Expression analysis of genetic loci linked with bakanae disease resistance in japonica rice of North Western Himalayas

Bakanae disease caused by Fusarium fujikuroi is emerging as a serious threat in the production of japonica rice under high altitudes of the western Himalayas and basmati rice in northern regions. To identify resistant sources for Bakanae disease of rice, a population of 165 doubled haploids (DHs) was screened through artificial inoculation using a uniform F. fujikuroi ‘A30'virulent isolate under controlled conditions. Out of 165 inbred lines, 105 were identified as resistant, 51 moderately susceptible and nine susceptible to disease. A polymorphism survey was conducted with the help of 502 KASP markers on 12 chromosomes. On chromosome 6, a 6.25% polymorphism was found between parents, GS-88 and K-332. Two DHs, D5-2 and D5-3, showed 6% polymorphism among themselves, while DHs D49-3 and D49-4 revealed just 3.6%. Further, 19 defense-related genes located between markers, ALK_SNP_ff_2 (6.8Mb) and RM19817_SNP_nn_3 (9.7 Mb), were identified through in silico. Primers for three transcripts (Os06g0279900, Os06g0249500 and Os06g0267400) were designed through Primer 3Plus. Based on the disease severity index, two extreme resistant and susceptible DH lines, along with parents, were selected for expression studies using reverse transcription polymerase chain reaction. Expression pattern between resistant and susceptible lines varied at two different stages, viz., 10 days post inoculation (dpi) and 24 dpi. Genes Os06g0279900 and Os06g0249500 were significantly enriched at 10 dpi and Os06g0267400 at 24 dpi in resistant lines, but were absent in susceptible lines. This indicates that the response shown by resistant DH against the pathogen was much faster than that of susceptible ones. These responses at 10 and 24 dpi are suggestive of an active defense system induced by the pathogen in resistant cultivars, which involves pathogenesis-related gene expression and enrichment pathways to defense of rice plants.