Phenotypic characterization of soybean genotypes for rust (Phakopsora pachyrhizi sydow) resistance

Introduction

Soybean (Glycine max (L.) Merr.) is an important oilseed and protein crop and is often described as a "miracle crop" or "golden bean" because its seed generally contains about 38-42% protein and 18-20% oil (Anonymous, 2022; Tiwari, 2022) [1,34] . Soybean protein has a favorable amino-acid profile and contributes substantially to human food, livestock feed and vegetable-oil requirements (Anonymous, 2022; Tiwari, 2022) [1,34] . Asian soybean rust, caused mainly by Phakopsora pachyrhizi Sydow, is one of the most destructive foliar diseases of soybean in tropical and subtropical soybean-growing regions (Bromfield, 1984; Goellner et al., 2010; Reis, 2022) [4,11,29] . The pathogen is an obligate biotroph, produces abundant urediniospores and can infect leaves rapidly under humid conditions, resulting in premature defoliation, reduced pod filling and heavy yield losses under favourable epidemics (Miles et al., 2003; Dalla Lana et al., 2015; Godoy et al., 2016) [24,7,12] . Rust symptoms commonly begin as small chlorotic to greyish lesions that later turn tan to reddish-brown, usually on the lower leaf surface, where uredinia develop and release spores (Miles et al., 2005; Hartman et al., 2015) [23,13] . Disease development is favoured by moderate temperature, high humidity and prolonged leaf wetness, and the pathogen can spread over long distances through wind-borne urediniospores (Bonde et al., 2006; Schmale and Ross, 2015; Belinelli et al., 2025) [3,32,2] . In India, soybean rust has been reported as an economically important disease in several soybean-growing areas, including Maharashtra, Karnataka and Madhya Pradesh (Rao et al., 1995; Mahajan et al., 2019) [28,20] . The epidemic occurrence of rust during favourable seasons has emphasized the need for systematic screening of germplasm and incorporation of resistance into adapted varieties (Khot et al., 2010; Kurundkar et al., 2011; Mahajan et al., 2019) [15,16,20] . Host resistance is considered a sustainable component of rust management; however, resistance governed by single major genes can be overcome by virulent pathogen populations (Pham et al., 2009; Twizeyimana and Hartman, 2012) [27,35] . Therefore, resistant donor identification, differential reaction studies, new Rpp-source discovery and integration with molecular characterization are required for durable resistance breeding (Whitham et al., 2016; Childs et al., 2018; Dormatey et al., 2020) [38,6,9] . Because soybean rust epidemics are influenced by airborne inoculum movement, host susceptibility and favourable weather, field screening remains important for identifying resistant donors that can be confirmed later through molecular and multilocation studies (Hartman et al., 2015; Martinelli et al., 2015; Mueller et al., 2016; Belinelli et al., 2025) [13,21,25,2] . Broadening the resistance base through wild and related legume sources, gene pyramiding and host-pathogen studies is important for improving the durability of soybean rust resistance (Kawashima et al., 2016; Dormatey et al., 2020) [14, 9] . Transfer of a pigeonpea-derived resistance gene into soybean demonstrated that related legumes can provide valuable resistance resources against Asian soybean rust (Kawashima et al., 2016) [14] . Accurate phenotypic screening remains essential because molecular tools, image-based phenotyping and advanced disease-detection methods require reliable field-based disease classification for validation ( [22,21,5,31] . Hence, the present study was undertaken to characterize soybean genotypes for rust reaction and to identify resistant or moderately resistant genotypes useful for further crop improvement (Mayee and Datar, 1986; Martinelli et al., 2015) [22,21] .

Material and Methods

Experimental material

The experimental material consisted of 30 soybean genotypes collected from different sources. The list of genotypes and their pedigree is presented in Table 1.

Experimental method

The field experiment was conducted at Agricultural Research Station, Kasbe-Digraj, Sangli, during Kharif 2018.

The experiment was laid out in a randomized block design with three replications and all recommended agronomic practices were followed to raise a healthy crop according to university recommendations.

