Drought response QTLs in a Super Basmati × Azucena population by high‐density GBS‐based SNP linkage mapping

Abstract

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 droughttolerant japonica cultivar, 'Azucena', a linkage map was constructed with 862 highquality 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.

Quantitative trait locus mapping for important yield traits of a sorghum-sudangrass hybrid using a high-density single nucleotide polymorphism map

“…They are also the preferred regions for fine mapping and candidate gene identification ( Xie et al., 2008 ). It can introduce genes related to crop quality, yield, and resistance into recipient crops simultaneously, control the correlation between traits in stable “QTL hotspots” or “QTL clusters” of different traits, and regulate pleiotropy of various traits through different metabolic pathways ( Huang and Yan, 2019 ; Waheed et al., 2021 ). Numerous studies have shown that the phenomenon of “QTL hotspots” or “QTL clusters” are prevalent in a variety of crops, such as crested wheatgrass ( Yang et al., 2022 ), wheat ( Cui et al., 2016 ), and sorghum ( Mace et al., 2012 ).…”

Breeding for Rice Aroma and Drought Tolerance: A Review

“…Selection of drought-tolerant genotypes may consider the targeted rice growth stage [65]. Screening under drought stress conditions allows selection of the drought-tolerant plants within each line.…”

“…However, they did not conduct any formal analysis for aroma in these lines. Waheed et al [65] reported one QTL on chromosome 7 and another on chromosome 11 for shoot dry weight and water uptake under drought conditions in recombinant inbred lines (RILs) developed from a cross between Super Basmati, an aromatic variety, and Azucena, a drought-tolerant cultivar. Nevertheless, they did not determine the aroma status in these lines.…”

Molecular mapping of drought-responsive QTLs during the reproductive stage of rice using a GBS (genotyping-by-sequencing) based SNP linkage map

“…The QTLs identi ed were thoroughly compared with previously identi ed QTLs for any colocalization using the Q-Taro (QTL Annotation Rice Online) database (Kulkarni et al, 2020). Cluster of QTLs governing various traits located within <30 cM (Waheed et al, 2021) on the linkage map were also reported.…”