Sporadic rice tungro virus disease outbreaks in India lead to a maximum production loss of 53% in a district and 2% in the country. An epidemic during 2001 in three districts of West Bengal caused an un-milled rice production loss of 0.5 million tons valued at US $ 65 million (Muralidharan et al. 2003a). Saito et al. (1976) and Hibino et al. (1978) assumed tungro disease to be caused by a unique combination of a spherical picorna virus (RTSV) and a bacilliform DNA pararetro virus (RTBV). Green leafhopper (GLH) species Nephotettix virescens is the most dominant vector that transmits virus particles in India (Siddiq et al. 1994). RTBV has been shown to be integrated with the host genome (Harper et al. 2002). Based on all the circumstantial evidence, Muralidharan et al. (2003b) showed tungro to be primarily caused by RTSV. Resistance to RTSV was suspected to be located on chr. 11 in Oryza officinalis (Kobayashi et al. 1992). In ARC 11554, resistance to both RTSV and GLH appeared to be tightly linked and controlled by a dominant gene located within 5.5 cM of RFLP marker RZ262 on chr. 4 (Sebastian et al. 1996). In Utri Rajappan, two dominant and complementary genes were shown to confer resistance to RTSV (Prasad et al. 2004). RTSV resistance in Utrimerah was reported to be monogenic recessive and located on chr. 7 near 78cM (~22 Mb) of marker RM336 (Choi et al. 2005). Two cultivars, Vikramarya (India, IET 7302) and Utri Rajapan (Indonesia, IRG ACC. No. 16684) were known to possess resistance (score 1) to RTSV (Ebron et al. 1994, Prasad et al. 2004). We studied the genetic basis of resistance to RTSV in these two cultivars by using QTL analysis. Two mapping populations were developed using susceptible cultivar TN1 (score 9) x Vikramarya, and TN1 x Utri Rajapan. The F₂ progenies of both mapping populations along with parents were screened for the reaction to RTSV in a glasshouse (28±2°C, >95% RH) using a locally virulent population of N. virescens. Seeds of each F₂ progeny and parents were sown singly in lines in plastic trays (60 x 40 cm) at a spacing of 5 cm between plants and 20 cm between lines. Initially GLH was provided with an acquisition feeding on RTSV infected plants for 12 h. Fifteen-days old seedlings were individually capped with a Mylar cage into which 2-3 viruliferous GLH were released for 24 h and the reaction was scored 15 days later. There was no mortality of insects in any of the inoculations made on using RTSV carrying GLH after acquisition feeding on infected plants or RTSV-free GLH. The parents TN1 succumbed to RTSV while Utri Rajapan and Vikramarya remained resistant. The RTSV resistance in both F₂ progeny populations showed continuous frequency distribution (Fig. 1).

Parental polymorphism was studied using 120 evenly distributed rice microsatellite markers covering the 12 chr. (Chen et al. 1997). In Utri Rajapan and Vikramarya, 58 and 63 markers were found polymorphic. As selective genotyping was shown to be effective to identify specific associated regions of the chromosomes (Nandi et al. 1997), 20 plants each showing extremely resistant and susceptible reactions to tungro were assayed individually with all these markers. Initially, markers RM 542 (chr. 7) and RM6844 (chr. 2) in Utri Rajapan, and RM427 (chr. 7) and RM6902 (chr. 1) in Vikramarya were found to be associated with RTSV resistance.

A 3 Mb region of the sequence encompassing the associated marker was considered and based on the number of repeats, ~50 microsatellite markers were selected. They were used to survey the parental polymorphism and to screen all 220 F₂ plants. A local linkage map was constructed using Mapmaker Exp 3.0 for each of the four genomic regions and QTLs were identified using Mapmaker QTL version 1.1 (Table 1, Fig. 2). Two QTLs controlling RTSV resistance were detected on chr. 7 and 2 in Utri Rajapan explaining 40.8 and 21.6 % of the phenotypic variance, respectively, and two on chr. 7 and 1 in Vikramarya explaining 18.7 and 16.4 %, respectively. From the sequence information (www.tigr.org), we have deduced the putative candidate genes for resistance in the mapped regions that included NB-ARC, LRR, protease inhibitors and serine threonine kinases. Further work is in progress to complete the high-resolution mapping.

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