Gene expression profiling
Transcriptome profiling of flag leaves in response to WD stress in TAM 111 and TAM 112 at different stages identified 5754 dif- ferentially expressed genes (Supplementary Fig. S4). Based on the physiological data, the grain filling stage in TAM 111 and TAM 112 was selected for detailed functional classification and analy- sis (Fig. 4). WD through the grain-filling stage resulted in altered expression of more genes in TAM 112 (3197 transcripts) com- pared to TAM 111 (2131 transcripts). A joint analysis indicated that 1657 transcripts were commonly altered in both cultivars, while 474 and 1540 transcripts were unique to TAM 111 and TAM 112 respectively (Fig. 4A). qRT-PCR analysis on selected candidate genes confirmed the gene expression patterns observed in microar- ray data (Supplementary Fig. 8). The unique genes differentially expressed in response to water deficit stress suggested distinct molecular responses. A detailed investigation of these genes was conducted to investigate the mechanisms underlying the drought responses.