CRY2 gene of rice (Oryza sativa subsp. indica) encodes a blue light sensory receptor involved in regulating flowering, plant height and partial photomorphogenesis in dark

Rice CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1-LIKE interacts with OsCRY2 and promotes flowering by upregulating Early heading date 1

Flowering time is a crucial adaptive response to seasonal variation in plants and is regulated by environmental cues such as photoperiod and temperature. In this study, we demonstrated the regulatory function of rice CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1-LIKE (OsCIBL1) in flowering time. Overexpression of OsCIB1L promoted flowering, whereas the oscib1l knockout mutation did not alter flowering time independent of photoperiodic conditions. Cryptochromes (CRYs) are blue light photoreceptors that enable plants to sense photoperiodic changes. OsCIBL1 interacted with OsCRY2, a member of the rice CRY family (OsCRY1a, OsCRY1b, and OsCRY2), and bound to the Early heading date 1 (Ehd1) promoter, activating the rice-specific Ehd1-Heading date 3a/RICE FLOWERING LOCUS T 1 pathway for flowering induction. Dual-luciferase reporter assays showed that the OsCIBL1-OsCRY2 complex required blue light to induce Ehd1 transcription. Natural alleles resulting from nonsynonymous single nucleotide polymorphisms in OsCIB1L and OsCRY2 may contribute to the adaptive expansion of rice cultivation areas. These results expand our understanding of the molecular mechanisms controlling rice flowering and highlight the importance of blue light-responsive genes in the geographic distribution of rice.

Genome-wide identification and characterization of flowering genes in Citrus sinensis (L.) Osbeck: a comparison among C. Medica L., C. Reticulata Blanco, C. Grandis (L.) Osbeck and C. Clementina

BACKGROUND

Flowering plays an important role in completing the reproductive cycle of plants and obtaining next generation of plants. In case of citrus, it may take more than a year to achieve progeny. Therefore, in order to fasten the breeding processes, the juvenility period needs to be reduced. The juvenility in plants is regulated by set of various flowering genes. The citrus fruit and leaves possess various medicinal properties and are subjected to intensive breeding programs to produce hybrids with improved quality traits. In order to break juvenility in Citrus, it is important to study the role of flowering genes. The present study involved identification of genes regulating flowering in Citrus sinensis L. Osbeck via homology based approach. The structural and functional characterization of these genes would help in targeting genome editing techniques to induce mutations in these genes for producing desirable results.

RESULTS

A total of 43 genes were identified which were located on all the 9 chromosomes of citrus. The in-silico analysis was performed to determine the genetic structure, conserved motifs, cis-regulatory elements (CREs) and phylogenetic relationship of the genes. A total of 10 CREs responsible for flowering were detected in 33 genes and 8 conserved motifs were identified in all the genes. The protein structure, protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed to study the functioning of these genes which revealed the involvement of flowering proteins in circadian rhythm pathways. The gene ontology (GO) and gene function analysis was performed to functionally annotate the genes. The structure of the genes and proteins were also compared among other Citrus species to study the evolutionary relationship among them. The expression study revealed the expression of flowering genes in floral buds and ovaries. The qRT-PCR analysis revealed that the flowering genes were highly expressed in bud stage, fully grown flower and early stage of fruit development.

CONCLUSIONS

The findings suggested that the flowering genes were highly conserved in citrus species. The qRT-PCR analysis revealed the tissue specific expression of flowering genes (CsFT, CsCO, CsSOC, CsAP, CsSEP and CsLFY) which would help in easy detection and targeting of genes through various forward and reverse genetic approaches.

OsCRY2 and OsFBO10 co-regulate photomorphogenesis and photoperiodic flowering in indica rice

Cryptochromes (CRYs) are a class of photoreceptors that perceive blue/ultraviolet-A light of the visible spectrum to mediate a vast number of physiological responses in bacteria, fungi, animals and plants. In the present study, we have characterized OsCRY2 in a photoperiod sensitive indica variety, Basmati 370, by generating and analyzing overexpression (OE) and knock-down (KD) transgenic lines. The OsCRY2^OE lines displayed dwarfism as shown in their reduced plant height and leaf length, attributed largely by an overall reduction in their cell size. The OsCRY2^OE lines flowered significantly earlier and showed shorter and broader seeds with an overall reduced seed weight. The OsCRY2^KD lines showed contrasting phenotypes, such as increased plant height and delayed flowering, however, decreased seed size and weight were also observed in the KD lines, along with reduced spikelet fertility and high seed shattering rate in mature panicles. Novel interactions were confirmed between OsCRY2 and members of ZEITLUPE family of blue/ultraviolet-A light photoreceptors, encoded by OsFBO8, OsFBO9 and OsFBO10 which are orthologous to ZEITLUPE (ZTL), LOV KELCH PROTEIN2 (LKP2) and FLAVIN BINDING, KELCH REPEAT F-BOX1 (FKF1), respectively, of Arabidopsis thaliana. Since FKF1 is known to play a role in regulating photoperiodic flowering, OsFBO10 was chosen for further studies. OsCRY2 and OsFBO10 interacted in the nucleus and cytoplasm of the cell and cross-regulated the expression of each other. They were also found to regulate the expression of several genes involved in photoperiodic flowering in rice. Both OsCRY2 and OsFBO10 played a positive role in photomorphogenic responses in different light conditions. The physical interaction of OsCRY2 with OsFBO10, their involvement in common physiological and developmental pathways and their cross-regulation of each other suggest that the two photoreceptors may regulate common developmental pathways in plants, either jointly or redundantly.

The Genomic Variation and Differentially Expressed Genes on the 6P Chromosomes in Wheat-Agropyron cristatum Addition Lines 5113 and II-30-5 Confer Different Desirable Traits

Wild relatives of wheat are essential gene pools for broadening the genetic basis of wheat. Chromosome rearrangements and genomic variation in alien chromosomes are widespread. Knowledge of the genetic variation between alien homologous chromosomes is valuable for discovering and utilizing alien genes. In this study, we found that 5113 and II-30-5, two wheat-A. cristatum 6P addition lines, exhibited considerable differences in heading date, grain number per spike, and grain weight. Genome resequencing and transcriptome analysis revealed significant differences in the 6P chromosomes of the two addition lines, including 143,511 single-nucleotide polymorphisms, 62,103 insertion/deletion polymorphisms, and 757 differentially expressed genes. Intriguingly, genomic variations were mainly distributed in the middle of the chromosome arms and the proximal centromere region. GO and KEGG analyses of the variant genes and differentially expressed genes showed the enrichment of genes involved in the circadian rhythm, carbon metabolism, carbon fixation, and lipid metabolism, suggesting that the differential genes on the 6P chromosome are closely related to the phenotypic differences. For example, the photosynthesis-related genes PsbA, PsbT, and YCF48 were upregulated in II-30-5 compared with 5113. ACS and FabG are related to carbon fixation and fatty acid biosynthesis, respectively, and both carried modification variations and were upregulated in 5113 relative to II-30-5. Therefore, this study provides important guidance for cloning desirable genes from alien homologous chromosomes and for their effective utilization in wheat improvement.