Skip to main content
SpringerLink
Log in

Evaluation and genome-wide association study of resistance to bacterial blight race 18 in U.S. Upland cotton germplasm

  • Original Article
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

Bacterial blight (BB), caused by Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease to cotton production in many countries. In the U.S., Xcm race 18 is the most virulent and widespread race and can cause serious yield losses. Planting BB-resistant cotton cultivars is the most effective method of controlling this disease. In this study, 335 U.S. Upland cotton accessions were evaluated for resistance to race 18 using artificial inoculations by scratching cotyledons on an individual plant basis in a greenhouse. The analysis of variance detected significant genotypic variation in disease incidence, and 50 accessions were resistant including 38 lines with no symptoms on either cotyledons or true leaves. Many of the resistant lines were developed in the MAR (multi-adversity resistance) breeding program at Texas A&M University, whereas others were developed before race 18 was first reported in the U.S. in 1973, suggesting a broad base of resistance to race 18. A genome-wide association study (GWAS) based on 26,301 single nucleotide polymorphic (SNP) markers detected 11 quantitative trait loci (QTL) anchored by 79 SNPs, including three QTL on each of the three chromosomes A01, A05 and D02, and one QTL on each of D08 and D10. This study has identified a set of obsolete Upland germplasm with resistance to race 18 and specific chromosomal regions delineated by SNPs for resistance. The results will assist in breeding cotton for BB resistance and facilitate further genomic studies in fine mapping resistance genes to enhance the understanding of the genetic basis of BB resistance in cotton.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Abdelraheem A, Thyssen GN, Fang DD, Jenkins JN, McCarty JC Jr, Wedegaertner ZJF (2020b) GWAS reveals consistent QTL for drought and salt tolerance in a MAGIC population of 550 lines derived from intermating of eleven Upland cotton (Gossypium hirsutum) parents. Mol Genet Genom. https://doi.org/10.1007/s00438-020-01733-2 (Online Oct 13, 2020)

    Article  Google Scholar 

  • Abdelraheem A, Elassbli H, Zhu Y, Kuraparthy V, Hinze L, Stelly D, Zhang JF (2020a) 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

    CAS  PubMed  Google Scholar 

  • Allen TW (2020) Cultivar response to inoculation with Xanthomonas citri subsp. malvacearum in Mississippi in 2019. In: Proc Beltwide Cotton Conf. p. 80–83. Austin, TX, January 8–10, 2020

  • Bayles MB, Johnson WM (1985) Growth of homologous and heterologous phytopathogenic bacteria in cotton lines susceptible, resistant, or immune to blight. Phytopathology 75:515–519

    Google Scholar 

  • Bayles MB, Verhalen LM (2007) Bacterial blight reactions of sixty-one upland cotton cultivars. J Cotton Sci 11:40–51

    Google Scholar 

  • Bird LS (1976) Registration of Tamcot SP21, Tamcot SP23 and Tamcot SP37 cottons. Crop Sci 16:884

    Google Scholar 

  • Bird LS (1979) Registration of Tamcot CAMD-E Cotton (Reg. No. 74). Crop Sci 29:411

    Google Scholar 

  • Bird LS (1982) The MAR (multi-adversity resistance) system for genetic improvement of cotton. Plant Dis 66:172–176

    Google Scholar 

  • Bourland FM (1996) Registration of ‘H1330’ cotton. Crop Sci 36:813

    Google Scholar 

  • Bourland FM, Benson NR (2002) Registration of Arkot 8606, an early-maturing cotton germplasm line. Crop Sci 42:1382

    Google Scholar 

  • Bourland FM, McGowen RE, Johnson JT (1997) Registration of Arkot 8102, Arkot 8506, and Arkot 8514 germplasm lines of cotton. Crop Sci 37:1936

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Brinkerhoff L (1970) Variation in Xanthomonas malvacearum and its relation to control. Annu Rev Phytopathol 8:85–110

    Google Scholar 

  • Brinkerhoff LA, Verhalen LA, Johnson WM, Essenberg M, Richardson PE (1984) Development of immunity to bacterial blight of cotton and its implications for other diseases. Plant Dis 68:168–173

    Google Scholar 

  • Culp TW, Moore RE, Pitner JB (1985) Registration of PD-1 cotton. Crop Sci 25:198

