Discovery of QTLs for water mining and water use efficiency traits in rice under water-limited condition through association mapping

Developing trait introgressed rice cultivars is essential to sustain yield under aerobic conditions. Here, we report DNA markers governing variability in root traits, water use efficiency (WUE) and other biometric traits like total leaf area by association mapping. A set of 173 diverse rice germplasm accessions were phenotyped for root traits in specially designed root structures and WUE using carbon isotope discrimination (Δ¹³C) during the monsoon season (July to October) of two consecutive years (2007 and 2008). The panel was genotyped using 291 SSR markers spanning the entire genome of rice. Root biomass varied between 1.8 and 16.3 g plant^?1 while root length between 22 and 78 cm representing significant genetic variability. Similarly, Δ¹³C varied from 18 to 23 ‰. The SSR markers showed extensive polymorphism with around 73 % of all the markers revealing polymorphism information content values more than 0.5. Model-based structure analysis using the squared-allele frequency correlations revealed six subgroups among the panel with an average LD decay of about 10–20 cM. The Benjamini–Hochberg analysis was carried out to compute the false discovery rate combined with the analysis of effective LD. A total of 82 markers were involved in 175 significant (corrected P values and Q values <0.05) marker–trait associations (MTAs) across experiment 1 and experiment 2 and for the pooled data. Out of these, 22 markers were found to be associated with more than one trait. Common markers with significant associations were discovered for root biomass, total leaf area and total biomass suggesting the interdependency of these traits. Finally, 12 markers showed significant and stable MTAs across the experiments for different traits. An in silico analysis indicated that 45 % of the MTAs overlapped with previously reported QTLs and can be used for QTL introgression through breeding.