Screening for rust resistance

Rust severity was recorded on five randomly selected plants from each plot using the 0-9 scale proposed for plant-disease assessment (Mayee and Datar, 1986) [22] . The rating scale used for rust assessment is given in Table 2. More than 50% area covered, lesions/pustules very common on all parts, defoliation common; death of plants common; damage more than 50%. Percent Disease Intensity (PDI) was calculated using the standard formula suggested by Wheeler (1969) [37] 𝑃𝐷𝐼 = Sum of individual disease ratings (Number of plants examined × Maximum disease grade) × 100

The categorization of soybean genotypes on the basis of PDI is presented in Table 3. [33,19,17] . [30, 20, 7] . The comparative performance of the top-yielding genotypes and the relationship between rust severity and seed yield are illustrated in Fig. 1 and Fig. 2.

References

1. Anonymous. Agricultural statistics and soybean production estimates for 2021-22. Government/official statistical sources; 2022.
2. Belinelli EO, Fantin LH, Canteri MG, Braga K, Cirilo ER, Romeiro NML, et al. Numerical simulation of atmospheric transport and dispersion of Phakopsora pachyrhizi urediniospores in South America using the state of Parana-Brazil as a model. arXiv. 2025:arXiv:2504.03433.
3. Bonde MR, Nester SE, Austin CN, Stone CL, Frederick RD, Hartman GL, et al. Evaluation of virulence of Phakopsora pachyrhizi and P. meibomiae isolates. Plant Dis. 2006;90:708-716.
4. Bromfield KR. Soybean rust. Monograph No. 11. St. Paul (MN): American Phytopathological Society; 1984.
5. Cavanagh H, Mosbach A, Scalliet G, Lind R, Endres RG. Physics-informed deep learning characterizes morphodynamics of Asian soybean rust disease. arXiv. 2021:arXiv:2110.07345.
6. Childs SP, King ZR, Walker DR, Harris DK, Pedley KF, Buck JW, et al. Discovery of a seventh Rpp soybean rust resistance locus in soybean accession PI 605823. Theor Appl Genet. 2018;131:27-41.
7. Dalla Lana F, Ziegelmann PK, Maia AHN, Godoy CV, Del Ponte EM. Meta-analysis of the relationship between crop yield and soybean rust severity. Phytopathology. 2015;105:307-315.
8. Devaraj L, Jahagirdar S, Basavaraja GT, Patil RH, Hundekar AR, Virupakshaprabhu H. Development of spray schedule involving fungicides and botanicals against Asian soybean rust caused by Phakopsora pachyrhizi Sydow. Karnataka J Agric Sci. 2013;26:6566.
9. Dormatey R, Sun C, Ali K, Coulter JA, Bi Z. Gene pyramiding for sustainable crop improvement against biotic and abiotic stresses. Agronomy. 2020;10:1255.
10. El-Hasan A, Walker F, Klaiber I, Schone J, Pfannstiel J, Voegele RT. New approaches to manage Asian soybean rust (Phakopsora pachyrhizi) using Trichoderma spp. or their antifungal secondary metabolites. Metabolites. 2022;12:507.
11. Goellner K, Loehrer M, Langenbach C, Conrath U, Koch E, Schaffrath U. Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Mol Plant Pathol. 2010;11:169-177.
12. Godoy CV, Seixas CDS, Soares RM, MarcelinoGuimaraes FC, Meyer MC, Costamilan LM. Asian soybean rust in Brazil: past, present, and future. Pesq Agropec Bras. 2016;51:407-421.
13. Hartman GL, Rupe JC, Sikora EJ, Domier LL, Davis JA, Steffey KL, editors. Compendium of soybean diseases and pests. 5th ed. St. Paul (MN): American Phytopathological Society; 2015.
14. Kawashima CG, Guimaraes GA, Nogueira SR, MacLean D, Cook DR, Steuernagel B, et al. A pigeonpea gene confers resistance to Asian soybean rust in soybean. Nat Biotechnol. 2016;34:661-665.
15. Khot GG, Kurundkar BP, Shinde VS, Mahajan SB, Tirmali AM, Deshmukh MP. Identification of soybean genotypes for slow rusting. J Plant Dis Sci. 2010;5:192194.
16. Kurundkar BP, Shinde VS, Mahajan SB, Deshmukh MP. Reaction of soybean genotypes against rust. J Plant Dis Sci. 2011;6:134-136.
