Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture

BACKGROUND

Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied.

RESULTS

To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits.

CONCLUSION

Our analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.

Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud

African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.

The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice

The architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. In particular, the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem governs the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in Oryza sativa (rice). Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq, we observed that two ALOG genes, OsG1-like 1 (OsG1L1) and OsG1L2, have expression profiles similar to that of TAW1. Here, we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes to the phenotype of the previously published taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the data sets were used for the construction of a gene regulatory network (GRN), proposing interactions among genes potentially involved in controlling inflorescence development in rice. In this GRN, we selected the homeodomain-leucine zipper transcription factor encoding the gene OsHOX14 for further characterization. The spatiotemporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new proteins involved in rice inflorescence development.

Identification of bacterial and fungal pathogens directly from clinical blood cultures using whole genome sequencing

Bloodstream infections are a major cause of morbidity and mortality worldwide. Early administration of appropriate antimicrobial therapy can improve patient survival and prevent antimicrobial resistance (AMR). Whole genome sequencing (WGS) can provide information for pathogen identification, AMR prediction and sequence typing earlier than current phenotypic diagnostic methods. WGS was performed on 97 clinical blood specimens and matched culture isolate pairs. Specimen/isolate pairs were MLST sequence-typed and further characterization was performed on Streptococcus species. WGS correctly identified 91.7% of clinical specimens and 93.2% of matched isolates representing 35 different microbial species. MLST types were assigned for 89.9% of matched cultures and 21.7% of blood specimens, with higher success for blood culture specimens extracted within 3 days (52% characterized) than 7 days (9.3%). This study demonstrates the potential use of WGS for identification and characterization of pathogens directly from blood culture specimens to facilitate timely initiation of appropriate antimicrobial therapies.

Micro-RNA-Regulated SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Expression and Cytokinin Accumulation Distinguish Early-Developing Male and Female Inflorescences in Oil Palm (Elaeis guineensis)

Sexual differentiation of inflorescences and flowers is important for reproduction and affects crop plant productivity. We report here on a molecular study of the process of sexual differentiation in the immature inflorescence of oil palm (Elaeis guineensis). This species is monoecious and exhibits gender diphasy, producing male and female inflorescences separately on the same plant in alternation. Three main approaches were used: small RNA-seq to characterise and study the expression of miRNA genes; RNA-seq to monitor mRNA accumulation patterns; hormone quantification to assess the role of cytokinins and auxins in inflorescence differentiation. Our study allowed the characterisation of 30 previously unreported palm MIRNA genes. In differential gene and miRNA expression studies, we identified a number of key developmental genes and miRNA-mRNA target modules previously described in relation to their developmental regulatory role in the cereal panicle, notably the miR156/529/535-SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) gene regulatory module. Gene enrichment analysis highlighted the importance of hormone-related genes, and this observation was corroborated by the detection of much higher levels of cytokinins in the female inflorescence. Our data illustrate the importance of branching regulation within the developmental window studied, during which the female inflorescence, unlike its male counterpart, produces flower clusters on new successive axes by sympodial growth.

Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote)

BACKGROUND AND AIMS

The pacaya palm is a dioecious neotropical palm species that is exploited in Latin America for its male inflorescence, which is edible when immature. It is cultivated, in a non-intensive manner, in Guatemala, where a morphotype occurs that produces much larger, more highly branched inflorescences compared with wild palms. We sought to identify molecular factors underlying this phenotypic divergence, which is likely to be a product of domestication.

METHODS

We performed RNA-seq-based studies on immature pacaya palm male inflorescences in order to identify genes that might be directly or indirectly affected in their expression in relation to domestication. We also measured the accumulation of a range of soluble sugar molecules to provide information on the biochemical status of the two different types of material.

KEY RESULTS

A total of 408 genes were found to display significantly different expression levels between the wild and cultivated morphotypes. Three different functional categories were found to be enriched in the gene set that was upregulated in the cultivated morphotype: redox balance; secondary metabolism; and transport. Several sugars were found to accumulate at higher levels in inflorescences of the cultivated morphotype, in particular myo-inositol, fructose and glucose.

CONCLUSIONS

The observed upregulation of redox-related genes in the cultivated morphotype is corroborated by the observation of higher myo-inositol accumulation, which has been shown to be associated with enhanced scavenging of reactive oxygen species in other plants and which may affect meristem activity.

Functional Diversification of euANT/PLT Genes in Oryza sativa Panicle Architecture Determination

Grain yield, which is one of the most important traits in rice breeding, is controlled in part by panicle branching patterns. Numerous genes involved in the control of panicle architecture have been identified through mutant and QTL characterization. Previous studies suggested the importance of several AP2/ERF transcription factor-encoding genes in the control of panicle development, including the AINTEGUMENTA/PLETHORA-like (euANT/PLT) genes. The ANT gene was specifically considered to be a key regulator of shoot and floral development in Arabidopsis thaliana. However, the likely importance of paralogous euANT/PLT genes in the regulation of meristem identities and activities during panicle architecture development has not to date been fully addressed in rice. In this study, we observed that the rice euANT/PLT genes displayed divergent temporal expression patterns during the branching stages of early panicle development, with spatial localization of expression in meristems for two of these genes. Moreover, a functional analysis of rice ANT-related genes using genome editing revealed their importance in the control of panicle architecture, through the regulation of axillary meristem (AM) establishment and meristem fate transition. Our study suggests that the paralogous euANT/PLT genes have become partially diversified in their functions, with certain opposing effects, since they arose from ancestral gene duplication events, and that they act in regulating the branching of the rice panicle.

Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice

Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study, we generated an atlas of genes expressed in developing crown root primordia in comparison with adjacent stem cortical tissue at three different developmental stages before emergence, using laser capture microdissection. We identified 3975 genes differentially expressed in crown root primordia. About 30% of them were expressed at the three developmental stages, whereas 10.5%, 19.5% and 12.8% were specifically expressed at the early, intermediate and late stages, respectively. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. Cross-analysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeling enzymes that are likely to play a key role during crown root primordia formation. This atlas constitutes an open primary data resource for further studies on the regulation of crown root initiation and development.

Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

BACKGROUND

African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species.

RESULTS

Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we found several association peaks, one of which co-localised with a well described gene in the Asian rice flowering pathway, OsGi, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting genomic regions and candidate genes. Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations.

CONCLUSION

Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

CRISPR-mediated accelerated domestication of African rice landraces

African Oryza glaberrima and Oryza sativa landraces are considered valuable resources for breeding traits due to their adaptation to local environmental and soil conditions. They often possess superior resistance to endemic pests and tolerance to drought and nutrient deficiencies when compared to the "imported" high production Asian rice varieties. In contrast, "domestication traits" such as seed shattering, lodging, and seed yield are not well established in these African landraces. Therefore, the use of these African varieties for high production agriculture is limited by unpredictable yield and grain quality. We are addressing this shortcoming by developing protocols for genetically transforming African landraces to allow the use of CRISPR-Cas mediated breeding approaches. Here we use as proof of concept the cultivated African landrace Kabre to target selected known "domestication loci" and improve the agronomic potential of Kabre rice. Stable genetic transformation with CRISPR-Cas9-based vectors generated single and simultaneous multiple gene knockouts. Plants with reduced stature to diminish lodging were generated by disrupting the HTD1 gene. Furthermore, three loci shown to control seed size and/or yield (GS3, GW2 and GN1A) were targeted using a multiplex CRISPR-Cas9 construct. This resulted in mutants with significantly improved seed yield. Our study provides an example of how new breeding technologies can accelerate the development of highly productive African landrace rice varieties, an important advancement considering that Africa is a hotspot for worldwide population growth and therefore prone to food shortage.

A set of AP2-like genes is associated with inflorescence branching and architecture in domesticated rice

Rice yield is influenced by inflorescence size and architecture, and inflorescences from domesticated rice accessions produce more branches and grains. Neither the molecular control of branching nor the developmental differences between wild and domesticated rice accessions are fully understood. We surveyed phenotypes related to branching, size, and grain yield across 91 wild and domesticated African and Asian accessions. Characteristics related to axillary meristem identity were the main phenotypic differences between inflorescences from wild and domesticated accessions. We used whole transcriptome sequencing in developing inflorescences to measure gene expression before and after the transition from branching axillary meristems to determinate spikelet meristems. We identified a core set of genes associated with axillary meristem identity in Asian and African rice, and another set associated with phenotypic variability between wild and domesticated accessions. AP2/EREBP-like genes were enriched in both sets, suggesting that they are key factors in inflorescence branching and rice domestication. Our work has identified new candidates in the molecular control of inflorescence development and grain yield, and provides a detailed description of the effects of domestication on phenotype and gene expression.

Risk of recurrence and death in patients with breast cancer after delayed deep inferior epigastric perforator flap reconstruction

Background

Postmastectomy reconstruction using a deep inferior epigastric perforator (DIEP) flap is increasingly being performed in patients with breast cancer. The procedure induces extensive tissue trauma, and it has been hypothesized that the release of growth factors, angiogenic agonists and immunomodulating factors may reactivate dormant micrometastasis. The aim of the present study was to estimate the risk of breast cancer recurrence in patients undergoing DIEP flap reconstruction compared with that in patients treated with mastectomy alone.

Methods

Each patient who underwent delayed DIEP flap reconstruction at Karolinska University Hospital, Sweden, between 1999 and 2013, was compared with up to four controls with breast cancer who did not receive a DIEP flap. The control patients were selected using incidence density matching with respect to age, tumour and nodal status, neoadjuvant therapy and year of mastectomy. The primary endpoint was breast cancer‐specific survival. Survival analysis was carried out using Kaplan–Meier survival estimates and Cox proportional hazard regression analysis.

Results

The analysis included 250 patients who had 254 DIEP flap reconstructions and 729 control patients. Median follow‐up was 89 and 75 months respectively (P = 0·053). Breast cancer recurrence developed in 50 patients (19·7 per cent) in the DIEP group and 174 (23·9 per cent) in the control group (P = 0·171). The 5‐year breast cancer‐specific survival rate was 92·0 per cent for patients with a DIEP flap and 87·9 per cent in controls (P = 0·032). Corresponding values for 5‐year overall survival were 91·6 and 84·7 per cent (P < 0·001). After adjustment for tumour and patient characteristics and treatment, patients without DIEP flap reconstruction had significantly lower overall but not breast cancer‐specific survival.

