Regulatory modules controlling early shade avoidance response in maize seedlings

Abstract

BackgroundOptimization of shade avoidance response (SAR) is crucial for enhancing crop yield in high-density planting conditions in modern agriculture, but a comprehensive study of the regulatory network of SAR is still lacking in monocot crops.ResultsIn this study, the genome-wide early responses in maize seedlings to the simulated shade (low red/far-red ratio) and also to far-red light treatment were transcriptionally profiled. The two processes were predominantly mediated by phytochrome B and phytochrome A, respectively. Clustering of differentially transcribed genes (DTGs) along with functional enrichment analysis identified important biological processes regulated in response to both treatments. Co-expression network analysis identified two transcription factor modules as potentially pivotal regulators of SAR and de-etiolation, respectively. A comprehensive cross-species comparison of orthologous DTG pairs between maize and Arabidopsis in SAR was also conducted, with emphasis on regulatory circuits controlling accelerated flowering and elongated growth, two physiological hallmarks of SAR. Moreover, it was found that the genome-wide distribution of DTGs in SAR and de-etiolation both biased toward the maize1 subgenome, and this was associated with differential retention of various cis-elements between the two subgenomes.ConclusionsThe results provide the first transcriptional picture for the early dynamics of maize phytochrome signaling. Candidate genes with regulatory functions involved in maize shade avoidance response have been identified, offering a starting point for further functional genomics investigation of maize adaptation to heavily shaded field conditions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2593-6) contains supplementary material, which is available to authorized users.

Molecular Mechanisms Governing Shade Responses in Maize

“…Interestingly, we identified 7 BBXs as core genes for SAS regulation (Table 1, S2). For example, ZmBBX20 was upregulated 2.9-fold (F1 vs. F0) and 12.7-fold (F3 vs. F0) in response to shade treatment in the current study, and 2.5-fold (1 h vs. 0h), 2.1-fold (3 h vs. 0 h) and 2.9-fold (6 h vs. 0 h) in the previous study (Wang et al, 2016).…”

“…To identify the important regulators of the shade response, we first listed the 226 genes overlapping in our DEG list (912, Dataset S2) and Wang’s DEG list (1105, Wang et al, 2016), eliminated the photosynthesis, secondary metabolism, stress, nucleotide metabolism, and function unknown genes from this list, added three genes, ZmGT1 ( Grassy tillers1 ), ZmTB1 ( Teosinte branched1 ), and ZmVT2 , which have already been shown to play important roles in maize SAS (Doebley et al, 1997; Sheehan et al, 2007; Phillips et al, 20011; Whipple et al, 2011), and identified 93 core genes for the shade response (Table1, S2). Most of these genes were significantly regulated by shade treatment.…”

“…In maize, although some of the early shade-responsive genes have been identified (Wang et al, 2016), their physiological functions and underlying mechanisms remain largely unknown. Here, we combined cytological and transcriptomic analysis with functional testing to investigate the anatomical and transcriptional dynamics of SAS in maize seedlings and predict the core responsive genes involved in the regulation of SAS.…”

From laboratory to field: yield stability and shade avoidance genes are massively differentially expressed in the field

“…The shade avoidance response is characterized by red:far-red ratio of the light experienced by the plants, resulting in changes in flowering time, plant growth and architecture, driven by auxin, GA and brassinosteroids responses (Carriedo et al, 2016) of which many genes were differentially expressed in our study. Using a hypergeometric test (phyper() function in R), we showed statistically significant (P = 2.25e-07) overlap between the genes that were robustly differentially expressed in our study and the early shade avoidance responses in maize triggered by a low red:far-red ratio (Wang et al, 2016).…”

Identification and cloning of GOLDEN2-LIKE1 (GLK1), a transcription factor associated with chloroplast development in Brassica napus L.

“…For example, the Lhca and Lhcb gene family encodes the light-harvesting chlorophyll a/b-binding proteins LHCI and LHCII, which capture light energy and transfer it to chlorophylls (Chls) in the core reaction centers of photosystems I and II (PSI and PSII) (Kobayashi et al, 2013). chlorophyll b binding proteins of the lightharvesting complexes (LHCB) and the small subunit of ribulose-1,5-bisphosphate carboxylase (SSU) modulate photosynthesis-related nuclear gene expression (Kakizaki et al, 2009), and HY5 and its homologs HYH and HFR1/REP1/RSF1 affect the expression of photosynthesisrelated genes and proplastid differentiation (Fairchild et al, 2000;Spiegelman et al, 2000;McCormac and Terry, 2002;Wang et al, 2016), which is the key target of the COP1/SPA complex (Xu et al, 2015). Therefore, subunits of the photosystem reaction center are encoded by multiple genes in plant proplastids.…”