17. Kuswantoro H. Genetic variability and selection of soybean genotypes for yield and agronomic traits. Biodiversitas. 2019;20:3564-3570.
18. Levy C, Techagwa JS, Tattersfield JR. The status of soybean rust in Zimbabwe and South Africa. In: International Journal of Advanced Biochemistry Research https://www.biochemjournal.com Proceedings of the Brazilian Soybean Congress; 2002; Foz do Iguacu, Parana, Brazil.
19. Li YH, Reif JC, Ma YS, Hong HL, Liu ZX, Chang RZ, et al. Targeted association mapping demonstrating the complex molecular genetics of phenotypic variation in soybean. Plant Genome. 2019;12:180053.
20. Mahajan SB, Deokar CD, Deshmukh MP, Khot GG, Deshmukh DP, Karade VM. Identification of phenotypic markers linked with rust resistance in soybean. Res J Life Sci Bioinform Pharm Chem Sci. 2019:180-192.
21. Martinelli F, Scalenghe R, Davino S, Panno S, Scuderi G, Ruisi P, et al. Advanced methods of plant disease detection: a review. Agron Sustain Dev. 2015;35:1-25.
22. Mayee CD, Datar VV. Phytopathometry. Technical Bulletin No. 1. Parbhani (India): Marathwada Agricultural University; 1986.
23. Miles MR, Hartman GL, Frederick RD. Management of Asian soybean rust. In: Proceedings of the 2005 Illinois Crop Protection Technology Conference; 2005; Urbana, IL. Urbana: University of Illinois Extension; 2005. p. 23-27.
24. Miles MR, Hartman GL, Levy C, Morel W. Current status of soybean rust control by fungicides. Pestic Outlook. 2003;14:197-200.
25. Mueller DS, Wise KA, Sisson AJ, Smith DL, Sikora EJ, Bradley CA, et al., editors. A farmer's guide to soybean diseases. St. Paul (MN): American Phytopathological Society; 2016.
26. Patil PV, Basavaraja GT, Hussain SM. Two genotypes of soybean as promising source of resistance to rust caused by Phakopsora pachyrhizi Sydow. Soybean Res. 2004;2:46-47.
27. Pham TA, Miles MR, Frederick RD, Hill CB, Hartman GL. Differential responses of resistant soybean entries to isolates of Phakopsora pachyrhizi. Plant Dis. 2009;93:224-228.
28. Rao VG, Raut VM, Patil PV. Outbreak of soybean rust in Maharashtra. J Maharashtra Agric Univ. 1995;20:479-480.
29. Reis EM. Phakopsora pachyrhizi (soyabean rust). CABI Compendium. Wallingford (UK): CAB International; 2022.
30. Rodrigues B, Serafim F, Nogueira APO, Hamawaki OT, de Sousa LB, Hamawaki RL. Correlation between traits in soybean naturally infected with Asian rust. Genet Mol Res. 2015;14:17718-17729.
31. Saleem N, Balu A, Jubery TZ, Singh AK, Singh A, Sarkar S, et al. Class-specific data augmentation for plant stress classification. arXiv. 2024:arXiv:2406.13081.
32. Schmale DG, Ross SD. Highways in the sky: scales of atmospheric transport of plant pathogens. Annu Rev Phytopathol. 2015;53:591-611.
33. Singh RJ, Vatsa VP. Genetic variability and character association in soybean. Legume Res. 2009;32:290-292.
34. Tiwari SP. Emerging trends in soybean industry. Indian Farming. 2022;72:3-7.
35. Twizeyimana M, Hartman GL. Pathogenic variation of Phakopsora pachyrhizi isolates on soybean entries with different resistance genes. Plant Dis. 2012;96:75-81.
36. Velasquez AC, Castroverde CDM, He SY. Plantpathogen warfare under changing climate conditions. Curr Biol. 2018;28.
37. Wheeler BEJ. An introduction to plant diseases. London: John Wiley and Sons Ltd.; 1969. p. 301.
38. Whitham SA, Qi M, Innes RW, Ma W, Lopes-Caitar V, Hewezi T. Molecular soybean-pathogen interactions. Annu Rev Phytopathol. 2016;54:443-468.
39. Yang XB, Tschanz AT, Dowler WM, Wang TC. Development of yield loss models in relation to reductions of components of soybean infected with Phakopsora pachyrhizi. Phytopathology. 1991;81:14201426.
40. Yorinori JT, Paiva WM, Frederick RD, Costamilan LM, Bertagnolli PF, Hartman GL, et al. Epidemics of soybean rust (Phakopsora pachyrhizi) in Brazil and Paraguay from 2001 to 2003. Plant Dis. 2005;89:675677.