Difference between revisions of "Time of bloom"

Revision as of 23:31, 5 March 2013

By Austin Mudd - Spring 2013

To Do

• Write introduction and procedure sections
• Aggregate all sequences into a single document in proper FASTA format

Flowering Introduction

The factors affecting time of flowering from the Max Planck Institute for Plant Breeding Research

Fornara et al., 2010

"Plants initiate flowering after a period of vegetative development. During this process, called floral induction, the shoot apical meristem starts to produce flowers instead of leaves. The timing of floral induction is controlled by sophisticated regulatory networks that monitor changes in the environment, ensuring that flowering occurs under conditions most likely to maximize reproductive success and seed production. In the model plant species Arabidopsis thaliana ?180 genes have been implicated in flowering-time control based on isolation of loss-of-function mutations or analysis of transgenic plants. This SnapShot presents a subset of these genes and proteins, each organized according to its spatial activity in the leaves or the shoot apical meristem of the plant. Strikingly, several genes act more than once and in several tissues during floral induction. Many of these genes occur in a network of six major pathways: the photoperiod and vernalization pathways control flowering in response to seasonal changes in day length and temperature; the ambient temperature pathway responds to daily growth temperatures; and the age, autonomous, and gibberellin pathways act more independently of environmental stimuli. The six pathways converge to regulate a small number of “floral integrator genes,” encoded by different classes of proteins, which govern flowering time by merging signals from multiple pathways. These integrator genes include FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), which both rapidly promote floral development. In addition, responses to other environmental stimuli, such as the balance of different wavelengths of light or nutrient availability, also influence flowering time, but how these processes interact with the pathways described here is not fully understood."

Higgins et al., 2010

"The switch from vegetative growth (the production of stems and leaves) to reproductive growth (the production of flowers) is an important developmental step in the life cycle of plants. Flowering needs to occur when conditions for pollination and seed development are optimal and consequently most plants restrict flowering to a specific time of year. They commonly achieve this by using reliable environmental cues such as day length (photoperiod) and temperature. In addition, nutrient and water availability and plant size can be important.

The genes and molecular mechanisms controlling flowering have been extensively studied in the model dicot Arabidopsis thaliana, subsequently Arabidopsis ... As part of this study the Arabidopsis flowering pathways were curated in Arabidopsis Reactome ... to provide an electronic knowledge resource allowing for further developments such as integration with protein-protein interaction datasets, overlaying with microarray data and electronic projection into all newly sequenced plant genomes. Using this we compiled a list of genes and gene families with a known role in flowering time in Arabidopsis.

Flowering time has also been extensively studied in crop species ... Flowering time is important for adaptation to specific environments and the world's major crop species provide a particularly interesting opportunity for study because they are grown in areas outside the ecogeographical limits of their wild ancestors. In addition, they are adapted to different farming practices such as fall (autumn) sowing or spring sowing in temperate regions. Adaptation to different environments and practices has been achieved by manipulation of flowering time responses and this makes flowering pathways an excellent system for comparison between and within domestic and wild species."

Jung et al., 2012

"Plants switch to the reproductive phase of development when environmental and endogenous factors are the most favourable for reproductive success and seed production. This proper timing is the result of elaborate regulatory networks that coordinate the external stimuli with endogenous cues, inducing the expression of genes that initiate the floral transition at the shoot apical meristem (SAM).

Much of our current understanding of the floral initiation process is derived from studies using Arabidopsis thaliana as the model system. More than 180 Arabidopsis genes have been identified that play a role in regulating flowering time, and these genes have been organised into six major pathways ... Although the photoperiod and vernalisation pathways monitor seasonal changes in day length or temperature and, hence, initiate flowering in response to exposure to long days or prolonged cold temperatures, the ambient temperature pathway coordinates the response to daily growth temperatures. The autonomous pathway together with those involving age or gibberellin constitutes the rest of the floral pathways, which function more independently of external stimuli. These pathways are integrated by downstream target genes including LEAFY (LFY), FLOWERING LOCUS T (FT) and SUPPRESSOR OF CONSTANS1 (SOC1), with their resulting outcomes conveyed to floral meristem identity genes such as APETALA1 (AP1) at the SAM that triggers the flowering process ...

