Charcoal Rot Resistance in Soybean: Current Understanding and Future Perspectives

  • Vennampally Nataraj
  • Sanjeev Kumar
  • Giriraj Kumawat
  • M. Shivakumar
  • Laxman Singh Rajput
  • Milind B. Ratnaparkhe
  • Rajkumar Ramteke
  • Sanjay Gupta
  • Gyanesh K. Satpute
  • Vangala Rajesh
  • Viraj Kamble
  • Subhash Chandra


Soybean (Glycine max L.) is a leading oil seed crop in the world. Owing to climate change, its production is challenged by many forms of biotic and abiotic stresses. Charcoal rot (Macrophomina phaseolina (Tassi) Goid) disease incidence is aggravated with the increase in soil and air temperatures. Charcoal rot disease in soybean is likely to gain its economic importance with the increase in global temperature. Apart from soybean, this pathogen has a wide host range including some economical crops like sorghum and maize. So far, complete resistance to this pathogen has not been identified in any of the crop species. Field screening techniques based on the colony-forming unit index (CFUI) and estimation of root stem severity (RSS) and glasshouse screening technique, such as cut-stem inoculation, are mainly employed in identifying charcoal rot resistance sources in soybean. High-throughput screening can be possible through cut-stem inoculation technique. There are reports indicating the correlation between field screening results and results obtained from this technique, and researchers have used this technique in understanding the genetic architecture of charcoal rot resistance and in identifying candidate genes and QTL governing charcoal rot resistance. Drought conditions are favourable for disease incidence and aggressiveness. Not all drought-tolerant genotypes are resistant to charcoal rot but some drought-tolerant genotypes are found to be moderately resistant to the disease. Significant yield losses are reported due to this disease even under irrigated conditions. Research is gaining momentum in developing high-throughput, reliable and repeatable glasshouse and in vitro screening techniques to identify stable sources of resistance and in understanding the genetic architecture of charcoal rot resistance. Breeding programs are under way for developing high-yielding, charcoal-rot-resistant and drought-tolerant cultivars.


Charcoal rot Macrophomina phaseolina (Tassi) Goid Resistance and soybean 


  1. Arelli PR, Shannon JG, Mengistu A et al (2017) Registration of conventional soybean germplasm JTN-4307 with resistance to nematodes and fungal diseases. Journal of Plant Registrations 11: 192–199CrossRefGoogle Scholar
  2. Bandara YMAY, Perumal R, Little CR (2015) Integrating resistance and tolerance for improved evaluation of sorghum lines against Fusarium stalk rot and charcoal rot. Phytoparasitica. Scholar
  3. Bao Y, Vuong T, Meinhardt C, Tiffin P et al (2014) Potential of association mapping and genomic selection to explore PI 88788 derived soybean cyst nematode resistance. Plant Genome 7:1–13. Scholar
  4. Bao Y, Kurle JE, Anderson G, Young ND (2015) Association mapping and genomic prediction for resistance to sudden death syndrome in early maturing soybean germplasm. Mol Breed 35:128. Scholar
  5. Bastien M, Sonah H, Belzile F (2014) Genome wide association mapping of Sclerotinia sclerotiorum resistance in soybean with a genotyping-by-sequencing approach. Plant Genome 7:1–13. Scholar
  6. Bellaloui N, Mengistu A, Zobiole L et al (2012) Resistance to toxin-mediated fungal infection: role of lignins, isoflavones, other seed phenolics, sugars, and boron in the mechanism of resistance to charcoal rot disease in soybean. Toxin Rev 31(1–2):16–26CrossRefGoogle Scholar
  7. Chang HX, Brown PJ, Lipka AE et al (2016) Genome-wide association and genomic prediction identifies associated loci and predicts the sensitivity of tobacco ring spot virus in soybean plant introductions. BMC Genomics 17:153. Scholar
  8. Cloud GL, Rupe JC (1991) Morphological instability on a chlorate medium of isolates of Macrophomina phaseolina from soybean and sorghum. Phytopathology 78:1563Google Scholar
  9. Contreras-Soto RI, de Oliveira MB, Costenaro-da-Silva D et al (2017) Population structure, genetic relatedness and linkage disequilibrium blocks in cultivars of tropical soybean (Glycine max). Euphytica.
