Genome-wide H3K9 Acetylation Level Increases with Age-Dependent Senescence of Flag Leaf in Rice (Oryza sativa)

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and epigenetic modification, but the precise mechanism is as of yet unclear. Here, we analyzed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq) and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac and gene expression and transcript elongation. A set of 1,249 up-regulated, differentially expressed genes (DEGs) and 996 down-regulated DEGs showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac was observed during rice flag leaf aging. We produced a landscape of H3K9 acetylation- modified gene expression targets that includes known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis- related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac and also elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.

The powdery mildew disease of rubber (Oidium heveae) mainly controlled by the winter temperature in the Xishuangbanna, China

Background: Rubber powdery mildew disease (Oidium heveae) is a serious threat to the natural rubber production in some rubber developing regions of the world. Many factors affect the powdery mildew disease. As many of these influencing factors found in previous studies are strongly correlated, unraveling their effects and their relative importance is a challenge. We assessed the three main groups of factors: temperature variables, the timing of leaf phenologies, and the duration of leaf development. In total, we investigated the effects of forty-one factors on the infection rate of powdery mildew of rubber trees (Hevea brasiliensis) by using Partial Least Squares (PLS) regression methods over 9-year records (2003–2011). Results: Among these factors, we found that the most influential variables were the temperature variables (winter and spring mean temperature, and daily temperature differences in winter) and the duration of leaf development to maturation, from copper brown stage to leaf aging, which explained 72% and 58% of the variations in the infection rate. We found the controlling role of winter mean temperature, for the first time, on the infection rate of powdery mildew, and the duration of leaf maturation was also influenced by the winter mean temperature. Conclusions: The controlling role of winter temperature may have directly increase the infection rate when winter temperature is high, and indirectly increase the infection rate through the prolongation of the leaf maturation duration, although the duration itself, from copper brown to leaf aging had smaller influences. We detected a warming trend of the winter temperatures from 2003 to 2011, which indicates that the rubber plantations will experience increasing of infection rate of powdery mildew if the winter warming continues.

Time-evolving genetic networks reveal a NAC troika that negatively regulates leaf senescence in Arabidopsis

Senescence is controlled by time-evolving networks that describe the temporal transition of interactions among senescence regulators. Here, we present time-evolving networks for NAM/ATAF/CUC (NAC) transcription factors in Arabidopsis during leaf aging. The most evident characteristic of these time-dependent networks was a shift from positive to negative regulation among NACs at a presenescent stage. ANAC017, ANAC082, and ANAC090, referred to as a “NAC troika,” govern the positive-to-negative regulatory shift. Knockout of the NAC troika accelerated senescence and the induction of other NACs, whereas overexpression of the NAC troika had the opposite effects. Transcriptome and molecular analyses revealed shared suppression of senescence-promoting processes by the NAC troika, including salicylic acid (SA) and reactive oxygen species (ROS) responses, but with predominant regulation of SA and ROS responses by ANAC090 and ANAC017, respectively. Our time-evolving networks provide a unique regulatory module of presenescent repressors that direct the timely induction of senescence-promoting processes at the presenescent stage of leaf aging.