Flowering is one of the most important agronomic traits influencing crop yield. There is thus a great necessity for research that examines the molecular control of this fundamental process in important crop species. This knowledge is critical for the breeding of climate change resilient crop varieties. Soybean, a major food crop, is also a member of the large and diverse legume family, which has the unique capability of forming nitrogen-fixing symbioses with soil microorganisms and has thus been used as part of sustainable agricultural practices for thousands of years. Soybean is distributed broadly across latitudes and is cultivated as different maturity groups, with each having a narrow range of latitudinal adaptation. Unlike Arabidopsis, soybean can undergo a reversion of flowering when plants are shifted from flowering inductive to non-inductive conditions ... In addition, soybean also follows a floral developmental plan that is distinct from that of Arabidopsis ... Therefore, an understanding of the molecular mechanisms underlying these soybean traits is of fundamental and practical interest."

• General plant anatomy / process of flowering
• Why flowering is important to study / general impact

Light Signaling Pathway

Jung et al., 2012

"Light is one of the main environmental regulators of flowering in plants. Plants sense the time of day and season of year by monitoring the light environment through light signalling pathways [23]. Soybean is a facultative short-day crop, but soybean cultivars also belong to different maturity groups depending upon their photoperiod sensitivity. This strong latitudinal cline is also observed in its undomesticated wild relative, Glycine soja (G. soja). In Arabidopsis, photoperiod pathway genes together with photoreceptor genes and circadian clock components take part in light signalling pathways. The number of known Arabidopsis flowering genes involved in these pathways is 48, which are clustered into 25 OGs. However, these OGs contain 53 Arabidopsis genes in total, suggesting that the additional 5 genes may also be involved in floral initiation (Table 1). In total, 121 soybean genes are identified as putative orthologues of 48 Arabidopsis flowering genes in 25 OGs (Table 1). The multiple sequence alignments followed by phylogenetic tree analyses for the Arabidopsis and soybean gene sequences in each of the 25 OGs revealed that 66 of the soybean genes are more closely located to their corresponding Arabidopsis genes than other soybean genes in the same OGs (Dataset S3). Furthermore, an in silico gene expression analysis of the identified soybean flowering genes determined that 115 of the 121 soybean orthologues are expressed, including 109 genes expressed in flowers [8], [9] (Figure S1 and Dataset S2).

The key Arabidopsis genes involved in the light signalling pathway include the CONSTANS (CO), PHYTOCHROME (PHY) and CRYPTOCHROME (CRY), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY) and PSEUDO-RESPONSE REGULATOR 1 [PRR1, also called TIMING OF CAB EXPRESSION 1 (TOC1)] genes. CO, along with CONSTANS-LIKE 1 (COL1) and CONSTANS-LIKE 2 (COL2), are contained in OG5_156319, which also contains four soybean genes as soybean orthologues (Glyma08g28370, Glyma13g07030, Glyma18g51320 and Glyma19g05170) (See Table S1). All four soybean-orthologue candidates of Arabidopsis CO are expressed in tested tissues/developmental stages in the two recent transcriptome datasets [8], [9], but only two candidates are expressed in flowers (Dataset S2). The CRY genes CRY1 and CRY2 are grouped into OG5_127186, which contains nine soybean genes (Table S1). The UV REPAIR DEFECTIVE 3 (UVR3) gene is also grouped into OG5_127186. In the phylogenetic tree of genes contained in OG5_127186, CRY1, CRY2 and UVR3 are all located in the same clade, along with 5 soybean genes (Figure 4A). Among these soybean genes, Glyma08g22400 is the closest orthologue of Arabidopsis UVR3, while Glyma18g07770, Glyma20g35220, Glyma10g32390 and Glyma02g00830 are closer to CRY2 (Figure 4A). Phylogenetic trees in Figure 4 include putative orthologues in Arabidopsis lyrata (A. lyrata), Medicago truncatula (Medicago) as well as a monocot Brachypodium distachyon (Brachypodium). All three Brachypodium genes and one Medicago genes clustered in the same OG are also found in the CRY1 clade, leaving four soybean genes and one Medicago gene in separate clades, indicating that these may have diverged functions (Figure 4A). Five PHY genes of Arabidopsis (PHYA, PHYB, PHYC, PHYD and PHYE) have eight soybean orthologue candidates, which are contained within OG5_136555 (Table S1). All of these soybean genes, except for Glyma15g23400, are expressed in flowers in one or both of the two transcriptome gene expression analyses integrated in this study [8], [9]. The MYB-transcription factor genes CCA1 and LHY are among the key circadian clock components in Arabidopsis and are regulated by TOC1 (also known as PRR1) [24]. CCA1 has a single soybean gene orthologue candidate (Glyma07g05410), while LHY and TOC1 have three and four soybean orthologue candidates, respectively (Table S1). All of the putative soybean orthologues of CCA1, LHY and TOC1 are expressed in the samples tested, including flowers, when analysed for their in silico gene expression [8], [9]. The GIGANTEA (GI) gene in OG5_190821 is a part of the evening loop in Arabidopsis and performs different functions through its interactions with other genes, including the FLAVIN-BINDING, KELCH REPEAT, F BOX 1 (FKF1), LOV KELCH PROTEIN 2 (LKP2) and ZEITLUPE (ZTL) genes contained within OG5_150244, which contains six soybean genes in total (Table S1) [12]. Higgins et al. (2011) reported that GI is a highly conserved single copy gene in Arabidopsis, rice, Brachypodium and barley [12], but it has three orthologous soybean genes (Glyma09g07240, Glyma10g36600, Glyma20g30980) (Table S1)."

