Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

<p>Abstract</p> <p>Background</p> <p>The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality.</p> <p>Results</p> <p>We describe and classify 108 members of the grape <it>R2R3 MYB </it>gene subfamily in terms of their genomic gene structures and similarity to their putative <it>Arabidopsis thaliana </it>orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across <it>Arabidopsis </it>and <it>Vitis</it>, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the <it>Arabidopsis </it>and rice MYB subfamilies. Two anthocyanin <it>MYBA </it>related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11.</p> <p>Conclusion</p> <p>This genome wide transcription factor analysis in <it>Vitis </it>suggests that clade-specific grape <it>R2R3 MYB </it>genes are expanded while other MYB genes could be well conserved compared to <it>Arabidopsis</it>. <it>MYB </it>gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions.</p

TRAUCO, a Trithorax-group gene homologue, is required for early embryogenesis in Arabidopsis thaliana

Embryogenesis is a critical stage during the plant life cycle in which a unicellular zygote develops into a multicellular organism. Co-ordinated gene expression is thus necessary for proper embryo development. Polycomb and Trithorax group genes are members of evolutionarily conserved machinery that maintains the correct expression patterns of key developmental regulators by repressing and activating gene transcription. TRAUCO (TRO), a gene homologous to the Trithorax group of genes that can functionally complement a BRE2P yeast mutant, has been identified in Arabidopsis thaliana. It is demonstrated that TRO is a nuclear gene product expressed during embryogenesis, and loss of TRO function leads to impaired early embryo development. Embryos that arrested at the globular stage in the tro-1 mutant allele were fully rescued by a TRO expression clone, a demonstration that the tro-1 mutation is a true loss-of-function in TRO. Our data have established that TRO is the first trithorax-group gene homologue in plants that is required for early embryogenesi

TRAUCO, a Trithorax-group gene homologue, is required for early embryogenesis in Arabidopsis thaliana

Embryogenesis is a critical stage during the plant life cycle in which a unicellular zygote develops into a multicellular organism. Co-ordinated gene expression is thus necessary for proper embryo development. Polycomb and Trithorax group genes are members of evolutionarily conserved machinery that maintains the correct expression patterns of key developmental regulators by repressing and activating gene transcription. TRAUCO (TRO), a gene homologous to the Trithorax group of genes that can functionally complement a BRE2P yeast mutant, has been identified in Arabidopsis thaliana. It is demonstrated that TRO is a nuclear gene product expressed during embryogenesis, and loss of TRO function leads to impaired early embryo development. Embryos that arrested at the globular stage in the tro-1 mutant allele were fully rescued by a TRO expression clone, a demonstration that the tro-1 mutation is a true loss-of-function in TRO. Our data have established that TRO is the first trithorax-group gene homologue in plants that is required for early embryogenesis

The photomorphogenic factors UV-B RECEPTOR 1, ELONGATED HYPOCOTYL 5, and HY5 HOMOLOGUE are part of the UV-B signalling pathway in grapevine and mediate flavonol accumulation in response to the environment

Grapevine (Vitis vinifera L.) is a species well known for its adaptation to radiation. However, photomorphogenic factors related to UV-B responses have not been molecularly characterized. We cloned and studied the role of UV-B RECEPTOR (UVR1), ELONGATED HYPOCOTYL 5 (HY5), and HY5 HOMOLOGUE (HYH) from V. vinifera We performed gene functional characterizations, generated co-expression networks, and tested them in different environmental conditions. These genes complemented the Arabidopsis uvr8 and hy5 mutants in morphological and secondary metabolic responses to radiation. We combined microarray and RNA sequencing (RNA-seq) data with promoter inspections to identify HY5 and HYH putative target genes and their DNA binding preferences. Despite sharing a large set of common co-expressed genes, we found different hierarchies for HY5 and HYH depending on the organ and stress condition, reflecting both co-operative and partially redundant roles. New candidate UV-B gene markers were supported by the presence of HY5-binding sites. These included a set of flavonol-related genes that were up-regulated in a HY5 transient expression assay. We irradiated in vitro plantlets and fruits from old potted vines with high and low UV-B exposures and followed the accumulation of flavonols and changes in gene expression in comparison with non-irradiated conditions. UVR1, HY5, and HYH expression varied with organ, developmental stage, and type of radiation. Surprisingly, UVR1 expression was modulated by shading and temperature in berries, but not by UV-B radiation. We propose that the UV-B response machinery favours berry flavonol accumulation through the activation of HY5 and HYH at different developmental stages at both high and low UV-B exposure

Inspection of the grapevine BURP superfamily highlights an expansion of RD22 genes with distinctive expression features in berry development and ABA-mediated stress responses

The RESPONSIVE TO DEHYDRATION 22 (RD22) gene is a molecular link between abscisic acid (ABA) signalling and abiotic stress responses. Its expression has been used as a reliable ABA early response marker. In Arabidopsis, the single copy RD22 gene possesses a BURP domain also located at the C-terminus of USP embryonic proteins and the beta subunit of polygalacturonases. In grapevine, a RD22 gene has been identified but putative paralogs are also found in the grape genome, possibly forming a large RD22 family in this species. In this work, we searched for annotations containing BURP domains in the Vitis vinifera genome. Nineteen proteins were defined by a comparative analysis between the two genome predictions and RNA-Seq data. These sequences were compared to other plant BURPs identified in previous genome surveys allowing us to reconceive group classifications based on phylogenetic relationships and protein motif occurrence. We observed a lineage-specific evolution of the RD22 family, with the biggest expansion in grapevine and poplar. In contrast, rice, sorghum and maize presented highly expanded monocot-specific groups. The Vitis RD22 group may have expanded from segmental duplications as most of its members are confined to a region in chromosome 4. The inspection of transcriptomic data revealed variable expression of BURP genes in vegetative and reproductive organs. Many genes were induced in specific tissues or by abiotic and biotic stresses. Three RD22 genes were further studied showing that they responded oppositely to ABA and to stress conditions. Our results show that the inclusion of RNA-Seq data is essential while describing gene families and improving gene annotations. Robust phylogenetic analyses including all BURP members from other sequenced species helped us redefine previous relationships that were erroneously established. This work provides additional evidence for RD22 genes serving as marker genes for different organs or stresses in grapevine

