Skip to main content

Genome Wide Association Study (GWAS) on Disease Resistance in Maize

Abstract

With the reduction in the genotyping cost of the sequencing technique, improved statistical methods, and increased computational efficiency, association mapping, especially genome wide association study (GWAS), is widely used to dissect the architecture of the several complex traits. Several review papers and chapters on QTL mapping of disease resistance in maize have been published so far. However, a general review and compilation of the recent GWAS studies in the disease resistance of maize is limited. This chapter compiles and integrates recent studies of the five major diseases of maize using GWAS. The economically important diseases in maize, along with the novel SNPs and QTLs’ hotspots, are highlighted in the chapter. The advantages of association mapping over QTL mapping, along with working model of GWAS, are briefly discussed. At the end, we discuss on the limitation of the GWAS and future perspectives on the identification of novel disease resistance genes.

Keywords

  • Maize
  • GWAS
  • Quantitative trait loci
  • Disease resistance
  • Association mapping

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-030-20728-1_6
  • Chapter length: 18 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   149.00
Price excludes VAT (USA)
  • ISBN: 978-3-030-20728-1
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   199.99
Price excludes VAT (USA)
Hardcover Book
USD   199.99
Price excludes VAT (USA)

References

  • Acuna TB, Rebetzke G, He X, Maynol E, Wade L (2014) Mapping quantitative trait loci associated with root penetration ability of wheat in contrasting environments. Mol Breed 34(2):631–642

    CrossRef  CAS  Google Scholar 

  • Balint-Kurti P, Carson M (2006) Analysis of quantitative trait loci for resistance to southern leaf blight in juvenile maize. Phytopathology 96(3):221–225

    CAS  PubMed  CrossRef  Google Scholar 

  • Balint-Kurti PJ, Johal GS (2009) Maize disease resistance. In: Handbook of maize: its biology. Springer, New York, pp 229–250

    CrossRef  Google Scholar 

  • Balint-Kurti P, Zwonitzer JC, Wisser RJ, Carson M, Oropeza-Rosas MA, Holland JB, Szalma SJ (2007) Precise mapping of quantitative trait loci for resistance to southern leaf blight, caused by Cochliobolus heterostrophus race O, and flowering time using advanced intercross maize lines. Genetics 176(1):645–657

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Bent AF, Kunkel BN, Dahlbeck D, Brown KL, Schmidt R, Giraudat J, Leung J, Staskawicz BJ (1994) RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. Science 265(5180):1856–1860

    CAS  PubMed  CrossRef  Google Scholar 

  • Bentolila S, Guitton C, Bouvet N, Sailland A, Nykaza S, Freyssinet G (1991) Identification of an RFLP marker tightly linked to theHt1 gene in maize. Theor Appl Genet 82(4):393–398

    CAS  PubMed  CrossRef  Google Scholar 

  • Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19(7):889–890

    CAS  PubMed  CrossRef  Google Scholar 

  • Castro A, Tacaliti M, Giménez D, Tocho E, Dobrovolskaya O, Vasicek A, Collado M, Snape J, Börner A (2008) Mapping quantitative trait loci for growth responses to exogenously applied stress induced hormones in wheat. Euphytica 164(3):719

    CAS  CrossRef  Google Scholar 

  • Causse M, Saliba-Colombani V, Lecomte L, Duffe P, Rousselle P, Buret M (2002) QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits. J Exp Bot 53(377):2089–2098

    CAS  PubMed  CrossRef  Google Scholar 

  • Causse M, Duffe P, Gomez M, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55(403):1671–1685

    CAS  PubMed  CrossRef  Google Scholar 

  • Chen Y, Chao Q, Tan G, Zhao J, Zhang M, Ji Q, Xu M (2008) Identification and fine-mapping of a major QTL conferring resistance against head smut in maize. Theor Appl Genet 117(8):1241

    CAS  PubMed  CrossRef  Google Scholar 

  • Chern M, Canlas PE, Fitzgerald HA, Ronald PC (2005) Rice NRR, a negative regulator of disease resistance, interacts with Arabidopsis NPR1 and rice NH1. Plant J 43(5):623–635