Conclusion

The present findings do not support the hypothesis that patients with breast cancer undergoing DIEP flap reconstruction have a higher rate of breast cancer recurrence than those who have mastectomy alone.

Deep inferior epigastric perforator is safe

Abstract P4-13-14: Risk of recurrence and death in breast cancer patients after delayed deep inferior epigastric perforator flap reconstruction

PURPOSE

Post-mastectomy reconstruction using the deep inferior epigastric perforator (DIEP) flap is increasingly performed in breast cancer patients. The procedure induces large tissue trauma and it has been hypothesized that the release of growth factors, angiogenic agonists and immunomodulating factors may reactivate dormant micrometastasis. The aim of our study was to contrast the risk of breast cancer recurrence in patients undergoing DIEP reconstruction to patients treated with mastectomy alone.

PATIENTS AND METHODS

We conducted a retrospective nested case-control study. Cases were defined as breast cancer patients operated with delayed DIEP reconstruction at Karolinska University Hospital, Sweden, between 1999-2013. Three controls, defined as breast cancer patients operated with conventional mastectomy without delayed reconstruction, were matched to each case based on age, tumour stage and year of mastectomy. The primary endpoint was breast cancer-specific survival. Survival analysis was carried out by Kaplan–Meier survival estimates and Cox proportional hazard regression analysis.

RESULTS

In all, 254 cases and 729 controls were included and had a median follow up of 134 and 122 months, respectively (p=0.004). Breast cancer recurrence occurred in 50 (19.7%) cases and 174 (23.9%) controls, respectively (p=0.171). Ten-year breast cancer-specific survival was 90.7% for cases and 85.2% in controls (p=0.067). The corresponding figures for 10-year overall survival was 89.6% and 80.0%, respectively (p&lt;0.001). Higher tumor stage and positive axillary lymph nodes, but not DIEP reconstruction, were independent risk factors for death due to breast cancer.

CONCLUSION

Our findings did not support the hypothesis that breast cancer patients undergoing DIEP reconstruction would have a higher rate of breast cancer recurrence than patients undergoing mastectomy alone.

Citation Format: Adam H, Docherty Skogh A-C, Edsander Nord Å, Schultz I, Gahm J, Hall P, Frisell J, Halle M, de Boniface J. Risk of recurrence and death in breast cancer patients after delayed deep inferior epigastric perforator flap reconstruction [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-13-14.

[French recommendations on control measures to reduce the infectious risk in immunocompromised patients]

The increase use of immunosuppressive treatments in patients with solid cancer and/or inflammatory diseases requires revisiting our practices for the prevention of infectious risk in the care setting. A review of the literature by a multidisciplinary working group at the beginning of 2014 wished to answer the following 4 questions to improve healthcare immunocompromised patients: (I) How can we define immunocompromised patients with high, intermediate and low infectious risk, (II) which air treatment should be recommended for this specific population? (III) What additional precautions should be recommended for immunocompromised patients at risk for infection? (IV) Which global environmental control should be recommended? Based on data from the literature and using the GRADE method, we propose 15 recommendations that could help to reduce the risk of infection in these exposed populations.

Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice

Background

The African rice Oryza glaberrima was domesticated from its wild relative Oryza barthii about 3000 years ago. During the domestication process, panicle complexity changed from a panicle with low complexity in O. barthii, to a highly branched panicle carrying more seeds in O. glaberrima. To understand the basis of this differential panicle development between the two species, we conducted morphological and molecular analyses of early panicle development.

Results

Using X-ray tomography, we analyzed the morphological basis of early developmental stages of panicle development. We uncovered evidence for a wider rachis meristem in O. glaberrima than in O. barthii. At the molecular level, spatial and temporal expression profiles of orthologs of O. sativa genes related to meristem activity and meristem fate control were obtained using in situ hybridization and qRT-PCR. Despite highly conserved spatial expression patterns between O. glaberrima and O. barthii, differences in the expression levels of these early acting genes were detected.

Conclusion

The higher complexity of the O. glaberrima panicle compared to that of its wild relative O. barthii is associated with a wider rachis meristem and a modification of expression of branching-related genes. Our study indicates that the expression of genes in the miR156/miR529/SPL and TAW1 pathways, along with that of their target genes, is altered from the unbranched stage of development. This suggests that differences in panicle complexity between the two African rice species result from early alterations to gene expression during reproductive development.

Electronic supplementary material

The online version of this article (doi:10.1186/s13227-017-0065-y) contains supplementary material, which is available to authorized users.

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

BACKGROUND

Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii.

RESULTS

Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems.

CONCLUSION

Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.

Rice panicle plasticity in Near Isogenic Lines carrying a QTL for larger panicle is genotype and environment dependent

BACKGROUND

Panicle architectural traits in rice (branching, rachis length, spikelet number) are established between panicle initiation and heading stages. They vary among genotypes and are prone to Genotype x Environment interactions. Together with panicle number, panicle architecture determines sink-based yield potential. Numerous studies analyzed genetic and environmental variation of plant morphology, but the plasticity of panicle structure is less well understood. This study addressed the response of rice panicle size and structure to limited light availability at plant level for near-isogenic lines (NILs) with IR64 or IRRI146 backgrounds, carrying the QTL qTSN4 (syn. SPIKE) for large panicles. Full light and shading in the greenhouse and two population densities in the field were implemented. The image analysis tool P-TRAP was used to analyze the architecture of detached panicles.

