*4.1. Plant Material, Cultivation and HNT Stress Treatment*

Eight *Oryza sativa* ssp. *indica* (IR123, IR62266-42-6-2, IR64 and IR72) and *japonica* (CT9993-5-10-1M, M202, Moroberekan and Taipei309) cultivars with different HNT tolerance in the vegetative stage under controlled environmental conditions [28] were used (Table 1). IR72, Taipei309 and Moroberekan were characterized as HNT tolerant; IR64, IR123 and CT9993-5-10-1M showed intermediate tolerance; and M202 and IR62266-42-6-2 were sensitive to HNT under these conditions [28]. The seeds for all cultivars were produced at the IRRI. The experiments were carried out during the WS and DS at the IRRI (14◦11'N, 121◦15'E, 21 MASL) in the Philippines. The seeds were pre-germinated in water after incubation at 50 ◦C for 3 d to break dormancy and were then sown in seeding trays. Fourteen-day old seedlings were transplanted to the field to a spacing of 0.2 × 0.2 m. The WS experiment was started in June 2011, with four seedlings per hill and each cultivar (42–48 hills) randomly assigned to

two replicate plots per treatment. Phosphorus (15 kg·ha−<sup>1</sup> p as single superphosphate), potassium (20 kg·ha−<sup>1</sup> K as KCl), and zinc (2.5 kg·ha−<sup>1</sup> Zn as zinc sulfate heptahydrate) were applied to all plots as a basal fertilizer a day before transplanting. Nitrogen (N as urea) was incorporated in four splits (30 kg·ha−<sup>1</sup> as basal, 20 kg·ha−<sup>1</sup> at mid-tillering, 30 kg·ha−<sup>1</sup> at panicle initiation (PI), and 20 kg·ha−<sup>1</sup> just before heading). For the DS experiment, seedlings were transplanted in a staggered approach with one batch in December 2013 and two batches in January 2014. The stagger sowing was based on the phenology data from the first experiment. Each cultivar was randomly assigned to five replicate plots per treatment with one seedling per hill and a total of 28–40 hills per plot. Basal fertilizer (30 kg·ha−<sup>1</sup> <sup>P</sup> as single superphosphate, 40 kg·ha−<sup>1</sup> K as KCl, and 5 kg·ha−<sup>1</sup> Zn as zinc sulfate heptahydrate) was applied one day before transplanting. N fertilizer as urea was applied in four splits (45 kg·ha−<sup>1</sup> as basal, 30 kg·ha−<sup>1</sup> at mid-tillering, 45 kg·ha−<sup>1</sup> at PI, and 30 kg·ha−<sup>1</sup> just before heading).

During the day (6 a.m–6 p.m.), plants were exposed to ambient conditions (compare Figure A2 and Table 1). Overnight (6 p.m.–6 a.m.), plants were exposed to the temperature treatments in manually-covered tents with temperature-control devices as described previously [25]. Air conditioners were programmed to maintain the temperature setting at control (22 ◦C) or HNT (28 ◦C). Temperature and relative humidity were monitored by sensors connected to data loggers (HOBO, Onset Computer Corporation, Bourne, MA, USA). Temperature treatments started at the panicle initiation stage and lasted until physiological maturity (Figure A1). During the flowering stage, panicles that had flowered for at least 50% were identified and tagged. These were then collected, together with the corresponding flag leaves, the next morning just before the tents were opened (~4 a.m.–6 a.m.). All samples were collected in liquid nitrogen and stored at −80 ◦C until use.

#### *4.2. Weather Data*

Weather data (radiation, sunshine duration, rainfall, relative humidity, maximum temperature (Tmax) and minimum temperature (Tmin)) recorded by the IRRI wetland agrometeorological station were obtained from the IRRI Climate Unit.
