*2.1. Plant Materials and Experimental Treatments*

Rice genotypes used in this study were: Swarna, a South Asian *indica* mega variety, susceptible to drought stress, and DTY-IL (designation IR 96321-1447-165-B-3-1-2), a highly drought-tolerant F7 introgression line containing N22 fragments in a Swarna background. DTY-IL is sister line of IR 96321-1447-651-B1-1-2, which was recently released as a drought-tolerant variety in Nepal [13].

Field experiments were conducted in the 2014 and 2015 dry season (DS), and were laid out in an augmented RCB design. The 2014 trial had 420 entries and 6 checks with 5 blocks in a single row per plot while the 2015 trial, had 46 entries and 2 checks with 4 blocks in four rows per plot. For both trials, only checks were repeated based on the number of blocks. For the drought screening, water was removed from the field around 28–30 days after transplanting by opening all drainage canals around the field. PVC pipes measuring 1.1 to 1.2-m long were installed in different parts of the field for water table measurements. The PVC pipes were placed 1 m below the soil surface. The water table was measured regularly starting 1 day after draining the field.

A pot experiment was arranged in a randomized complete block design with two treatments (well-watered and 2-weeks drought-stressed), two genotypes, and six replications in a greenhouse at the International Rice Research Institute (Los Baños, Philippines) from July to November 2015. Three pre-germinated seeds of the two genotypes were initially seeded on white porcelain pots filled with 15 kg of clean puddled field soil (not sterilized). Upon seedling establishment, a healthy seedling was retained in each pot and grown under a well-watered condition in the greenhouse until the booting stage before initiating a dry-down experiment. A day before imposing stress, all the pots were saturated with water and allowed to drain excess water for 24 h to maintain the field capacity (FC) so that the soil moisture amount in each pot was uniform. Then each pot was weighed to know the amount of water at FC. The temperature inside the greenhouse during the stress induction was at a maximum of 30–34 ◦C and a minimum of 23–26 ◦C, and a day-time relative humidity of 69%–95% (Figure S1A). During the drought stress period, the pots were weighed daily, and the difference in weight on subsequent days was corrected by adding water to maintain the required FC [49]. For RDS, water was withheld at the reproductive R2 stage, on discrete morphological criteria as described by [50], until the soil moisture level dropped to 75% FC and was maintained for nine days, whereas control plants were well-watered. At day 10, FC was reduced to 50% for three more days (Figure S1B). Flag-leaf and whole panicle samples of well-watered and drought-stressed treatments were collected at the R3 stage [50] on the 12th day of RDS and immediately flash-frozen in liquid nitrogen. Four independent biological replicates for each tissue and each genotype sample were harvested.