    Google Scholar 

  • Delannoy E, Lyon BR, Marmey P, Jalloul A, Daniel JF, Montillet JL, Essenberg M, Nicole M (2005) Resistance of cotton towards Xanthomonas campestris pv. malvacearum. Ann Rev Phytopath 43:63–82

    CAS  Google Scholar 

  • Du X, Huang G, He S, Yang Z, Sun G, Ma X, Li N, Zhang X, Sun J, Liu M, Jia Y, Pan Z, Gong W, Liu Z, Zhu H, Ma L, Liu F, Yang D, Wang F, Fan W, Gong Q, Peng Z, Wang L, Wang X, Xu S, Shang H, Lu C, Zheng H, Huang S, Lin T, Zhu Y, Li F (2018) Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nat Genet 50:796–802

    CAS  PubMed  Google Scholar 

  • Elassbli H, Abdelraheem A, Zhu Y, Teng T, Sanogo S, Wheeler TA, Wedegaertner T, Zhang JF (2021) Evaluation and analysis of commercial cultivars and elite breeding lines for resistance to the bacterial blight pathogen race 18 in cotton. Euphytica 21:21

    Google Scholar 

  • El-Zik K, Thaxton P (1994) Breeding for resistance to bacterial blight of cotton in relation to races of the pathogen. In: challenging the future: World Cotton Research Conference-1, Brisbane, Australia, pp 236- 241

  • El-Zik KM, Thaxton PM (1997) Registration of seven multi-adversity resistant (MAR-5) germplasm lines of upland cotton. Crop sci 37:1394–1395

    Google Scholar 

  • Fang L, Wang Q, Hu Y, Jia Y, Chen J, Liu B, Zhang Z, Guan X, Chen S, Zhou B, Mei G, Sun J, Pan Z, He S, Xiao S, Shi W, Gong W, Liu J, Ma J, Cai C, Zhu X, Guo W, Du X, Zhang T (2017) Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nature Genet 49:1089–1098

    CAS  PubMed  Google Scholar 

  • Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Mitchell SE, Buckler ES (2005) Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44:1054–1064

    CAS  PubMed  Google Scholar 

  • Follin JC, Girardot B, Mangano V, Benitez R (1988) New results on inheritance of immunity to bacterial blight (Xanthomonas campestris pv. malvacearum (Smith) Dye, race 18 and 20) in the cotton plant (Gossypium hirsutum L.). Coton et Fibres Tropicales 43:167–175

    Google Scholar 

  • Hillocks RJ (1992) Cotton diseases. CAB International, Wallingford, p 415

    Google Scholar 

  • Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM (2017) Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol 17:37

    PubMed  PubMed Central  Google Scholar 

  • Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Stelly D (2015) Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. Genes Genome Genet 5:1187–1209

    Google Scholar 

  • Hunter R, Brinkerhoff L, Bird LS (1968) The development of a set of Upland cotton lines for differentiating races of Xanthomonas malvacearum. Phytopathology 58:830–832

    Google Scholar 

  • Islam MS, Thyssen GN, Jenkins JN, Zeng L, Delhom CD, McCarty JC, Fang DD (2016) A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC Genom 17:903

    Google Scholar 

  • Jalloul A, Sayegh M, Champion A, Nicole M (2015) Bacterial blight of cotton. Phytopathol Mediterr 54:3–20

    CAS  Google Scholar 

  • Jones JE, Wright SL, Bewsom LD (1958) Sources of tolerance to and inheritance of resistance to root-knot nematodes in cotton. In: 11th annual Cotton Improvement Conference, Dec 15–16, 1958. Houston, TX, USA. National Cotton Council of America, Memphis, TN. pp 34–39

  • Kappelman AJ (1982) Registration of three okra-leaf, frego-bract disease resistant cotton germplasms (Reg. No. GP 183, GP 184, and GP 185). Crop Sci 22:693–694

    Google Scholar 

  • Li T, Ma X, Li N, Zhou L, Liu Z, Han H, Gui Y, Bao Y, Chen J, Dai X (2017) Genome-wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). Plant Biotechnol J 15:1520–1532

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li B, Chen L, Sun W, Wu D, Wang M, Yu Y, Chen G, Yang W, Lin Z, Zhang X, Duan L, Yang X (2020) Phenomics-based GWAS analysis reveals the genetic architecture for drought resistance in cotton. Plant Biotechnol J 18:2533–2544

