Fine mapping of qBK1.2, a major QTL governing resistance to bakanae disease in rice

Amar Kant Kushwaha; Ranjith Kumar Ellur; Sarvesh Kumar Maurya; Gopala Krishnan S; Bishnu Maya Bashyal; Prolay Kumar Bhowmick; K K Vinod; Haritha Bollinedi; Nagendra Kumar Singh; Ashok Kumar Singh

doi:10.3389/fpls.2023.1265176

Fine mapping of qBK1.2, a major QTL governing resistance to bakanae disease in rice

Front Plant Sci. 2023 Nov 10:14:1265176. doi: 10.3389/fpls.2023.1265176. eCollection 2023.

Affiliations

¹ Division of Crop Improvement and Biotechnology, Indian Council of Agricultural Research (ICAR)-Central Institute for Subtropical Horticulture, Lucknow, India.
² Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India.
³ Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India.
⁴ National Professor B.P. Pal Chair, Indian Council of Agricultural Research (ICAR)-National Institute of Plant Biotechnology, New Delhi, India.

Abstract

Bakanae disease caused by Fusarium fujikuroi is an emerging disease of rice causing losses in all rice-growing regions around the world. A BC₂F₂ population was developed by backcrossing the recurrent parent Pusa Basmati 1121 (PB1121) with the recombinant inbred line RIL28, which harbors a major quantitative trait locus (QTL) governing resistance to bakanae, qBK1.2. MassARRAY-based single-nucleotide polymorphism (SNP) assays targeting the genomic region of qBK1.2 helped in fine mapping the QTL to a region of 130 kb between the SNP markers rs3164311 and rs3295562 using 24 recombinants. In-silico mining of the fine-mapped region identified 11 putative candidate genes with functions related to defense. The expression analysis identified two significantly differentially expressed genes, that is, LOC_Os01g06750 and LOC_Os01g06870, between the susceptible genotype PB1121 and the resistant genotypes Pusa1342 and R-NIL4. Furthermore, the SNPs identified in LOC_Os01g06750 produced minor substitutions of amino acids with no major effect on the resistance-related functional motifs. However, LOC_Os01g06870 had 21 amino acid substitutions, which led to the creation of the leucine-rich repeat (LRR) domain in the resistant genotype Pusa1342, thereby making it a potential candidate underlying the major bakanae-resistant QTL qBK1.2. The markers used in the fine mapping program are of immense utility in marker-assisted breeding for bakanae resistance in rice.

Keywords: NILs (Near isogenic lines); QTL; SNPs; bakanae; candidate genes; fine-mapping; resistance; rice.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The research work was funded by the Indian Council of Agricultural Research, New Delhi, India, under the project Incentivizing Research in Agriculture.