Genome-Wide Association Mapping in BAAP highlights multiple Genes driving seasonal phenotypic variation against Sheath Blight in Rice

Naveenkumar R^1,2SIDDHARTH PANDA^1,3Challa Vijaya Kumar Reddy⁴Prabhukarthikeyan S. R¹SANGEETHA G⁵Anthony John Travis⁶Gareth John Norton⁶Adam Huw Price⁶Anandan Annamalai^1,7*LICON KUMAR ACHARYA^8,9*

• ¹ICAR - National Rice Research Institute, Cuttack, India
• ²Amrita Vishwa Vidyapeetham, Coimbatore, India
• ³Siksha O Anusandhan, Bhubaneswar, India
• ⁴Odisha University of Agriculture and Technology, Bhubaneswar, India
• ⁵ICAR - Indian Institute of Horticultural Research, Bengaluru, India
• ⁶University of Aberdeen School of Biological Sciences, Aberdeen, United Kingdom
• ⁷ICAR-National Institute of Seed Science & Technology, Mau, India
• ⁸ICAR - National Research Institute for Integrated Pest Management, New Delhi, India
• ⁹ICAR - Indian Agricultural Research Institute, New Delhi, India

Sheath blight in rice caused by Rhizoctonia solani is one of the deadliest diseases penalising yield by almost half under severe infections. Complete and durable resistance has not yet been found making it essential to understand the genetic basis of partial or quantitative resistance. In this study, we used Genome Wide Association Studies in the diverse rice genotypes of the Bengal-Assam-Aus Panel, evaluated across three growing seasons (Wet season 2018, Wet season 2019, and Dry season 2019), to identify genomic regions linked to sheath blight tolerance. Disease severity was measured through Ppercent Ddisease Iindex (PDI) and aArea Uunder Ddisease Pprogress Ccurve (AUDPC). The genotypes showed wide variation and near-normal trait distributions, suggesting multiple genes controlling resistance. Combined analysis revealed strong genotype × environment interactions, so separate GWAS were conducted for each season. Twenty seven different loci associated with sheath blight response were detected, with three consistent, high-confidence peaks located on chromosomes 1, 9, and 10. Within these regions, three genes stood out, LOC_Os01g03360 (Bowman–Birk protease Formatted: Font: Italic This is a provisional file, not the final typeset article inhibitor, BBTI4), LOC_Os09g11790 (defensin-like peptide, DEFL14), and LOC_Os10g04860 (aldehyde oxidase, AO2). These genes likely contribute through protease inhibition, antifungal activity, and hormone regulation. When combined together, they can form multi-layered defense system that helps rice manage sheath blight stress. The findings provide new insights into the genetic and biochemical basis of sheath blight tolerance and identify practical targets for breeding.