RESULTS

The qTSN4 increased total branch length, branching frequency and spikelet number per panicle in IRRI146 background in the field and greenhouse, and in IR64 background in the greenhouse, but not for IR64 in the field. In the field, however, qTSN4 reduced panicle number, neutralizing any potential yield gains from panicle size. Shading during panicle development reduced spikelet and branch number but qTSN4 mitigated partly this effect. Spikelet number over total branch length (spikelet density) was a stable allometry across genotypes and treatments with variation in spikelet number mainly due to the frequency of secondary branches. Spikelet number on the main tiller was correlated with stem growth rate during panicle development, indicating that effects on panicle size seemed related to resources available per tiller.

CONCLUSIONS

The qTSN4 effects on panicle spikelet number appear as indirect and induced by upstream effects on pre-floral assimilate resources at tiller level, as they were (1) prone to G x E interactions, (2) non-specific with respect to panicle architectural traits, and (3) associated with pre-floral stem growth rate.

Micafungin as primary antifungal prophylaxis in patients presenting with acute myeloid leukemia

OBJECTIVE

To study the efficacy and safety of micafungin for prophylaxis of invasive fungal infections in patients undergoing induction chemotherapy for acute myeloid leukemia.

PATIENTS AND METHODS

A prospective observational single-center study of 41 patients from the hematology department between May 2012 and April 2015. Micafungin was administered once daily from the first day of induction chemotherapy to the end of the neutropenic phase.

RESULTS

Neither Candida nor Aspergillus infection was documented in our 41 patients from the first day of micafungin infusion to the end of the neutropenic phase. Patients were followed for three months after discontinuation of micafungin and none of them contracted an invasive fungal infection. Only one patient presented with grade III-IV hepatic and ionic toxicities.

CONCLUSION

Micafungin is associated with a good safety profile and is an interesting option for preventing invasive fungal infections in the high-risk population of patients presenting with hematological disorders.

Gene expression profiling of reproductive meristem types in early rice inflorescences by laser microdissection

In rice, inflorescence architecture is established at early stages of reproductive development and contributes directly to grain yield potential. After induction of flowering, the complexity of branching, and therefore the number of seeds on the panicle, is determined by the activity of different meristem types and the timing of transitions between them. Although some of the genes involved in these transitions have been identified, an understanding of the network of transcriptional regulators controlling this process is lacking. To address this we used a precise laser microdissection and RNA-sequencing approach in Oryza sativa ssp. japonica cv. Nipponbare to produce quantitative data that describe the landscape of gene expression in four different meristem types: the rachis meristem, the primary branch meristem, the elongating primary branch meristem (including axillary meristems), and the spikelet meristem. A switch in expression profile between apical and axillary meristem types followed by more gradual changes during transitions in axillary meristem identity was observed, and several genes potentially involved in branching were identified. This resource will be vital for a mechanistic understanding of the link between inflorescence development and grain yield.

Identification of CROWN ROOTLESS1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation

In monocotyledons, the root system is mostly composed of postembryonic shoot-borne roots called crown roots. In rice (Oryza sativa), auxin promotes crown root initiation via the LOB-domain transcription factor (LBD) transcription factor CROWN ROOTLESS1 (CRL1); however, the gene regulatory network downstream of CRL1 remains largely unknown. We tested CRL1 transcriptional activity in yeast and in planta, identified CRL1-regulated genes using an inducible gene expression system and a transcriptome analysis, and used in situ hybridization to demonstrate coexpression of a sample of CRL1-regulated genes with CRL1 in crown root primordia. We show that CRL1 positively regulates 277 genes, including key genes involved in meristem patterning (such as QUIESCENT-CENTER SPECIFIC HOMEOBOX; QHB), cell proliferation and hormone homeostasis. Many genes are homologous to Arabidopsis genes involved in lateral root formation, but about a quarter are rice-specific. Our study reveals that several genes acting downstream of LBD transcription factors controlling postembryonic root formation are conserved between monocots and dicots. It also provides evidence that specific genes are involved in the formation of shoot-derived roots in rice.

An extensive analysis of the African rice genetic diversity through a global genotyping

We present here the first curated collection of wild and cultivated African rice species. For that, we designed specific SNPs and were able to structure these very low diverse species. Oryza glaberrima, the cultivated African rice, is endemic from Africa. This species and its direct ancestor, O. barthii, are valuable tool for improvement of Asian rice O. sativa in terms of abiotic and biotic stress resistance. However, only a few limited studies about the genetic diversity of these species were performed. In the present paper, and for the first time at such extend, we genotyped 279 O. glaberrima, selected both for their impact in current breeding and for their geographical distribution, and 101 O. barthii, chosen based on their geographic origin, using a set of 235 SNPs specifically designed for African rice diversity. Using those data, we were able to structure the individuals from our sample in three populations for O. barthii, related to geography, and two populations in O. glaberrima; these two last populations cannot be linked however to any currently phenotyped trait. Moreover, we were also able to identify misclassification in O. glaberrima as well as in O. barthii and identified new form of O. sativa from the set of African varieties.

Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima)

The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA-seq technology, we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using approximate Bayesian computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived nonsynonymous substitution that we detected suggests that the O. glaberrima population suffered from the 'cost of domestication'. In addition, we used this genome-scale data set to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.

Re-evaluation of rejection criteria for endotracheal tube (ETT) specimens from adult patients

The purpose of this study was to determine optimal criteria for microbiology laboratory screening of endotracheal tube (ETT) specimens submitted for bacterial culture from adult patients. ETT specimens from adult patients that were received by two microbiology laboratories were prospectively evaluated and subdivided into one of three study arms with the following criteria: <10 squamous epithelial cells (SECs) per low-power field with bacteria seen on Gram staining (arm 1), >10 SECs per low-power field with bacteria seen on Gram staining (arm 2) and <10 SECs per low-power field with no bacteria seen on Gram staining (arm 3). A fourth study arm (>10 SECs per low-power field with no bacteria seen on Gram staining) was planned but this arm was terminated due to the paucity of specimens meeting these criteria. Isolate evaluation was performed using standard microbiology protocols. A limited chart review was undertaken at one of the institutions, only reviewing patients from which a potential pathogen was recovered on culture. In total, 141 ETT specimens were evaluated. A potential respiratory pathogen was recovered from 54, 37 and 10 % of specimens in study arms 1, 2, and 3, respectively (P<0.0001, comparing between arm 1 and arm 3). For the 23 patients included in the chart review from whom a potential pathogen was recovered on culture, respiratory infection was considered to be present in 50 % (6/12) of patients in arm 1, 66.6 % (6/9) of patients in arm 2 and 100 % (2/2) of patients in arm 3. Therapy was rarely altered based on culture results. In this study, the ETT specimens submitted for bacterial culture were of limited benefit to clinicians. The data presented here support the use of an absence of bacteria on Gram staining as a rejection criterion for ETT specimens. The criterion of >10 SECs per low-power field should be further evaluated in a prospective study of patients with an unequivocal clinical diagnosis of pneumonia.

Change in antimicrobial susceptibility of Escherichia coli urinary tract isolates at a single institution over a period of 10 years

Urinary tract infections are common. Few published studies have demonstrated the change in Escherichia coli urinary isolate antimicrobial susceptibility over time within a given area and (or) population. The purpose of this study was to evaluate the change in susceptibility of E. coli clinical isolates obtained from urine specimens at a single institution over a period of 10 years. The microbiology laboratory information system at St. Boniface Hospital (Winnipeg, Manitoba, Canada) was searched retrospectively from 1 January 2000 to 31 December 2009, for all E. coli isolates from either a midstream or catheter urine source that had susceptibility testing performed. Only one isolate per patient was included during the entire study period. Antimicrobial susceptibility testing was carried out with either a Microscan instrument (pre-April 2004) or a Vitek instrument (May 2004 onwards). In total, 7353 E. coli urinary isolates were included for evaluation. Ciprofloxacin susceptibility declined significantly, from 99% in 2000 to 85% in 2009 (p < 0.0001). A small but statistically significant decline in susceptibility was also observed for ampicillin, cefazolin, trimethoprim-sulfamethoxazole, gentamicin, and nitrofurantoin. These data suggest that certain antimicrobials recommended for the treatment of urinary tract infections (ciprofloxacin, trimethoprim-sulfamethoxazole) may no longer be optimal.

Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae

BACKGROUND AND AIMS

Molecular phylogenetic studies of palms (Arecaceae) have not yet provided a fully resolved phylogeny of the family. There is a need to increase the current set of markers to resolve difficult groups such as the Neotropical subtribe Bactridinae (Arecoideae: Cocoseae). We propose the use of two single-copy nuclear genes as valuable tools for palm phylogenetics.

METHODS

New primers were developed for the amplification of the AGAMOUS 1 (AG1) and PHYTOCHROME B (PHYB) genes. For the AGAMOUS gene, the paralogue 1 of Elaeis guineensis (EgAG1) was targeted. The region amplified contained coding sequences between the MIKC K and C MADS-box domains. For the PHYB gene, exon 1 (partial sequence) was first amplified in palm species using published degenerate primers for Poaceae, and then specific palm primers were designed. The two gene portions were sequenced in 22 species of palms representing all genera of Bactridinae, with emphasis on Astrocaryum and Hexopetion, the status of the latter genus still being debated.

KEY RESULTS

The new primers designed allow consistent amplification and high-quality sequencing within the palm family. The two loci studied produced more variability than chloroplast loci and equally or less variability than PRK, RPBII and ITS nuclear markers. The phylogenetic structure obtained with AG1 and PHYB genes provides new insights into intergeneric relationships within the Bactridinae and the intrageneric structure of Astrocaryum. The Hexopetion clade was recovered as monophyletic with both markers and was weakly supported as sister to Astrocaryum sensu stricto in the combined analysis. The rare Astrocaryum minus formed a species complex with Astrocaryum gynacanthum. Moreover, both AG1 and PHYB contain a microsatellite that could have further uses in species delimitation and population genetics.

