Unveiling key genetic determinants of charcoal rot resistance in soybean via genome wide association studies

Vennampally Nataraj¹Pawan Kumar Amrate²Milind B. Ratnaparkhe^1*Shivakumar Maranna¹Laxman Rajput^1,3Nisha Agrawal¹Rishi Raghuvanshi¹Kriti Pathak¹Saloni Mandloi^1,2Salikram Mohre²BHOJARAJA NAIK K⁴Manoj Kumar Srivastava²Giriraj Kumawat¹VANGALA RAJESH¹SANJAY Gupta¹Annapurna Chitikineni⁵Rajeev K Varshney⁵K.H Singh¹

• ¹ICAR - Indian Institute of Soybean Research, Indore, India
• ²Jawaharlal Nehru Krishi Vishwavidyalaya, Jabalpur, Madhya Pradesh, India, Jabalpur, India
• ³ICAR - Central Arid Zone Research Institute, Indra Colony, India
• ⁴ICAR - Indian Institute of Seed Science, Bengaluru, Karnataka, India, Bengaluru, India
• ⁵International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India

Abstract: Charcoal rot is a soil and seed-borne disease caused by a necrotrophic fungal pathogen-Macrophomina phaseolina. To understand the genetic architecture of resistance against it, a genome-wide association study (GWAS) was conducted based on a glasshouse experiment and a three-year field experiment using 214 diverse soybean accessions. In glasshouse experiment at seedling stage, eight SNPs were identified; one SNP each on chromosome (chr) 8 (S8_16817767), chr 10 (S10_52066337), chr 14 (S14_50857981), chr 15 (S15_32620059), chr 17 (S17_1689021) and chr 18 (S18_9413708), while two SNPs (S16_34569104 and S16_37878937) were located on chr 16. In case of field experiment at reproductive stage, ten SNPs were identified; one SNP each on chr 12 (S12_14977708), chr 14 (S14_51754926) and chr 16 (S16_33491560). Two SNPs each were identified on chr 6 (S6_41109641 and S6_41863847) and chr 10 (S10_40644409 and S10_44768495), while three SNPs (S18_25004105, S18_55655188 and S18_56366541) were located on chr 18. The SNP S14_50857981 associated with seedling resistance, and S14_51754926 associated with adult plant resistance, are present within 1 Mb region and will be of immense importance for charcoal rot resistance breeding. The putative candidate gene analysis for identified SNPs revealed 23 genes with annotations associated with defense response pathways. Three genes encoding a NB-ARC domain associated with defence response, were present near S14_50857981. The genotype PI 159923 was found to be resistant both under field and glasshouse conditions, it will be employed as parents in breeding for high-yielding and charcoal rot resistance. Our study provides new insights into charcoal rot resistance in soybean, identifying key SNPs and genes that can aid future breeding programs for developing climate-resilient crops.