Mapping aluminum tolerance loci in cereals: A tool available for crop breeding

Aluminum (Al) toxicity is the main factor limiting crop productivity in acidic soils around the world. In cereals, this problem reduces crop yields by 30-40%. The use of DNA-based markers linked to phenotypic traits is an interesting alternative approach. Strategies such as molecular marker-assisted selection (MAS) in conjunction with bioinformatics-based tools such as graphical genotypes (GGT) have been important for confirming introgression of genes or genomic regions in cereals but also to reduce the time and cost of identifying them through genetic selection. These biotechnologies also make it possible to identify target genes or quantitative trait loci (QTL) that can be potentially used in similar crops to increase their productivity. This review presents the main advances in the genetic improvement of cereals for Al-tolerance

Stomata regulation by tissue-specific expression of the Citrus sinensis MYB61 transcription factor improves water-use efficiency in Arabidopsis

Water-use efficiency (WUE) is a quantitative measurement of biomass produced per volume of water transpired by a plant. WUE is an important physiological trait for drought response to mitigate the water deficiency. In this work, a cisgenic construction from Citrus sinensis was developed and its function in the improvement of WUE was evaluated in Arabidopsis. Sequences of the CsMYB61 coding region, a transcription factor implicated in the closure of stomata, together with a putative stomata-specific promoter from CsMYB15, were identified and cloned. The protein encoded in the CsMYB61 locus harbors domains and motifs characteristic of MYB61 proteins. In addition, a 1.2 kb promoter region of the gene CsMYB15 (pCsMYB15) containing regulatory elements for expression in guard cells and in response to Abscisic Acid (ABA) and light was isolated. In Arabidopsis, pCsMYB15 directs the expression of the reporter gene GUS in stomata in the presence of light. In addition, transgenic lines expressing the CsMYB61 coding region under transcriptional control of pCsMYB15 have a normal phenotype under in vitro and greenhouse conditions. These transgenic lines exhibited a smaller opening of the stomata pore, lower stomatal conductance and respiration rate, enhanced sensitivity to exogenous ABA, and high drought stress tolerance. Our results indicate that stomata-specific expression of CsMYB61 enhances water use efficiency under drought conditions in Arabidospi

The photomorphogenic factors UV-B RECEPTOR 1, ELONGATED HYPOCOTYL 5, and HY5 HOMOLOGUE are part of the UV-B signalling pathway in grapevine and mediate flavonol accumulation in response to the environment

Grapevine (Vitis vinifera L.) is a species well known for its adaptation to radiation. However, photomorphogenic factors related to UV-B responses have not been molecularly characterized. We cloned and studied the role of UV-B RECEPTOR (UVR1), ELONGATED HYPOCOTYL 5 (HY5), and HY5 HOMOLOGUE (HYH) from V. vinifera. We performed gene functional characterizations, generated co-expression networks, and tested them in different environmental conditions. These genes complemented the Arabidopsis uvr8 and hy5 mutants in morphological and secondary metabolic responses to radiation. We combined microarray and RNA sequencing (RNA-seq) data with promoter inspections to identify HY5 and HYH putative target genes and their DNA binding preferences. Despite sharing a large set of common co-expressed genes, we found different hierarchies for HY5 and HYH depending on the organ and stress condition, reflecting both co-operative and partially redundant roles. New candidate UV-B gene markers were supported by the presence of HY5-binding sites. These included a set of flavonol-related genes that were up-regulated in a HY5 transient expression assay. We irradiated in vitro plantlets and fruits from old potted vines with high and low UV-B exposures and followed the accumulation of flavonols and changes in gene expression in comparison with non-irradiated conditions. UVR1, HY5, and HYH expression varied with organ, developmental stage, and type of radiation. Surprisingly, UVR1 expression was modulated by shading and temperature in berries, but not by UV-B radiation. We propose that the UV-B response machinery favours berry flavonol accumulation through the activation of HY5 and HYH at different developmental stages at both high and low UV-B exposures. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology

Role of boron and its interaction with other elements in plants

Boron (B) is an essential microelement for plants, and its deficiency can lead to impaired development and function. Around 50% of arable land in the world is acidic, and low pH in the soil solution decreases availability of several essential mineral elements, including B, magnesium (Mg), calcium (Ca), and potassium (K). Plants take up soil B in the form of boric acid (H3BO3) in acidic soil or tetrahydroxy borate [B(OH)4]- at neutral or alkaline pH. Boron can participate directly or indirectly in plant metabolism, including in the synthesis of the cell wall and plasma membrane, in carbohydrate and protein metabolism, and in the formation of ribonucleic acid (RNA). In addition, B interacts with other nutrients such as Ca, nitrogen (N), phosphorus (P), K, and zinc (Zn). In this review, we discuss the mechanisms of B uptake, absorption, and accumulation and its interactions with other elements, and how it contributes to the adaptation of plants to different environmental conditions. We also discuss potential B-mediated networks at the physiological and molecular levels involved in plant growth and development