    CAS  PubMed  CrossRef  Google Scholar 

  • Clements M, Maragos C, Pataky J, White D (2004) Sources of resistance to fumonisin accumulation in grain and Fusarium ear and kernel rot of corn. Phytopathology 94(3):251–260

    CAS  PubMed  CrossRef  Google Scholar 

  • Dhugga KS (2005) Plant Golgi cell wall synthesis: from genes to enzyme activities. Proc Natl Acad Sci U S A 102(6):1815–1816

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Ding J-Q, Wang X-M, Chander S, Yan J-B, Li J-S (2008) QTL mapping of resistance to Fusarium ear rot using a RIL population in maize. Mol Breed 22(3):395–403

    CrossRef  Google Scholar 

  • Doerge RW (2002) Multifactorial genetics: mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3(1):43

    CAS  PubMed  CrossRef  Google Scholar 

  • Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES (2005) Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44(6):1054–1064

    CAS  PubMed  CrossRef  Google Scholar 

  • Flor HH (1971) Current status of the gene-for-gene concept. Annu Rev Phytopathol 9(1):275–296

    CrossRef  Google Scholar 

  • Foolad M (1999) Comparison of salt tolerance during seed germination and vegetative growth in tomato by QTL mapping. Genome 42(4):727–734

    CAS  CrossRef  Google Scholar 

  • Gowda M, Das B, Makumbi D, Babu R, Semagn K, Mahuku G, Olsen MS, Bright JM, Beyene Y, Prasanna BM (2015) Genome-wide association and genomic prediction of resistance to maize lethal necrosis disease in tropical maize germplasm. Theor Appl Genet 128(10):1957–1968

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Hammond-Kosack KE, Jones JD (1997) Plant disease resistance genes. Annu Rev Plant Biol 48(1):575–607

    CAS  CrossRef  Google Scholar 

  • Ishikawa A, Tanaka H, Nakai M, Asahi T (2003) Deletion of a chaperonin 60β gene leads to cell death in the Arabidopsis lesion initiation 1 mutant. Plant Cell Physiol 44(3):255–261

    CAS  PubMed  CrossRef  Google Scholar 

  • Johal GS, Briggs SP (1992) Reductase activity encoded by the HM1 disease resistance gene in maize. Science 258(5084):985–987

    CAS  PubMed  CrossRef  Google Scholar 

  • Jones JD, Dangl JL (2006) The plant immune system. Nature 444(7117):323

    CAS  PubMed  CrossRef  Google Scholar 

  • Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178(3):1709–1723

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, Zwonitzer JC, Kresovich S, McMullen MD, Ware D (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43(2):163

    CAS  PubMed  CrossRef  Google Scholar 

  • Levings CS, Siedow JN (1992) Molecular basis of disease susceptibility in the Texas cytoplasm of maize. In: 10 years plant molecular biology. Springer, Dordrecht, pp 135–147

    Google Scholar 

  • Li X, Wang Z, Gao S, Shi H, Zhang S, George M, Li M, Xie C (2008) Analysis of QTL for resistance to head smut (Sporisorium reiliana) in maize. Field Crop Res 106(2):148–155

    CrossRef  Google Scholar 

  • Liu X, Huang M, Fan B, Buckler ES, Zhang Z (2016) Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genet 12(2):e1005767

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Lu X, Brewbaker J (1999) Molecular mapping of QTLs conferring resistance to Sphacelotheca reiliana (Kühn) Clint. Maize Genetics Cooperation Newsletter (73)

    Google Scholar 

  • Lübberstedt T, Xia X, Tan G, Liu X, Melchinger A (1999) QTL mapping of resistance to Sporisorium reiliana in maize. Theor Appl Genet 99(3–4):593–598

    PubMed  CrossRef  Google Scholar 

  • Mammadov J, Sun X, Gao Y, Ochsenfeld C, Bakker E, Ren R, Flora J, Wang X, Kumpatla S, Meyer D (2015) Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.). BMC Genomics 16(1):916

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262(5138):1432–1436

    CAS  PubMed  CrossRef  Google Scholar 

  • McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C (2009) Genetic properties of the maize nested association mapping population. Science 325(5941):737–740