  10. Coser SM, Reddy RVC, Zhang J et al (2017) Genetic architecture of charcoal rot (Macrophomina phaseolina) resistance in soybean revealed using a diverse panel. Front Plant Sci 8:1626. Scholar
  11. Das IK, Prabhakar Indira S (2008) Role of stalk-anatomy and yield parameters in development of charcoal rot caused by Macrophomina phaseolina in winter sorghum. Phytoparasitica 36:199–208CrossRefGoogle Scholar
  12. Dhingra OD, Sinclair JB (1978) Biology and pathology of Macrophomina phaseolina. Universidade Federal de Viçosa, ViçosaGoogle Scholar
  13. Fehr WR, Caviness CE, Burmood DT, Pennington JS (1971) Stage of development descriptions for soybeans, Glycine max (L.) Merr. Crop Sci 11:929–931CrossRefGoogle Scholar
  14. Francl LJ, Wyllie TD, Rosenbrock SM et al (1988) Influence of crop rotation on population density of Macrophomina phaseolina in soil infested with Heterodera glycines. Plant Dis 72:760–764CrossRefGoogle Scholar
  15. Garcia-Olivares JG, Lopez-Salina EL, Cumpian-Gutierrez J et al (2012) Grain yield and charcoal rot resistance in common beans under terminal drought conditions. J Phytopathol 160:98–105CrossRefGoogle Scholar
  16. Gary FA, Mihail JD, Lavigne RJ et al (1991) Incidence of charcoal rot of sorghum and soil populations of Macrophomina phaseolina associated with sorghum and native vegetation in Somalia. Mycopathologia 114:145–151CrossRefGoogle Scholar
  17. Gillen AM, Mengistu A, Smith JR et al (2016) Registration of DT99 16864 soybean germplasm line with moderate resistance to Charcoal Rot [Macrophomina phaseolina (Tassi) Goid.]. J Plant Reg 10:309–315. Scholar
  18. Hanson AA, Lorenz AJ, Hesler LS et al (2018) Genome-wide association mapping of host-plant resistance to soybean aphid. Plant Genome 11:180011. Scholar
  19. Hernández-Delgado S, Reyes-Valdés MH, Rosales-Serna R et al (2009) Molecular markers associated with resistance to Macrophomina phaseolina (tassi) goid. in common bean. J Plant Pathol 91(1):163–170Google Scholar
  20. Iquira E, Humira S, Francois B (2015) Association mapping of QTLs for sclerotinia stem rot resistance in a collection of soybean plant introductions using a genotyping by sequencing (GBS) approach. BMC Plant Biol 15:5. Scholar
  21. Islam MS, Haque MS, Islam MM et al (2012) Tools to kill: genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina. BMC Genomics 13:493CrossRefGoogle Scholar
  22. James WC (1974) Assessment of plant disease losses. Annu Rev Phytopathol 12:27–48CrossRefGoogle Scholar
  23. Johnson HW (1958) Registration of soybean varieties: VI. Agron J 50:690–691CrossRefGoogle Scholar
  24. Kang S, Lebrun MH, Farrall L et al (2001) Gain of virulence caused by insertion of a Pot3 transposon in a Magnaporthe grisea avirulence gene. Mol Plant-Microbe Interact 14:671–674CrossRefGoogle Scholar
  25. Korte A, Farlow A (2013) The advantages and limitations of trait analysis with GWAS: a review. Plant Methods 29:9. Scholar
  26. Li H, Rodda M, Gnanasambandam A et al (2015) Breeding for biotic stress resistance in chickpea: progress and prospects. Euphytica 204:257–288CrossRefGoogle Scholar
  27. Luna MPR, Mueller D, Mengistu A et al (2017) Advancing our understanding of charcoal rot in soybeans. J Integr Pest Manag 8(1):1–8CrossRefGoogle Scholar