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ma Z, He S, Wang X, Sun J, Zhang Y, Zhang G, Wu L, Li Z, Liu Z, Sun G, Yan Y, Jia Y, Yang J, Pan Z, Gu Q, Li X, Sun Z, Dai P, Liu Z, Gong W, Wu J, Wang M, Liu H, Feng K, Ke H, Wang J, Lan H, Wang G, Peng J, Wang N, Wang L, Pang B, Peng Z, Li R, Tian S, Du X (2018) Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield. Nat Genet 50:803–813

    CAS  PubMed  Google Scholar 

  • Ma J, Liu J, Pei W, Ma Q, Wang N, Zhang X, Cui Y, Li D, Liu G, Wu M, Zang X, Song J, Zhang J, Yu S, Yu J (2019) Genome-wide association study of the oil content in upland cotton (Gossypium hirsutum L.) and identification of GhPRXR1, a candidate gene for a stable QTLqOC-Dt5-1. Plant Sci 286:89–97

    CAS  PubMed  Google Scholar 

  • Mihelich NT, Mulkey SE, Stec AO, Stupar RM (2020) Characterization of genetic heterogeneity within accessions in the USDA soybean germplasm collection. Plant Genome 3:e20000

    Google Scholar 

  • Naoumkina M, Thyssen GN, Fang DD, Jenkins JN, McCarty JC, Florane CB (2019) Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population. BMC Genom 20:112

    Google Scholar 

  • Nie X, Wen T, Shao P, Tang B, Nuriman-Guli A, Yu Y, Du X, You C, Lin Z (2020) High-density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China. Plant J 103:677–689

    CAS  PubMed  PubMed Central  Google Scholar 

  • Phillips AZ, Berry JC, Wilson MC, Vijayaraghavan A, Burke J, Bunn JI, Allen TW, Wheeler T, Bart RS (2017) Genomics-enabled analysis of the emergent disease cotton bacterial blight. PLoS Genet 13:e1007003

    PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rungis D, Llewellyn D, Dennis E, Lyon B (2002) Investigation of the chromosomal location of the bacterial blight resistance gene present in an Australian cotton (Gossypium hirsutum L.) cultivar. Crop Pasture Sci 53:551–560

    CAS  Google Scholar 

  • Said JI, Lin ZX, Zhang XL, Song MZ, Zhang JF (2013) A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton. BMC Genom 14:776

    CAS  Google Scholar 

  • Said JI, Knapka JA, Song MZ, Zhang JF (2015a) Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum × G. barbadense populations. Mol Genet Genom 290:1615–1625

    CAS  Google Scholar 

  • Said JI, Song MZ, Wang H, Lin Z, Zhang X, Fang DD, Zhang JF (2015b) A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations. Mol Genet Genom 290:1003–1025

    CAS  Google Scholar 

  • Su J, Ma Q, Li M, Hao F, Wang C (2018) Multi-locus genome-wide association studies of fiber-quality related traits in Chinese early-maturity upland cotton. Front Plant Sci 9:1169

    PubMed  PubMed Central  Google Scholar 

  • Sun H, Meng M, Yan Z, Lin Z, Nie X, Yang X (2019) Genome-wide association mapping of stress-tolerance traits in cotton. Crop J 7:77–88

    Google Scholar 

  • Thaxton PM, El-Zik K (1998) Host plant resistance to pathogens in MAR cotton germplasm. In: Proceedings World Cotton Research Conference-2, Athens, Greece. pp 113–119

  • Thaxton PM, El-Zik KM (2004) Registration of eight multi-adversity resistant (MAR-7B) germplasm lines of upland cotton. Crop Sci 44:1494–1495

    Google Scholar 

  • Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V (2014) Genetic diversity and population structure in the US upland cotton (Gossypium hirsutum L.). Theor Appl Genet 127:283–295

    PubMed  Google Scholar 

  • Verma JP (1986) Bacterial blight of cotton. CRC Press, Boca Raton

    Google Scholar 

  • Verma J, Singh R (1974) Recent studies on the bacterial diseases of fibre and oil seed crops in India. Curr Trends Plant Pathol 342:134–145

