Marker Aided Incorporation of Saltol, a Major QTL Associated with Seedling Stage Salt Tolerance, into Oryza sativa 'Pusa Basmati 1121'.

Pusa Basmati 1121 (PB1121), an elite Basmati rice cultivar is vulnerable to salinity at seedling stage. A study was undertaken to impart seedling-stage salt tolerance into PB1121 by transferring a quantitative trait locus (QTL), Saltol, using FL478 as donor, through marker assisted backcrossing. Sequence tagged microsatellite site (STMS) marker RM 3412, tightly linked to Saltol was used for foreground selection. Background recovery was estimated using 90 genome-wide STMS markers. Systematic phenotypic selection helped in accelerated recovery of recurrent parent phenome (RPP). A set of 51 BC3F2 lines homozygous for Saltol were advanced to develop four improved near isogenic lines (NILs) of PB1121 with seedling stage salt tolerance. The background genome recovery in the NILs ranged from 93.3 to 99.4%. The improved NILs were either similar or better than the recurrent parent PB1121 for yield, grain and cooking quality and duration. Biochemical analyses revealed significant variation in shoot and root Na+ and K+ concentrations. Correlation between shoot and root Na+ concentration was stronger than that between root and shoot K+ concentration. The effect of QTL integration into the NILs was studied through expression profiling of OsHKT1;5, one of the genes present in the Saltol region. The NILs had significantly higher OsHKT1;5 expression than the recurrent parent PB1121, but lower than FL478 on salt exposure validating the successful introgression of Saltol in the NILs. This was also confirmed under agronomic evaluation, wherein the NILs showed greater salt tolerance at seedling stage. One of the NILs, Pusa1734-8-3-3 (NIL3) showed comparable yield and cooking quality to the recurrent parent PB1121, with high field level seedling stage salinity tolerance and shorter duration. This is the first report of successful introgression of Saltol into a Basmati rice cultivar.

Mapping quantitative trait loci responsible for resistance to Bakanae disease in rice.

BACKGROUND: Bakanae or foot rot disease caused by Fusarium fujikuroi [teleomorph: Gibberella fujikuroi (Sawada) Ito] is emerging as a serious disease in rice. The disease causes both quantitative and qualitative losses to the grains under the field conditions. Breeding for resistance to Bakanae disease is a promising strategy to manage this emerging disease. In this study, we used a population of 168 F14 recombinant inbred lines (RILs) derived from two indica rice parents Pusa 1342, a highly resistant variety and Pusa Basmati 1121, a highly susceptible variety to map quantitative trait loci (QTLs) governing resistance against Bakanae disease. RESULTS: The disease reaction of 168 F14 RILs were measured on the seedlings inoculated using Fusarium fujikuroi culture using high-throughput screening protocol under glasshouse conditions. Utilizing inclusive composite interval mapping, three QTLs governing resistance to Bakanae were identified, namely qBK1.1, qBK1.2 and qBK1.3 which accounted 4.76, 24.74 and 6.49 % of phenotypic variation, respectively. The major effect QTL designated qBK1.2 was mapped in 0.26 Mb region between RM5336 and RM10153. A total of 55 annotated genes were identified within the identified QTL region qBK1.2. CONCLUSIONS: The novel QTLs identified in this study are useful resource for efficiently breeding rice cultivars resistant to Bakanae disease. This is the first report on identification of QTLs governing resistance against Bakanae in rice using inclusive composite interval mapping strategy in a RIL population.

Analysis of differentially expressed genes in leaf rust infected bread wheat involving seedling resistance gene Lr28.

Genome-wide transcriptome analysis of seedling resistance to leaf rust conferred by Lr28 gene in wheat (Triticum aestivum L.) was conducted to identify differentially expressed genes during incompatible interaction. A virulent leaf rust race 77-5 was used for inoculation of resistant (HD2329+Lr28) and susceptible (HD2329 - Lr28) wheat NILs and cDNA-AFLP analyses was carried out. As many as 223 differential transcripts appeared following leaf rust inoculation; these included 122 transcripts that appeared exclusively in resistant NIL, whereas 39 transcripts appeared both in resistant and susceptible NILs. Sequence analyses of 37 transcripts, which appeared in the resistant NIL revealed that 15 transcripts had homology with genes involved in protein synthesis, signal transduction, transport, disease resistance and metabolism. The functions of remaining 22 transcripts could not be determined; these included six novel genes reported for the first time in wheat. Specific primers could be designed for 18 of the 37 transcripts, which included genes with putative and unknown functions. Quantitative real time PCR analysis was conducted using these 18 pairs of primers. A majority (13) of these transcripts appeared within 48h reaching a peak value at 96h in resistant NIL signifying their role in providing leaf rust resistance.