Drought Response QTLs in a Super Basmati × Azucena Population by High-density GBS-based SNP Linkage Mapping

Basmati rice is favoured for its grain type and aroma, but its production is vulnerable due to climate change and freshwater accessibility. Discovery and refinement of genomic regions conferring drought tolerance are needed to develop new drought tolerant Basmati varieties. Using Recombinant Inbred Lines (RILs) derived from a cross between drought-sensitive elite Basmati variety, ‘Super Basmati’, and drought-tolerant japonica cultivar, ‘Azucena’, a linkage map was constructed with 862 high-quality GBS-based SNP markers. Thirty-three QTLs were detected for yield-related and physiological traits. Of five QTL clusters, two were identified as novel on chromosome 7 and 11 for shoot dry weight and water uptake that could be designated as promising QTLs, and their candidate gene analysis suggested contributions to yield in the ‘Super Basmati’ background. Comparing the greenhouse and field results, this study suggests that selection of drought tolerance donor varieties must be matched with the target growth stage of drought tolerance needed. Along with fine mapping and functional marker selection, the QTL clusters identified can be further tested to contribute to Basmati rice improvement.