CONCLUSIONS

AG1 and PHYB provide additional phylogenetic information within the palm family, and should prove useful in combination with other genes to improve the resolution of palm phylogenies.

Environmental regulation of sex determination in oil palm: current knowledge and insights from other species

BACKGROUND

The African oil palm (Elaeis guineensis) is a monoecious species of the palm subfamily Arecoideae. It may be qualified as 'temporally dioecious' in that it produces functionally unisexual male and female inflorescences in an alternating cycle on the same plant, resulting in an allogamous mode of reproduction. The 'sex ratio' of an oil palm stand is influenced by both genetic and environmental factors. In particular, the enhancement of male inflorescence production in response to water stress has been well documented.

SCOPE

This paper presents a review of our current understanding of the sex determination process in oil palm and discusses possible insights that can be gained from other species. Although some informative phenological studies have been carried out, nothing is as yet known about the genetic basis of sex determination in oil palm, nor the mechanisms by which this process is regulated. Nevertheless new genomics-based techniques, when combined with field studies and biochemical and molecular cytological-based approaches, should provide a new understanding of the complex processes governing oil palm sex determination in the foreseeable future. Current hypotheses and strategies for future research are discussed.

Insights from ANA-grade angiosperms into the early evolution of CUP-SHAPED COTYLEDON genes

BACKGROUND AND AIMS

The closely related NAC family genes NO APICAL MERISTEM (NAM) and CUP-SHAPED COTYLEDON3 (CUC3) regulate the formation of boundaries within and between plant organs. NAM is post-transcriptionally regulated by miR164, whereas CUC3 is not. To gain insight into the evolution of NAM and CUC3 in the angiosperms, we analysed orthologous genes in early-diverging ANA-grade angiosperms and gymnosperms.

METHODS

We obtained NAM- and CUC3-like sequences from diverse angiosperms and gymnosperms by a combination of reverse transcriptase PCR, cDNA library screening and database searching, and then investigated their phylogenetic relationships by performing maximum-likelihood reconstructions. We also studied the spatial expression patterns of NAM, CUC3 and MIR164 orthologues in female reproductive tissues of Amborella trichopoda, the probable sister to all other flowering plants.

KEY RESULTS

Separate NAM and CUC3 orthologues were found in early-diverging angiosperms, but not in gymnosperms, which contained putative orthologues of the entire NAM + CUC3 clade that possessed sites of regulation by miR164. Multiple paralogues of NAM or CUC3 genes were noted in certain taxa, including Brassicaceae. Expression of NAM, CUC3 and MIR164 orthologues from Am. trichopoda was found to co-localize in ovules at the developmental boundary between the chalaza and nucellus.

CONCLUSIONS

The NAM and CUC3 lineages were generated by duplication, and CUC3 was subsequently lost regulation by miR164, prior to the last common ancestor of the extant angiosperms. However, the paralogous NAM clade genes CUC1 and CUC2 were generated by a more recent duplication, near the base of Brassicaceae. The function of NAM and CUC3 in defining a developmental boundary in the ovule appears to have been conserved since the last common ancestor of the flowering plants, as does the post-transcriptional regulation in ovule tissues of NAM by miR164.

Divergent expression patterns of miR164 and CUP-SHAPED COTYLEDON genes in palms and other monocots: implication for the evolution of meristem function in angiosperms

In order to understand how the morphology of plant species has diversified over time, it is necessary to decipher how the underlying developmental programs have evolved. The regulatory network controlling shoot meristem activity is likely to have played an important role in morphological diversification and useful insights can be gained by comparing monocots and eudicots. These two distinct monophyletic groups of angiosperms diverged 130 Ma and are characterized by important differences in their morphology. Several studies of eudicot species have revealed a conserved role for NAM and CUC3 genes in meristem functioning and pattern formation through the definition of morphogenetic boundaries during development. In this study, we show that NAM- and CUC3-related genes are conserved in palms and grasses, their diversification having predated the radiation of monocots and eudicots. Moreover, the NAM-miR164 posttranscriptional regulatory module is also conserved in palm species. However, in contrast to the CUC3-related genes, which share a similar expression pattern between the two angiosperm groups, the expression domain of the NAM-miR164 module differs between monocot and eudicot species. In our studies of spatial expression patterns, we compared existing eudicot data with novel results from our work using two palm species (date palm and oil palm) and two members of the Poaceae (rice and millet). In addition to contrasting results obtained at the gene expression level, major differences were also observed between eudicot and monocot NAM-related genes in the occurrence of putative cis-regulatory elements in their promoter sequences. Overall, our results suggest that although NAM- and CUC3-related proteins are functionally equivalent between monocots and eudicots, evolutionary radiation has resulted in heterotopy through alterations in the expression domain of the NAM-miR164 regulatory module.

