Transcriptomic divergence between upland and lowland ecotypes contributes to rice adaptation to a drought‐prone agroecosystem

INTRODUCTION: Transcriptomic divergence drives plant ecological adaptation. Upland rice is differentiated in drought tolerance from lowland rice during its adaptation to the drought‐prone environment. They provide a good system to learn the evolution of drought tolerance in rice. METHODS AND RESULTS: We estimate morphological differences between the two rice ecotypes under well‐watered and drought conditions, as well as their genetic and transcriptomic divergences by the high‐throughput sequencing. Upland rice possesses higher expression diversity than lowland rice does. Thousands of genes exhibit expression divergences between the two rice ecotypes, which contributes to their morphological differences in drought tolerance. These transcriptomic divergences contribute to drought adaptation of upland rice during its domestication. Mutations in transcriptional regulatory regions, which cause presence and absence of cis‐elements, are the cause of expression divergence. About 15.3% transcriptionally selected genes also receive sequence‐based selection in upland or lowland ecotype. Some highly differentiated genes promote the transcriptomic divergence between rice ecotypes via gene co‐expression network. In addition, we also detected transcriptomic trade‐offs between drought tolerance and productivity. DISCUSSION: Many key genes, which promote transcriptomic adaptation to drought in upland rice, have great prospective in breeding water‐saving and drought‐resistant rice. Meanwhile, appropriate strategies are required in breeding to overcome the potential transcriptomic trade‐off.