    Google Scholar 

  • Wallace T, El-Zik K (1989) Inheritance of resistance in three cotton cultivars to the HV1 isolate of bacterial blight. Crop Sci 29:1114–1119

    Google Scholar 

  • Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L, Zhou X, Nie X, Li Z, Guo K, Ma Y, Huang C, Jin S, Zhu L, Yang X, Min L, Yuan D, Zhang Q, Lindsey K, Zhang X (2017) Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet 49:579–587

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Wendel JF, Brubaker C, Percival A (1992) Genetic diversity in Gossypium hirsutum and the origin of Upland cotton. Am J Bot 79:1291–1310

    Google Scholar 

  • Wheeler T (2018) Bacterial blight on cotton. In: Proc Beltwide Cotton Conf., San Antonio, TX, January 3–5, 2018. Natl. Cotton Counc. Am., Memphis, TN

  • Wheeler TA, Dever JK (2020) Effects of verticillium wilt and bacterial blight on commercial varieties. pp 73–79. In: Proc Beltwide Cotton Conferences, Austin, TX, January 8–10, 2020

  • Wheeler TA, Sagaram US, Schuster GL, Gannaway JR (2007) Identification of factors that influence screening for bacterial blight resistance. J Cotton Sci 11:91–97

    Google Scholar 

  • Wright RJ, Thaxton PM, El-Zik KM, Paterson AH (1998) D subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploidy formation has created novel avenues for evolution. Genetics 149:1987–1996

    CAS  PubMed  PubMed Central  Google Scholar 

  • Xiao J, Fang D, Bhatti M, Hendrix B, Cantrell R (2010) A SNP haplotype associated with a gene resistant to Xanthomonas axonopodis pv. malvacearum in upland cotton (Gossypium hirsutum L.). Mol Breed 25:593–602

    CAS  Google Scholar 

  • Zhang JF, Abdelraheem A, Flynn R (2019) Genetic gains of Acala 1517 cotton since 1926. Crop Sci 59:1052–1061

    CAS  Google Scholar 

  • Zhang JF, Bourland FM, Wheeler TA, Wallace TP (2020a) Bacterial blight resistance in cotton: genetic basis and molecular mapping. Euphytica 216:111

    CAS  Google Scholar 

  • Zhang J, Abdelraheem A, Thyssen GN, Fang DD, Jenkins JN, McCarty JC, Wedegaertner T (2020b) 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

    CAS  Google Scholar 

  • Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20

    CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Cotton Incorporated and New Mexico State University Agricultural Experiment Station for funding support.

Funding

Cotton Incorporated (Grant 12-257) and New Mexico State University Agricultural Experiment Station.

Author information

Authors and Affiliations

  1. Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA

    Hanan Elassbli, Abdelraheem Abdelraheem, Yi Zhu, Zonghua Teng & Jinfa Zhang

  2. Texas A&M AgriLife Research, 1102 E. Drew St, Lubbock, TX, 79403, USA

    Terry A. Wheeler

  3. Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695-7620, USA

    Vasu Kuraparthy

  4. Crop Germplasm Research Unit, USDA, Agricultural Research Service, College Station, TX, 77845, USA

    Lori Hinze

  5. Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA

    David M. Stelly

  6. Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA

    Tom Wedegaertner

Authors
  1. Hanan Elassbli
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Abdelraheem Abdelraheem
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yi Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zonghua Teng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Terry A. Wheeler
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Vasu Kuraparthy
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Lori Hinze
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. David M. Stelly
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Tom Wedegaertner
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jinfa Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

HE, AA, YZ and ZT performed the screening for bacterial blight resistance. AA and HE performed the GWAS analysis. HE drafted the manuscript. TW developed the screening techniques and assisted in germplasm screening. VK developed the association mapping panel. LH and DS genotyped part of the panel. TW, LH and DS edited the MS. JZ conceived and directed the study, and helped draft and finalized the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Jinfa Zhang.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Disclaimer

Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

Additional information

Communicated by Stefan Hohmann.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (XLSX 28 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Elassbli, H., Abdelraheem, A., Zhu, Y. et al. Evaluation and genome-wide association study of resistance to bacterial blight race 18 in U.S. Upland cotton germplasm. Mol Genet Genomics 296, 719–729 (2021). https://doi.org/10.1007/s00438-021-01779-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-021-01779-w

Keywords

Search

Navigation