang JF, Abdelraheem A, Thyssen GN, Fang DD, Jenkins JN, McCarty JC Jr, Wedegaertner T (2020) Evaluation and genome-wide association study of Verticillium wilt resistance in a MAGIC population derived from intermating of eleven Upland cotton (Gossypium hirsutum) parents. Euphytica 216:9

    Article  CAS  Google Scholar 

  • Zhao Y, Wang H, Chen W, Li Y (2014) Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L) germplasm population. PLoS One 9:e86308

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhu HQ, Wu ZB, Zhou K, Feng ZL (2007) The national identification method for Verticillium wilt and Fusarium wilt resistance in cotton cultivar regional test. China Cotton 34(11):9–24

    Google Scholar 

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Ackonwledgements

The authors thank professor Heqin Zhu for supplying the pathogenic strain of V. dahliae and the technical support in identifying disease resistance, and thank Dr Yuhui Xu for giving professional advices in analysing the data using different models.This study was supported by the National Key R&D Program of China (2018YFD0100301 and 2017YFD0101600) and the Central Public-interest Scientific Institution Basal Research Fund (No. 1610162020040905).

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Authors and Affiliations

  1. State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China

    Yunlei Zhao, Wei Chen, Yanli Cui, Xiaohui Sang, Jianhua Lu, Huijuan Jing, Wenju Wang, Pei Zhao & Hongmei Wang

  2. Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China

    Yunlei Zhao & Hongmei Wang

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  1. Yunlei Zhao
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  2. Wei Chen
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  3. Yanli Cui
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  4. Xiaohui Sang
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  5. Jianhua Lu
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  7. Wenju Wang
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Contributions

HW, PZ, and YZ conceived and designed the experiments; YZ, WC, YC, XS, and JL executed the experiments; YZ analysed the data and wrote the paper; HJ and WW contributed reagents, materials, and analysis tools.

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Correspondence to Pei Zhao or Hongmei Wang.

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Communicated by Brent Hulke.

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Zhao, Y., Chen, W., Cui, Y. et al. Detection of candidate genes and development of KASP markers for Verticillium wilt resistance by combining genome-wide association study, QTL-seq and transcriptome sequencing in cotton. Theor Appl Genet 134, 1063–1081 (2021). https://doi.org/10.1007/s00122-020-03752-4

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