  28. Ma J, Hill CB, Hartman GL (2010) Production of Macrophomina phaseolina conidia by multiple soybean isolates in culture. Plant Dis 94(9):1088–1092. Scholar
  29. Madden LV, Hughes G, van den Bosch F (2007) The study of plant disease epidemics. APS Press, St. PaulGoogle Scholar
  30. Mah KM, Uppalapati SR, Tang Y et al (2012) Gene expression profiling of Macrophomina phaseolina infected Medicago truncatula roots reveals a role for auxin in plant tolerance against the charcoal rot pathogen. Physiol Mol Plant Pathol 79:21–30CrossRefGoogle Scholar
  31. Manici LM, Caputo FA, Cerato C (1995) Temperature responses of isolates of Macrophomina phaseolina from different climatic regions of sunflower production in Italy. Plant Dis 79:934–938CrossRefGoogle Scholar
  32. Mengistu A, Ray JD, Smith JR, Paris RL (2007) Charcoal rot disease assessment of soybean genotypes using a colony-forming unit index. Crop Sci 47:2453–2461CrossRefGoogle Scholar
  33. Mengistu A, Arelli PA, Bond JP et al (2011a) Evaluation of soybean genotypes for resistance to charcoal rot. Online Plant Health Prog. Scholar
  34. Mengistu A, Smith JR, Ray JD (2011b) Seasonal progress of charcoal rot and its impact on soybean productivity. Plant Dis 95:1159–1166CrossRefGoogle Scholar
  35. Mengistu A, Bond J, Nelson R et al (2013) Identification of soybean accessions resistant to Macrophomina phaseolina by field screening and laboratory validation. Online Plant Health Prog. Scholar
  36. Mengistu A, Ray JD, Smith JR et al (2014) Maturity effects on colony-forming units of Macrophomina phaseolina infection as measured using near-isogenic lines of soybeans. J Crop Improv 28:38–56. Scholar
  37. Mengistu A, Ray JD, Smith JR et al (2018) Effect of charcoal rot on selected putative drought tolerant soybean genotypes and yield. Crop Prot 105:90–10CrossRefGoogle Scholar
  38. Meyer WA, Sinclair JB, Khare MM (1974) Factors affecting charcoal rot of soybean seedlings. Phytopathology 64:845–849CrossRefGoogle Scholar
  39. Moellers TC, Singh A, Zhang J et al (2017) Main and epistatic loci studies in soybean for Sclerotinia sclerotiorum resistance reveal multiple modes of resistance in multi-environments. Sci Rep 7:3554. Scholar
  40. Muchero W, Ehlers JD, Close TJ et al (2009) Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L) Walp]. Theor Appl Genet 118:849–863CrossRefGoogle Scholar
  41. Muchero W, Ehlers JD, Close TJ et al (2011) Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L) Walp.]. BMC Genomics 12:8Google Scholar
  42. Olaya G, Abawi GS, Weeden NF (1996) Inheritance of resistance to Macrophomina phaseolina and identification of RAPD markers linked to the resistance genes in beans. Phytopathology 86:674–679CrossRefGoogle Scholar
  43. Paris RL, Mengistu A, Tyler JM et al (2006) Registration of soybean germplasm line DT97-4290 with moderate resistance to charcoal rot. Crop Sci 46:2324–2325CrossRefGoogle Scholar
  44. Pastor-Corrales MA, Abawi GS (1988) Reactions of selected bean accessions to infection by Macrophomina phaseolina. Plant Dis 72:39–41CrossRefGoogle Scholar
  45. Pawlowski ML, Hill CB, Hartman GL (2015) Resistance to charcoal rot identified in ancestral soybean germplasm. Crop Sci 55:1230–1235. Scholar