Genetic basis of pearl millet adaptation along an environmental gradient investigated by a combination of genome scan and association mapping

Identifying the molecular bases of adaptation is a key issue in evolutionary biology. Genome scan is an efficient approach for identifying important molecular variation involved in adaptation. Association mapping also offers an opportunity to gain insight into genotype-phenotype relationships. Using these two approaches coupled with environmental data should help to come up with a refined picture of the evolutionary process underlying adaptation. In this study, we first conducted a selection scan analysis on a transcription factor gene family. We focused on the MADS-box gene family, a gene family which plays a crucial role in vegetative and flower development. Twenty-one pearl millet populations were sampled along an environmental gradient in West Africa. We identified one gene, i.e. PgMADS11, using Bayesian analysis to detect selection signatures. Polymorphism at this gene was also associated with flowering time variation in an association mapping framework. Finally, we found that PgMADS11 allele frequencies were closely associated with annual rainfall. Overall, we determined an efficient way to detect functional polymorphisms associated with climate variation in non-model plants by combining genome scan and association mapping. These results should help monitor the impact of recent climatic changes on plant adaptation.

Cell cycle arrest characterizes the transition from a bisexual floral bud to a unisexual flower in Phoenix dactylifera

BACKGROUND AND AIMS

Phoenix dactylifera (date palm) is a dioecious species displaying strong dimorphism between pistillate and staminate flowers. The mechanisms involved in the development of unisexual flowers are as yet unknown.

METHODS

This paper describes the results of inflorescence and flower development studies using different histological and molecular cytological approaches. Nuclear integrity and cell division patterns in reproductive organs were investigated through DAPI staining and in situ hybridization using a histone H4 gene probe.

KEY RESULTS

The earliest sex-related difference in flower buds is observed at an otherwise 'bisexual' stage, at which the number of cells in the gynoecium of pistillate flowers is higher than in their staminate counterparts. In the pistillate flower, staminodes (sterile stamens) display precocious arrest of development followed by cell differentiation. In the staminate flower, pistillodes (sterile gynoecium) undergo some degree of differentiation and their development ceases shortly after the ovule has been initiated. Staminode and pistillode cells exhibit nuclear integrity although they did not show any accumulation of histone H4 gene transcripts.

CONCLUSIONS

These results strongly suggest that the developmental arrest of sterile sex organs and the subsequent unisexuality of date palm flowers result from a cessation of cell division and precocious cell differentiation rather than from cell death.

Graft-transmissible induction of potato tuberization by the microRNA miR172

The photoreceptor phytochrome B (PHYB) and the homeodomain protein BEL5 are involved in the response of potato tuber induction to the photoperiod. However, whether they act in the same tuberization pathway is unknown. Here we show the effect of a microRNA, miR172, on this developmental event. miR172 levels are higher under tuber-inducing short days than under non-inductive long days and are upregulated in stolons at the onset of tuberization. Overexpression of this microRNA in potato promotes flowering, accelerates tuberization under moderately inductive photoperiods and triggers tuber formation under long days. In plants with a reduced abundance of PHYB, which tuberize under long days, both BEL5 mRNA and miR172 levels are reduced in leaves and increased in stolons. This, together with the presence of miR172 in vascular bundles and the graft transmissibility of its effect on tuberization, indicates that either miR172 might be mobile or it regulates long-distance signals to induce tuberization. Consistent with this, plants overexpressing miR172 show increased levels of BEL5 mRNA, which has been reported to be transmissible through grafts. Furthermore, we identify an APETALA2-like mRNA containing a miR172 binding site, which is downregulated in plants overexpressing miR172 and plants in which PHYB is silenced. Altogether, our results suggest that miR172 probably acts downstream of the tuberization repressor PHYB and upstream of the tuberization promoter BEL5 and allow us to propose a model for the control of tuberization by PHYB, miR172 and BEL5.

The endocrine status of gossypol - treated male rats

Male adult Wistar rats were exposed daily or every other day to oral gossypol acetic acid (GAA) concentrations of 2.5-30 mg/kg for 10-20 weeks. Controls received the GAA-suspension medium or were left completely untreated. The serum concentrations of testosterone, LH and FSH as well as the weight of testis, epididymis, prostate, seminal vesicle, coagulating gland, and pituitary were determined. The accessory sex organs were prepared for light microscopy. Significant antifertility effect in these animals was achieved at GAA-dosage of 15 mg/kg and higher. GAA-administration neither altered the serum hormonal profiles nor the reproductive organ weights in comparison to the controls. Accordingly, light microscopical examination revealed no alterations in the histological picture of prostate, seminal vesicle and coagulating gland when compared with the controls. The results indicate that GAA does not interfere with the hypothalamic-pituitary-gonadal axis in male adult rats.

Conversion from carbamazepine or oxcarbazepine to topiramate in adolescents and adults with epilepsy

OBJECTIVE

To explore effectiveness, tolerability and changes in quality of life in patients with epilepsy converting to topiramate (TPM) from carbamazepine (CBZ) or oxcarbazepine (OXC) due to insufficient effectiveness and/or tolerability.

METHODS

A multicenter, open-label, non-interventional trial was used to examine patients (> or = 12 years) with epilepsy, changing to TPM monotherapy from baseline mono- or combination therapy with CBZ or OXC. TPM was added to the existing antiepileptic drug (AED) treatment and started at a dose of 25 mg once daily. The dose was titrated up with 25 mg/day increments, once every 1-2 weeks, until a final dose between 50 and 200 mg/day was reached. On the basis of clinical judgment, the treating physician decided whether or not the existing AED treatment with CBZ or OXC could then be withdrawn. Type and number of seizures, preferred TPM dose, quality of life (QOLIE-10 questionnaire), subjective perception of improvement and adverse events (AE) were documented.