Vernalization Pathway

Jung et al., 2012

"Vernalisation involves plants that require prolonged periods of low temperature to initiate flowering. The vernalisation pathway in Arabidopsis involves 32 genes clustered into 23 OGs (Table 1). Among these, 30 Arabidopsis genes in 21 OGs have 81 soybean orthologue candidates (Table 1), of these 81 genes, 71 show evidence of transcription (Dataset S2). However, the orthologous counterparts of the Arabidopsis VERNALISATION INSENSITIVE 3 (VIN3) gene in OG5_AT5G57380 and AGAMOUS-LIKE24 (AGL24) gene in OG5_AT4G24540 were not identified in soybean (Table S1) by this method. Nonetheless, a BLAST analysis suggests the potential existence of their soybean orthologues (see below and the Discussion). Among the OGs containing Arabidopsis genes associated with the vernalisation pathway, the ratio of the number of soybean genes to that of Arabidopsis genes is highest in OG5_212406, in which the ratio is 14 soybean genes to 1 Arabidopsis gene, REDUCED VERNALISATION RESPONSE 1 (VRN1) (Table S1). In contrast, the six Arabidopsis genes in OG5_139532, which includes a MADS-box transcription factor gene, FLOWERING LOCUS C (FLC), that negatively regulates flowering [25], share only one soybean gene as a putative orthologue (Glyma05g28130), resulting in the lowest soybean-to-Arabidopsis gene count ratio among the vernalisation-related OGs (Table S1). In the phylogenetic tree of OG5_139532, Glyma05g28130 is most closely related to FLC (Figure 4B). Interestingly, no Medicago and Brachypodium genes are found in this OG. As mentioned above, VIN3 (in OG5_AT5G57380), which is a repressor of FLC in cold temperatures [26], and a flowering promoter gene, AGL24 [27], [28], [29] [reviewed by Alexandre and Hennig (2008) [30]] in OG5_AT4G24540, are not assigned with putative soybean orthologues (Table S1), but share closely related soybean genes with other flowering genes (see below and Discussion)."