  46. Pearson CAS, Schwenk FW, Crowe FJ et al (1984) Colonization of soybean roots by Macrophomina phaseolina. Plant Dis 68:1086–1088CrossRefGoogle Scholar
  47. Qin J, Song Q, Shi A et al (2017) Genome-wide association mapping of resistance to Phytophthora sojae in a soybean (Glycine max (L.) Merr.) germplasm panel from maturity groups IV and V. PLoS One 12(9):e0184613. Scholar
  48. Radwan O, Rouhana LV, Hartman GL et al (2014) Genetic mechanisms of host-pathogen interactions for charcoal rot in soybean. Plant Mol Biol Rep 32:617–629CrossRefGoogle Scholar
  49. Rao DNV, Shinde VK (1985) Inheritance of charcoal rot resistance in sorghum. J Maharashtra Agric Univ 10:54–56Google Scholar
  50. Reznikov S, Chiesa MA, Pardo EM et al (2019) Soybean-Macrophomina phaseolina-specific interactions and identification of a novel source of resistance. Phytopathology 109(1):63–73. Scholar
  51. Ritchie SW, Hanway JJ, Thompson HE et al (1989) How a soybean plant develops. Spec. Rep. No. 53. Iowa State Univ. Sci. Technol. Coop. Ext. Serv., Ames, IAGoogle Scholar
  52. Saleh AA, Ahmed HU, Todd TC et al (2010) Relatedness of Macrophomina phaseolina isolates from tallgrass prairie, maize, soybean and sorghum. Mol Ecol 19:79–91CrossRefGoogle Scholar
  53. Schmitt DP, Shannon G (1992) Differentiating soybean response to Heterodera glycines races. Crop Sci 32:275–277CrossRefGoogle Scholar
  54. Schneider R, Rolling W, Song Q et al (2016) Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea. BMC Genomics 17:607. Scholar
  55. Shivakumar M, Kumawat G, Gireesh C et al (2018) Soybean MAGIC population: a novel resource for genetics and plant breeding. Curr Sci 114:906–908. Scholar
  56. Short GE, Wyllie TD, Bristow PR (1980) Survival of Macrophomina phaseolina in soil and in residue of soybean. Phytopathology 70:13–17CrossRefGoogle Scholar
  57. Silva MP, Klepadlo M, Gbur EE et al (2019) QTL mapping of charcoal rot resistance in PI 567562A soybean accession. Crop Sci 59:1–6CrossRefGoogle Scholar
  58. Smith GS, Carvil ON (1997) Field screening of commercial and experimental soybean cultivars for their reaction to Macrophomina phaseolina. Plant Dis 81:363–368CrossRefGoogle Scholar
  59. Smith GS, Wyllie TD (1999) Charcoal rot. In: Hartman GL, Sinclair JB, Rupe JC (eds) Compendium of soybean disease, 4th edn. American Phytopathological Society, St. Paul, pp 29–31Google Scholar
  60. Smith JR, Ray JD, Mengistu A (2018) Genotypic differences in yield loss of irrigated soybean attributable to charcoal rot. J Crop Improv. Scholar
  61. Su G, Suh SO, Schneider RW et al (2001) Host specialization in the charcoal rot fungus, Macrophomina phaseolina. Phytopathology 91:120–126CrossRefGoogle Scholar
  62. Sun J, Li L, Zhao J et al (2014) Genetic analysis and fine mapping of RpsJS, a novel resistance gene to Phytophthora sojae in soybean [Glycine max (L.) Merr]. Theor Appl Genet 127:913–919. Scholar
  63. Talukdar A, Verma K, Gowda DSS et al (2009) Molecular breeding for charcoal rot resistance in soybean I. Screening and mapping population development. Indian J Genet 69:367–370Google Scholar
  64. Tenkouano A, Miller FR, Frederiksen RA et al (1993) Genetics of non senescence and charcoal rot resistance in sorghum. Theor Appl Genet 85(5):644–648CrossRefGoogle Scholar