RESULTS

140 patients (53.5% women, mean age 47 years) decided to switch to TPM due to insufficient effectiveness (75% of patients) and/or poor tolerability (80%) of the CBZ/OXC treatment. Average duration of follow-up was 24 weeks with an overall discontinuation rate of 19.3%, mainly due to AEs (12.1%). At study endpoint, the intended shift to TPM monotherapy was achieved in 73% of patients at a median TPM dose of 100 mg/day. A seizure reduction of > or = 50% was achieved in 91% of patients in the last scheduled period (weeks 12-26); 62% of patients entering that period remained seizure free. Quality of life at endpoint improved significantly when compared with baseline for all domains of QOLIE-10 (P < 0.001). Most frequent AEs (reported by > or = 5% of patients) were paresthesia (9.3%), weight loss (7.9%), convulsions (5.7%) and memory disorders (5.0%).

CONCLUSION

In patients with epilepsy, previously not satisfactorily treated with CBZ or OXC, conversion to TPM may result in an improvement in seizure control as well as in quality of life.

Overexpression of TaVRN1 in Arabidopsis promotes early flowering and alters development

TaVRN1, a member of the APETALA1 (AP1) subfamily of MADS-box transcription factors, is a key gene that controls transition from vegetative to reproductive phase in wheat. The accumulation of TaVRN1 transcripts in winter wheat probably requires the down-regulation of TaVRT2, a MADS-box factor that binds and represses the TaVRN1 promoter, and of the flowering repressor TaVRN2. However, the molecular mechanisms by which TaVRN1 functions as an activator of phase transition is unknown. To address this, a combination of gene expression and functional studies was used. RNA in situ hybridization studies showed that TaVRN1 transcripts accumulate in all meristems and primordia associated with flower development. An interaction screen in yeast revealed that TaVRN1 interacts with several proteins involved in different processes of plant development such as transcription factors, kinases and a cyclophilin. Arabidopsis plants overexpressing TaVRN1 flower early and show various levels of modified plant architecture. The ectopic expression causes an overexpression of the AP1 and MAX4 genes, which are associated with flowering and auxin regulation, respectively. The induction of gene expression probably results from the binding of TaVRN1 to CArG motifs present on the AP1 and MAX4 promoters. In contrast, Arabidopsis plants that overexpress TaVRT2, which encodes a putative flowering repressor, show an opposite late flowering phenotype. Together, the data provide molecular evidence that TaVRN1 may have pleiotropic effects in various processes such as control of axillary bud growth, transition to flowering and development of floral organs.

TaVRT2 represses transcription of the wheat vernalization gene TaVRN1

In wheat, VRN1/TaVRN1 and VRN2/TaVRN2 determine the growth habit and flowering time. In addition, the MADS box transcription factor VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (TaVRT2) is also associated with the vernalization response in a manner similar to TaVRN2. However, the molecular relationship between these three genes and their products is unknown. Using transient expression assays in Nicotiana benthamiana, we show that TaVRT2 acts as a repressor of TaVRN1 transcription. TaVRT2 binds the CArG motif in the TaVRN1 promoter and represses its activity in vivo. In contrast, TaVRN2 does not bind the TaVRN1 promoter and has no direct effect on its activity, but it can enhance the repression effect of TaVRT2. This suggests that a repressor complex regulates the expression of TaVRN1. In winter wheat, TaVRT2, TaVRN2 and TaVRN1 transcripts accumulate in the shoot apical meristem and young leaves, and temporal expression is consistent with TaVRT2 and TaVRN2 being repressors of floral transition, whereas TaVRN1 is an activator. Non-vernalized spring wheat grown under a short-day photoperiod accumulates TaVRT2 and shows a delay in flowering, suggesting that TaVRT2 is regulated independently by photoperiod and low temperature. The data presented suggest that TaVRT2, in association with TaVRN2, represses the transcription of TaVRN1.

Interaction network of proteins associated with abiotic stress response and development in wheat

Wheat is the most widely adapted crop to abiotic stresses and considered an excellent system to study stress tolerance in spite of its genetic complexity. Recent studies indicated that several hundred genes are either up- or down-regulated in response to stress treatment. To elucidate the function of some of these genes, an interactome of proteins associated with abiotic stress response and development in wheat was generated using the yeast two-hybrid GAL4 system and specific protein interaction assays. The interactome is comprised of 73 proteins, generating 97 interactions pairs. Twenty-one interactions were confirmed by bimolecular fluorescent complementation in Nicotiana benthamiana. A confidence-scoring system was elaborated to evaluate the significance of the interactions. The main feature of this interactome is that almost all bait proteins along with their interactors were interconnected, creating a spider web-like structure. The interactome revealed also the presence of a "cluster of proteins involved in flowering control" in three- and four-protein interaction loops. This network provides a novel insight into the complex relationships among transcription factors known to play central roles in vernalization, flower initiation and abscisic acid signaling, as well as associations that tie abiotic stress with other regulatory and signaling proteins. This analysis provides useful information in elucidating the molecular mechanism associated with abiotic stress response in plants.