Genomic and Genetic Comparison of Flowering Pathways in Rice and Arabidopsis

The model plant, Arabidopsis thaliana is a long day-plant, while rice is a short-day plant. Arabidopsis is a dicot while rice is a monocot. In their habit, vegetative and floral morphology, they look very different and belong to two widely divergent taxa. In spite of such a phylogenetic divergence, the two species show that a majority of genes controlling flowering pathways such as such as Hd1 (Heading date1)/CO (CONSTANS), Hd3a (Heading date3)/FT (FLOWERING LOCUS T), are orthologues, indicating that these genes are conserved between rice and Arabidopsis.

In a review article published in the April 2003 issue of Current Opinion in Plant Biology (vol. 6:113–120), Masahiro Yano, and collaborators at the National Institute of Agrobiological Sciences, Japan, have discussed how the combined study of genomics and molecular genetics has helped in elucidating flowering pathways conserved between rice and Arabidopsis thaliana.

The review begins by describing the advantages gained by completion of base sequencing in Arabidopsis and rice. The review then points out, that the current information, based on complete genome sequencing of the above two species, would enable researchers to compare genomes of different organisms more thoroughly and do map-based cloning. The authors further describe factors that have contributed to natural variations in the flowering-time genes and their impact on the speciation and diversity of flowering plants.

Photoreceptors involved in floral induction: A good deal of similarity exists between Arabidopsis and rice photoreceptors that are involved in floral induction. Compared to five PHY (PHYTOCHROME) genes in Arabidopsis, the number is three in rice, PHYD and PHYE being absent in its genome. On the other hand, the number of CRY (CRYPTOCHROME) genes, which encode blue light receptor, is higher in rice; it is three compared to two in Arabidopsis. Of the three CRY genes in rice, two are of CRY 1 type and the third of the CRY2 type. The SE5 (PHOTOPERIOD SENSITIVITY5) gene, essential for chromophore biosynthesis in rice, is an Arabidopsis orthologue, HY1 (LONG HYPOCOTYL1). This SE5 gene is exclusively required to elicit full response to photoperiod in rice, but its Arabidopsis orthologue HY1 is not essential to induce full photoperiodic response. The authors hypothesize that such photo- receptors may be involved differently in the control of flowering time in the two species. In long- day Arabidopsis plants, PHYB may inhibit flowering under short-day conditions, while CRY2 functions for floral induction under long days, in which the interaction of CRY2 with PHYB may be necessary. In contrast, in rice, PHYB inhibits flowering under long days. In the light of such an observation, it is assumed that light-stable PHYB action may repress FT (or its rice orthologs) expression in both rice and Arabidopsis. Meanwhile, blue light signals may play different roles for floral induction in those taxa.

Circadian clock-related genes: The other conserved flowering-time genes common to both the species are circadian-clock genes. They are: (a) TIMING OF CHLOROPHYLL A/B BINDING PROTEIN (CAB) EXPRESSION 1 abbreviated to TOC1 (b) GIGANTEA (GI) (called OsGI in rice) (c) orthologues of other members of Arabidopsis such as Arabidopsis PSEUDO RESPONSE REGULATOR (APRR) family. Of the two MYB-related clock genes in Arabidopsis, namely, LHY (LATE ELONGATED HYPOCOTYL) and CCA1 (CIRCADIAN CLOCK ASSOCIATED1) genes, only  one LHY (CIRCADIAN CLOCK ASSOCIATED)-like  gene was found to be an orthologue of rice. Of the two Arabidopsis clock-related genes, ELF3 and ELF4, only ELF3 has an orthologue in rice. In addition, two more Arabidopsis genes that function in the circadian clock have been identified in rice. These orthologues are: ZEITLUPE (ZTL), and FLAVIN-BINDING, KELCH-REPEATS, F-BOX1 (FKF1) The biological function of those orthologous genes in rice largely remains to be tested.