  65. Todd TC, Pearson CAS, Schwenk FW (1987) Effect of Heterodera glycines on charcoal rot severity in soybean cultivars resistant and susceptible to soybean cyst nematode. Ann Appl Nematol 1:35–40Google Scholar
  66. Tooley PW, Grau CR (1984) Field characterization of rate reducing resistance to Phytophthora megasperma f. sp. glycines in soybean. Phytopathology 74:1201–1208CrossRefGoogle Scholar
  67. Twizeyimana M, Hill CB, Pawlowski M et al (2012) A cut stem inoculation technique to evaluate soybean for resistance to Macrophomina phaseolina. Plant Dis 96:1210–1215CrossRefGoogle Scholar
  68. Vinholes P, Rosado R, Roberts P et al (2019) Single nucleotide polymorphism-based haplotypes associated with charcoal rot resistance in Brazilian soybean germplasm. Agron J 111:182–192CrossRefGoogle Scholar
  69. Vuong TD, Sonah H, Meinhardt CG et al (2015) Genetic architecture of cyst nematode resistance revealed by genome wide association study in soybean. BMC Genomics 16:593. Scholar
  70. Wei W, Mesquita ACO, Figueiró AA (2017) Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil. BMC Genomics 18:849. Scholar
  71. Weiss MG, Stevenson TM (1955) Registration of soybean varieties: V. Agron J 47:541–543CrossRefGoogle Scholar
  72. Wen Z, Tan R, Yuan J et al (2014) Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean. BMC Genomics 15:11. Scholar
  73. Williams A, Hector PQ, Victor MG (2009) Grain sorghum varieties reaction [Sorghum bicolor (L.) Moench] to Macrophomina phaseolina (Tassi) Goid. Revista Mexicana de Fitopatología 27:148–155Google Scholar
  74. Wrather JA, Anderson TR, Arsyad DM et al (2001) Soybean disease loss estimates for the top ten soybean-producing countries in 1998. Canadian J Plant Pathol 23:115–121CrossRefGoogle Scholar
  75. Wrather JA, Shannon JG, Carter TE (2008) Reaction of drought-tolerant soybean genotypes to Macrophomina phaseolina. Plant Health Prog. Scholar
  76. Young PA (1949) Charcoal rot of plants in east Texas. Bulletin Texas Agricultural Experimental Station No. 33Google Scholar
  77. Zhang J, Singh A, Mueller DS et al (2015) Genomewide association and epistasis studies unravel the genetic architecture of sudden death syndrome resistance in soybean. Plant J 84:1124–1136. Scholar
  78. Zhang H, Li C, Davis EL et al (2016) Genome-Wide Association Study of resistance to soybean cyst nematode (Heterodera glycines) HG type 2.5.7 in wild soybean (Glycine soja). Front Plant Sci 7:1214. Scholar
  79. Zhao X, Han Y, Li Y et al (2015) Loci and candidate gene identification for resistance to Sclerotinia sclerotiorum in soybean (Glycine max L. Merr.) via association and linkage maps. Plant J 82:245–255. Scholar
  80. Zveibil A, Mor N, Gnayem N et al (2012) Survival, host–pathogen interaction, and management of Macrophomina phaseolina on strawberry in Israel. Plant Dis 96:265–272CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Vennampally Nataraj
    • 1
  • Sanjeev Kumar
    • 1
  • Giriraj Kumawat
    • 1
  • M. Shivakumar
    • 1
  • Laxman Singh Rajput
    • 1
  • Milind B. Ratnaparkhe
    • 1
  • Rajkumar Ramteke
    • 1
  • Sanjay Gupta
    • 1
  • Gyanesh K. Satpute
    • 1
  • Vangala Rajesh
    • 1
  • Viraj Kamble
    • 1
  • Subhash Chandra
    • 1
  1. 1.ICAR- Indian Institute of Soybean ResearchIndoreIndia

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