Abstract
Sheath blight is an emerging disease of rice that appears in rice production areas worldwide. A total of 294 O. nivara accessions along with susceptible check PR114, the cultivated rice, were screened against sheath blight under field conditions for three consecutive years. Based on screening, 15 accessions were identified that showed moderate resistance reaction to sheath blight across the years. However, none of the accession showed highly resistant reaction. Sheath blight resistance was found to be quantitative controlled based on near normal distribution of lesion length. These 15 accessions further showed same level of resistance in detached tiller culture method and are proposed as the candidate donors for resistance to sheath blight, to be used in rice breeding programme. Further Multi locus-GWAS implemented using the 3VmrMLM model in 294 O. nivara accessions using 22,261 SNPs identified 11 marker-trait associations (MTAs) on 8 different chromosomes with the LOD score ranging from 3.34 to 20.58, while 10 out of 11 significant showed significant statistical difference based on Kruskal–Wallis test. Based on the LD decay in the panel, an interval of ± 300 kb of each significant MTA was investigated to identify candidate genes governing resistance to sheath blight. Among 11 QTL regions, a total of 19 candidate genes were found to be differentially expressed in response to the sheath blight pathogen based on in-depth in silico analysis, including those encoding lignin biosynthesis proteins, calcineurin B, thaumatin proteins, protein kinase domains, NBS-LRR domains, and cytochrome P450 oxidoreductases. The study highlighted 15 sheath blight resistant donors along with 10 QTL regions and 19 candidate genes that will provide a platform for understanding genetic basis of sheath blight resistance in rice.
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Acknowledgements
The authors are grateful to Dr Kumari Neelam, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana for sharing the O. nivara germplasm.
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The study was funded by the Science and Engineering Research Board, Department of Science and Technology, Govt. of India with project no. EMR/2017/003069 funded to Dr Dharminder Bhatia.
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DB conceived the idea, planned, and supervised the experiments. JSL, AK, DB screened all the experimental material against sheath blight and analyzed the data. RSRG, DB did analysis of genotype, GWAS, candidate gene analysis. DB, JSL, RSRG wrote the manuscript.
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Bhatia, D., Lore, J.S., Kamboj, A. et al. Genome wide association study identifies donors and candidate genes underlying QTLs for resistance to sheath blight in a collection of Oryza nivara (Sharma et Shastry) accessions. Euphytica 220, 65 (2024). https://doi.org/10.1007/s10681-024-03325-2
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DOI: https://doi.org/10.1007/s10681-024-03325-2