Bünning model explaining that light enables plants to measure day length: Recent studies have shown that mRNA expression of rice FT (flowering locus T) orthologues is dependent on Hd1 (Heading date1) that functions as a repressor in response to light-stable phytochrome signaling. Unlike Hd1, CO promotes the transcription of FT mRNA in response to CRY2 and light-labile PHYA-mediated light signaling. The authors further develop the model proposed by Bünning and later modified by Pittendrigh and Minis. The model describes a 2-step process by which light enables plants to measure day length. First light resets the circadian clock, so called entrainment*. This step turns on the expression of the two genes, Hd1 and CO (CONSTANS) from dusk till dawn. The second role of the light is to modify  the transcription factors, Hd1and CO. The action of external light signals on Hd1/CO determines the difference between rice and Arabidopsis.

Function of some flowering-time orthologues between Arabidopsis and rice: Earlier work on CONSTANS (CO) suggests that it is a circadian clock-related floral regulator in Arabidopsis.   It has two modified versions (paralogs): COL1 (CONSTANS-LIKE1) and COL2 (CONSTANS-LIKE2)COL1 and COL2 are similar to rice HD1. Recent studies on the above two genes reveal, that they are involved in circadian clock systems rather than flowering-time induction. Describing the role of the Arabidopsis FT (FLOWERING LOCUS T) gene, the authors point out that that it acts as one of the integrators controlled by CO. Rice has 10 FT-like genes, one of which is Hd3a. It acts as one of the integrators also controlled by Hd1. . The authors point out that more work is necessary to define the roles of so many copies (= orthologues) of FTgenes in the rice genome. One possibility is that these orthologues have acquired novel functions. Beside FT, a MADS-box gene SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CO 1) has been reported inArabidopsis. This gene is affected by CO directly and serves as another integrator. The rice orthologue of this gene has been identified, although its biological function in rice is unknown.

Interestingly, some of the flowering-time genes present in Arabidopsis have no orthologue in the rice genome. Such genes are FLC (FLOWERING LOCUSC), FRIGIDA, VRN1 (VERNALIZATION1), and VRN2 (VERNALIZATION2). While FRIGIDA is an activator of FLC, the last two in the list, VRN1 and VRN2, are involved in the vernalization process of Arabidopsis through regulation of FLC expression.  The authors assume that these genes were present early in the evolutionary history of the rice genome but they were lost in the absence of any selection pressure such as requirement of a low temperature treatment for germination of rice grains. In contrast, Arabidopsis seed of some ecotypes must be exposed to low temperature to break its dormancy.

The Polycomb group of genes in Arabidopsis and their rice orthologues: Turning to the Polycomb group of genes that act on chromatin structure to repress gene expression, the authors refer to two such genes in Arabidopsis in addition to VRN2: EMF2 (EMBRYONIC FLOWERING2) and  FIE (FERTILIZATION INDEPENDENT ENDOSPERM). The rice genome showed two orthologues each of Arabidopsis EMF2 and FIE genes and one orthologue of LHP1 (LIKE HETEROCHROMATIN PROTEIN1 The two taxa lack gene order and chromosome structure conservation and yet they possess a number of related Polycomb orthologues. This similarity has led the authors to pose the question whether the biological function of such chromatin-related genes is conserved among plant species.

Natural variation in flowering-time genes: The authors also discuss the importance of a wide range of natural allelic variation in flowering-time genes under pressure of a wide range of environmental factors such as photoperiod and temperature. They are referring to different alleles of the FLC and FRIGIDA floral regulators, characterizing the Columbia and Landsberg erecta ecotypes of Arabidopsis, The identification of a novel CRY2 allele in the tropical Cape Islands ecotype of Arabidpsis has further supported their hypothesis. While Kasalath, a cultivar of  indica rice, has a null-function allele of Hd1, the japonica rice cultivar Nipponbare, has a functional allele of the same gene. On the other hand, Hd6 in Kasalath is functional while its allele in Nipponbare is defective. These variations may cause differential flowering responses within and between species.

Conclusion: The comparative study of genomic sequences within and between rice and Arabidopsis has opened up lots of  possibilities of gaining deep insights about the evolutionary forces that have led to the diversity among flowering plants. The present review points the way forward and promotes a reverse and transgene-based genetics approach to solve some of the evolutionary mysteries facing flowering plants.
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*The process by which a change in external stimuli resets the circadian cycle and adjusts the clock to a different temperature and light regime within the same 24-hr period.

 

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