Modeling the response of gene expression to multiple abiotic fluctuations in nature Event

Abstract: Plants have evolved to respond to complex environmental fluctuations that take place at time-scales that go from seconds to years and shape plant developmental and physiological responses. To better understand how plants respond to abiotic conditions, we used RNA-Seq and examined global gene expression patterns under natural fluctuating conditions, in two irrigated and rainfed fields typical of the main modes of rice (Oryza sativa) cultivation, over two seasons (wet and dry), each comprising 15 time-points. We designed a model selection approach to relate the main variations in global gene expression to variation in several environmental/developmental parameters with simple linear equations and detect differences in gene expression patterns between fields or seasons. Our results show extensive impact of the field environment on the gene expression response to meteorological conditions, especially under limited water availability, for groups of co-expressed abiotic stress response, photosynthesis and developmental genes. We found that short-term effects of solar radiation and temperature were the most consistent across different fields and seasons. Our approach identifies regulatory mechanisms that have evolved under multiple fluctuating conditions that would not be detected in controlled laboratory/greenhouse settings, where the effect of only one or a few drastic changes is measured.