QTL mapping and candidate gene mining for sheath blight resistance in rice (Oryza sativa L.) using QTLseqr approach

Abstract

Sheath blight (ShB) caused by Rhizoctonia solani is a devastating disease that poses a major threat to rice (Oryza sativa L.) production worldwide. In this study, next generation sequencing assisted bulk segregant analysis (BSA) integrated with R package i.e. QTLseqr was utilized to identify QTL regions controlling the sheath blight resistance trait. F3 mapping progenies for ShB resistance trait was derived from the cross between susceptible rice cultivar PR121 and resistant donor IET 22769. Based on sheath blight screening of F3 progenies under artificial inoculation conditions, fifteen resistant (20-30 cm lesion height) and fifteen highly susceptible (70-85 cm lesion height) progenies were selected. DNA of the selected progenies were extracted and bulked respectively to constitute ShB-R and ShB-S bulks respectively. The two bulks along with parents were sequenced at > 20 X read depth. A total of 11,45,820 high-quality single nucleotide polymorphism (SNPs) were used for QTL-seq analysis using QTLseqr package. QTL analysis identified five QTLs namely qShB1, qShB3, qShB5.1, qShB5.2 and qShB6 on chromosome 1, 3, 5 and 6, respectively for resistance to ShB. A total of 69 candidate genes were identified within the QTL regions including leucine-rich repeat receptor-like kinase, coiled-coil nucleotide-binding and transcription factor protein etc. which might play a significant role in defense mechanism against R. solani. The identified QTLs and candidate genes can be further studied to understand genetics of ShB resistance in rice and to develop ShB resistant varieties.