    CAS  PubMed  CrossRef  Google Scholar 

  • Nimchuk Z, Eulgem T, Holt Iii BF, Dangl JL (2003) Recognition and response in the plant immune system. Annu Rev Genet 37(1):579–609

    CAS  PubMed  CrossRef  Google Scholar 

  • Nordborg M, Tavaré S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18(2):83–90

    CAS  PubMed  CrossRef  Google Scholar 

  • Olukolu BA, Negeri A, Dhawan R, Venkata BP, Sharma P, Garg A, Gachomo E, Marla S, Chu K, Hasan A (2013) A connected set of genes associated with programmed cell death implicated in controlling the hypersensitive response in maize. Genetics 193(2):609–620

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Park KJ, Sa KJ, Kim BW, Koh H-J, Lee JK (2014) Genetic mapping and QTL analysis for yield and agronomic traits with an F2: 3 population derived from a waxy corn× sweet corn cross. Genes Genomics 36(2):179–189

    CrossRef  Google Scholar 

  • Parlevliet JE (2002) Durability of resistance against fungal, bacterial and viral pathogens; present situation. Euphytica 124(2):147–156

    CAS  CrossRef  Google Scholar 

  • Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335(6192):721

    CAS  PubMed  CrossRef  Google Scholar 

  • Pérez Brito D, Jeffers D, González de León D, Khairallah M, Cortés C, Velázquez C, Azpíroz S, Srinivasan G (2001) QTL mapping of Fusarium moniliforme ear rot resistance in highland maize. Agrociencia, Mexico, 35(2)

    Google Scholar 

  • Perkins J, Pedersen W (1987) Disease development and yield losses associated with northern leaf blight on corn. Plant Dis 71(10):940–943

    CrossRef  Google Scholar 

  • Poland JA, Balint-Kurti PJ, Wisser RJ, Pratt RC, Nelson RJ (2009) Shades of gray: the world of quantitative disease resistance. Trends Plant Sci 14(1):21–29

    CAS  PubMed  CrossRef  Google Scholar 

  • Poland JA, Bradbury PJ, Buckler ES, Nelson RJ (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci 108(17):6893–6898

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Pratt RC, Gordon SG (2006) Breeding for resistance to maize foliar pathogens. Plant Breed Rev 27:119

    CAS  Google Scholar 

  • Price AH (2006) Believe it or not, QTLs are accurate! Trends Plant Sci 11(5):213–216

    CAS  PubMed  CrossRef  Google Scholar 

  • Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8):904

    CAS  PubMed  CrossRef  Google Scholar 

  • Pring DR, Lonsdale DM (1989) Cytoplasmic male sterility and maternal inheritance of disease susceptibility in maize. Annu Rev Phytopathol 27(1):483–502

    CrossRef  Google Scholar 

  • Quarrie S, Gulli M, Calestani C, Steed A, Marmiroli N (1994) Location of a gene regulating drought-induced abscisic acid production on the long arm of chromosome 5A of wheat. Theor Appl Genet 89(6):794–800

    CAS  PubMed  CrossRef  Google Scholar 

  • Ray J, Yu L, McCouch S, Champoux M, Wang G, Nguyen H (1996) Mapping quantitative trait loci associated with root penetration ability in rice (Oryza sativa L.). Theor Appl Genet 92(6):627–636

    CAS  PubMed  CrossRef  Google Scholar 

  • Rodríguez-Gacio MDC, Iglesias-Fernández R, Carbonero P, Matilla ÁJ (2012) Softening-up mannan-rich cell walls. J Exp Bot 63(11):3976–3988

    CrossRef  CAS  Google Scholar 

  • Romay MC, Millard MJ, Glaubitz JC, Peiffer JA, Swarts KL, Casstevens TM, Elshire RJ, Acharya CB, Mitchell SE, Flint-Garcia SA (2013) Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol 14(6):R55

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Sax K (1923) The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8(6):552–560

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, Long Q, Nordborg M (2012) An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat Genet 44(7):825

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM (2011) Genome-wide atlas of transcription during maize development. Plant J 66(4):553–563

