Identification of Soybean Genes Involved in Circadian Clock Mechanism and Photoperiodic Control of Flowering Time by In Silico Analyses

Abstract

Glycine max is a photoperiodic short‐day plant and the practical consequence of the response is latitude and sowing period limitations to commercial crops. Genetic and physiological studies using the model plants Arabidopsis thaliana and rice (Oryza sativa) have uncovered several genes and genetic pathways controlling the process, however information about the corresponding pathways in legumes is scarce. Data mining prediction methodologies, including multiple sequence alignment, phylogenetic analysis, bioinformatics expression and sequence motif pattern identification, were used to identify soybean genes involved in day length perception and photoperiodic flowering induction. We have investigated approximately 330 000 sequences from open‐access databases and have identified all bona fide central oscillator genes and circadian photoreceptors from A. thaliana in soybean sequence databases. We propose a working model for the photoperiodic control of flowering time in G. max, based on the identified key components. These results demonstrate the power of comparative genomics between model systems and crop species to elucidate the several aspects of plant physiology and metabolism.

Analysis of clock gene homologs using unifoliolates as target organs in soybean (Glycine max)

“…It suggests what we cloned may be LHY or CCA1 homologs. Both LHY and CCA1 in Arabidopsis encode MYB-related transcriptional factors and they have highly conserved sequences (Ding et al, 2007;Hecht et al, 2005;Murakami et al, 2007;Quecini et al, 2007). So it is difficult to conclude that the genes cloned were LHY or CCA1 homologs in soybean.…”

“…Clock genes, LHY, CCA1, and TOC1 control flowering and show conserved circadian expression patterns in various plants (Ding et al, 2007;Hecht et al, 2005;Murakami et al, 2007;Quecini et al, 2007;Serikawa et al, 2008). We studied the expression patterns of GmLCL1, GmLCL2, and GmTOC1 in short days and long days and found that all three genes exhibited the circadian expression patterns regardless of photoperiodic conditions (Figures 4 and 5).…”

“…Late Elongated Hypocotyl (LHY), Circadian Clock Associated 1 (CCA1), and Timing Of CAB Expression 1 (TOC1) comprise the major components of the main circadian clock in Arabidopsis and control photoperiodic flowering (Ding et al, 2007). Accumulating evidence shows that this scheme is widely conserved in various plants including monocots and dicots, long-day plants and short-day plants (Hecht et al, 2005(Hecht et al, , 2007Murakami et al, 2007;Quecini et al, 2007;Serikawa et al, 2008).…”

“…However, the mechanism of flowering is poorly understood. Recently, Quecini et al (2007) identified by in silico analyze 33 soybean EST contigs corresponding to Arabidopsis genes involved in the circadian clock mechanism and photoperiodic flowering control. Among them, 10 are homologs to components of the central oscillatory mechanism including CCA1, LHY, and TOC1 homolgs.…”

In silico characterization of 1,2-diacylglycerol cholinephosphotransferase and lysophospha­tidylcholine acyltransferase genes in Glycine max L. Merrill

“…This pattern of differential gene expression is due to transcriptional regulation, and for this reason, many studies have been carried out to improve our understanding of gene expression in soybean under different conditions, including excess water (Komatsu et al, 2009), soybean cyst nematode infection (Yeckel et al, 2007), circadian expression, and flowering controlled by photoperiod (Quecini et al, 2007). Table 1 shows the presence of binding sites for DNA-binding with one finger (DOF) proteins in promoter regions of the gene models encoding CPT and LPCAT.…”