Identification of significant SNPs and candidate loci for blast disease resistance via GWAS and population structure analysis in ARC panel of Oryza sativa

Parinda Barua; Munmi Phukon; Sunita Munda; Vipin Ranga; R Sruthi; Jyoti Lekha Borah; Janardan Das; Pompi Dutta; Ashok Bhattacharyya; Mahendra Kumar Modi; Sanjay Kumar Chetia

doi:10.1007/s12298-024-01518-6

Identification of significant SNPs and candidate loci for blast disease resistance via GWAS and population structure analysis in ARC panel of Oryza sativa

Physiol Mol Biol Plants. 2024 Oct;30(10):1673-1689. doi: 10.1007/s12298-024-01518-6. Epub 2024 Oct 26.

Authors

Affiliations

¹ Assam Agricultural University-Assam Rice Research Institute (AAU-ARRI), Titabar, Jorhat, Assam 785630 India.
² DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India.
³ Assam Agricultural University, Jorhat, Assam 785013 India.
⁴ Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India.

PMID: 39506992
PMCID: PMC11535146 (available on 2025-10-01)
DOI: 10.1007/s12298-024-01518-6

Abstract

Pyricularia (syn. Magnaporthe) oryzae is responsible for the blast disease in rice resulting in a greater extent of yield loss. However, some of the cultivars of rice have the ability to survive this devastating infection due to the presence of R (resistance) genes. Therefore, genome wide association study (GWAS) was undertaken using a panel of 400 rice landraces (ARC panel) and a set of filtered 38,723 single nucleotide polymorphisms (SNPs). The highest SNPs were mapped to chromosome 1 with a number of 4332 SNPs and lowest (2252) in chromosome 12. The ARC panel was evaluated phenotypically which revealed that 6% of the selected cultivars has resistance to rice blast disease with SES score of 1. The majority of the resistant cultivars belong to the group Asra of the panel. The population structure analysis was executed wherein three genetic subpopulations were identified namely RC1, RC2, RC3 and an admixture population constituting 48 accessions. Further, GWAS detected 15 significant association signal with P value in the range of 1.03E-05 to 1.03E-04, effect ranged from - 1.18 to 1.06, phenotypic variance explained was from 0 to 7.14%, R² of 0.047 to 0.058, and minor allele frequency of 0.107 to 0.444. Eleven (Os01g39980, Os01g56130, Os01g67100, Os01g67110, Os03g41030, Os04g33310, Os07g42104, Os09g06464, Os09g08920, Os09g38800, Os12g37680) out of these 15 significant associations were identified as the candidate loci for the blast resistance in rice that will serve as an important genetic resistance source to be introgressed into an elite rice line in future breeding programs for deciphering blast resistance in rice. The GWAS study presented in this article helped to uncover significant gene regions which encode proteins to resist blast infection in rice plant. This is the first report on the GWAS analysis for blast resistance in unique landraces of rice from Northeast India employing single nucleotide polymorphism.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-024-01518-6.

Keywords: Blast resistance; Candidate loci; Genome wide association study; Population structure; Pyricularia (syn. Magnaporthe) oryzae.

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