Autonomous Pathway

Jung et al., 2012

"Autonomous pathways in plants are activated in response to endogenous changes that are independent from the environmental cues leading to flowering [31]. There are 17 genes, grouped into 16 OGs, involved in the Arabidopsis autonomous pathway (Table 1). Each OG has a single Arabidopsis gene that is known to be functional during floral initiation, except for OG5_129164, which contains two Arabidopsis flowering genes: CURLY LEAF (CLF) and SWINGER (SWN) (Table S1). Three other OGs (OG5_147254, OG5_127148 and OG5_131236) also include one or two additional Arabidopsis genes, raising the total number of Arabidopsis genes in the autonomous pathway-related OGs to 23 (Table 1). The total number of orthologous soybean genes to the 17 Arabidopsis genes (or 23 if the additional genes are included) is 49, of which 46 genes are transcriptionally active (Table 1). OG5_163423 has six soybean genes that are orthologous to AT3G04610 [FLOWERING LOCUS KH DOMAIN (FLK)], a repressor of FLC expression [32], which is the highest soybean-to-Arabidopsis gene count ratio among the OGs for autonomous pathways. The subsequent phylogenetic tree analyses revealed that only two soybean genes (Glyma03g40840 and Glyma19g43540) are located in the same clade with Arabidopsis FLK, indicating that they are likely true orthologues of FLK (Figure 4C). Similarly, in OG5_131236 and OG5_147254, only one (Glyma02g18610) and two (Glyma15g18450 and Glyma09g07120) soybean genes, respectively, are found and thus are also likely to be true orthologues of their Arabidopsis counterparts involved in autonomous pathways (Figure 4D,E). OG5_131236 has three Arabidopsis genes, including FLOWERING LOCUS D (FLD), which down-regulates FLC and has Glyma02g18610 as its closest orthologue according to the phylogenetic tree (Figure 4D), and FVE [also known as MULTICOPY SUPPRESSOR OF IRA1 4 (MSI4)] in OG5_147254, which also down-regulates FLC and has Glyma15g18450 and Glyma09g07120 as its closest orthologues (Figure 4E). In comparison, four soybean orthologue candidates of Arabidopsis FPA, which has a redundant role with FLD, FVE, and LD [33], are equally distant from their Arabidopsis counterpart (data not shown). Because the minimum number of sequences for the generation of a phylogenetic tree is four, we are unable to generate phylogenetic trees for four OGs (OG5_128052, OG5_155119, OG5_169591 and OG5_170601) (Table S1). Therefore, all of the soybean genes in these OGs are regarded as the closest homologues of the Arabidopsis genes contained in the corresponding groups. Each of VEL2, VEL3 and VIN3 are grouped into a singleton OG and are not assigned orthologous counterparts in soybean (Table S1) but do have homologous genes in soybean according to the direct BLAST analysis (see below and Discussion)."

Ambient Temperature Pathway

Jung et al., 2012

"Plants respond to ambient temperature changes to modulate their flowering times [34]. The ambient temperature pathway in Arabidopsis involves 16 genes that are clustered into 8 OGs that have 38 soybean genes in total (Table 1). Three OGs (OG5_131236, OG5_147254 and OG5_155119) are also involved in autonomous pathways, and the Arabidopsis genes contained in OG5_139532, OG5_129661 and OG5_177438 are also involved in its vernalisation pathway (Table S1). In most of the OGs related to the ambient temperature pathway, the numbers of soybean genes are greater than those of Arabidopsis genes; however, the opposite findings are observed in the cases for OG5_139532 and OG5_190004. OG5_139532 contains six Arabidopsis genes (including FLC) that are orthologous to only one soybean gene, Glyma05g28130 (see above and Figure 4B). Similarly, Glyma01g36810 is the only soybean orthologue of the Arabidopsis genes AT4G35900 (FD) and AT2G17770 (FDP) in OG5_190004, which encode for the basic leucine zipper (bZIP) domain protein and positively regulate flowering [35]. Arabidopsis AT4G16280 (FCA) in OG5_155119 has one putative soybean orthologue (Glyma17g03960) (Table S1)."

Procedure

• Overall procedure for finding the genes, running with GenSAS, determining SSRs, etc

Gallery of Arabidopsis Flowering Pathways

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  Izawa et al., 2003

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  Sung et al., 2003

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  Boss et al., 2004

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  Boss et al., 2004

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  Henderson and Dean, 2004

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  Amasino, 2005

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  He and Amasino, 2005

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  Yamaguchi et al., 2005

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  Bäurle and Dean, 2006

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  Farrona et al., 2008

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  Farrona et al., 2008

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  Liu et al., 2009

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  Schneitz, 2009

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  Amasino, 2010

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  Higgins et al., 2010

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  Kim and Sung, 2010

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  Taiz and Zeiger, 2010

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  Wellmer and Riechmann, 2010 and Ferrier et al., 2011

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  Ballerini and Kramer, 2011

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  Zhang et al., 2011

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  Jung et al., 2012

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  Posé et al., 2012

105 Flowering Genes

This table lists all of the genes involved in the ambient temperature, autonomous, light signaling, and vernalization pathways. All Arabidopsis genes are compiled from Jung et al., 2012. All potential orthologs are found via UniProt Grape or UniProt Strawberry nomenclature search.