    CAS  PubMed  CrossRef  Google Scholar 

  • Simcox KD, Bennetzen JL (1993) The use of molecular markers to study Setosphaeria turcica resistance in maize. Phytopathology 83(12):1326–1330

    CAS  CrossRef  Google Scholar 

  • Singh B, Singh AK (2015) Marker-assisted plant breeding: principles and practices. Springer

    Google Scholar 

  • Song W-Y, Wang G-L, Chen L-L, Kim H-S, Pi L-Y, Holsten T, Gardner J, Wang B, Zhai W-X, Zhu L-H (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270(5243):1804–1806

    CAS  PubMed  CrossRef  Google Scholar 

  • Tan Y, Sun M, Xing Y, Hua J, Sun X, Zhang Q, Corke H (2001) Mapping quantitative trait loci for milling quality, protein content and color characteristics of rice using a recombinant inbred line population derived from an elite rice hybrid. Theor Appl Genet 103(6–7):1037–1045

    CAS  CrossRef  Google Scholar 

  • Technow F, Bürger A, Melchinger AE (2013) Genomic prediction of northern corn leaf blight resistance in maize with combined or separated training sets for heterotic groups. G3 3(2):197–203

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES IV (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28(3):286

    CAS  PubMed  CrossRef  Google Scholar 

  • Tian Y, Zhang H, Xu P, Chen X, Liao Y, Han B, Chen X, Fu X, Wu X (2015) Genetic mapping of a QTL controlling leaf width and grain number in rice. Euphytica 202(1):1–11

    CrossRef  Google Scholar 

  • Ullstrup A (1972) The impacts of the southern corn leaf blight epidemics of 1970-1971. Annu Rev Phytopathol 10(1):37–50

    CrossRef  Google Scholar 

  • Wang J, Levy M, Dunkle LD (1998) Sibling species of Cercospora associated with gray leaf spot of maize. Phytopathology 88(12):1269–1275

    CAS  PubMed  CrossRef  Google Scholar 

  • Wang S, Basten C, Zeng Z (2007) Windows QTL cartographer 2.5. Department of statistics. North Carolina state university, Raleigh

    Google Scholar 

  • Wang M, Yan J, Zhao J, Song W, Zhang X, Xiao Y, Zheng Y (2012) Genome-wide association study (GWAS) of resistance to head smut in maize. Plant Sci 196:125–131

    CAS  PubMed  CrossRef  Google Scholar 

  • Wisser RJ, Balint-Kurti PJ, Nelson RJ (2006) The genetic architecture of disease resistance in maize: a synthesis of published studies. Phytopathology 96(2):120–129

    CAS  PubMed  CrossRef  Google Scholar 

  • Xiao W, Zhao J, Fan S, Li L, Dai J, Xu M (2007) Mapping of genome-wide resistance gene analogs (RGAs) in maize (Zea mays L.). Theor Appl Genet 115(4):501–508

    CAS  PubMed  CrossRef  Google Scholar 

  • Yin X, Wang Q, Yang J, Jin D, Wang F, Wang B, Zhang J (2003) Fine mapping of the Ht2 (Helminthosporium turcicum resistance 2) gene in maize. Chin Sci Bull 48(2):165–169

    CAS  CrossRef  Google Scholar 

  • Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38(2):203

    CAS  PubMed  CrossRef  Google Scholar 

  • Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178(1):539–551

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Zhang Z, Ersoz E, Lai C-Q, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42(4):355

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

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

    CAS  CrossRef  Google Scholar 

  • Zila CT, Samayoa LF, Santiago R, Butrón A, Holland JB (2013) A genome-wide association study reveals genes associated with Fusarium ear rot resistance in a maize core diversity panel. G3 3(11):2095–2104

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Vivek Shrestha .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Verify currency and authenticity via CrossMark

Cite this chapter

Shrestha, V., Awale, M., Karn, A. (2019). Genome Wide Association Study (GWAS) on Disease Resistance in Maize. In: Wani, S.H. (eds) Disease Resistance in Crop Plants. Springer, Cham. https://doi.org/10.1007/978-3-030-20728-1_6

Download citation