Arabidopsis microarrays identify conserved and differentially expressed genes involved in shoot growth and development from distantly related plant species

Morphological and Genetic Diversity of Cucumber (Cucumis sativus L.) Fruit Development

Cucumber (Cucumis sativus L.) fruits, which are eaten at an immature stage of development, can vary extensively in morphological features such as size, shape, waxiness, spines, warts, and flesh thickness. Different types of cucumbers that vary in these morphological traits are preferred throughout the world. Numerous studies in recent years have added greatly to our understanding of cucumber fruit development and have identified a variety of genetic factors leading to extensive diversity. Candidate genes influencing floral organ establishment, cell division and cell cycle regulation, hormone biosynthesis and response, sugar transport, trichome development, and cutin, wax, and pigment biosynthesis have all been identified as factors influencing cucumber fruit morphology. The identified genes demonstrate complex interplay between structural genes, transcription factors, and hormone signaling. Identification of genetic factors controlling these traits will facilitate breeding for desired characteristics to increase productivity, improve shipping, handling, and storage traits, and enhance consumer-desired qualities. The following review examines our current understanding of developmental and genetic factors driving diversity of cucumber fruit morphology.

The Formation of Fruit Quality in Cucumis sativus L

Cucumber is one of the most widely grown vegetables in China and an indispensable fresh fruit in the diet. With the development of society, the demand of people for cucumber quality is higher and higher. Therefore, cultivating high-quality cucumber varieties is one of the main goals of cucumber breeding. With the rapid development of biotechnology such as molecular marker, cucumber quality control network is becoming clear. In this review, we describe the formation mechanism of cucumber fruit quality from three aspects: (1) the commercial quality of cucumber fruit, (2) nutritional quality formation, and (3) flavor quality of cucumber fruit. In addition, the determinants of cucumber fruit quality were summarized from two aspects of genetic regulation and cultivation methods in order to provide ideas for cucumber researchers and cultivators to improve fruit quality.

Brassinosteroid signaling may regulate the germination of axillary buds in ratoon rice

BACKGROUND

Rice ratooning has traditionally been an important component of the rice cropping system in China. However, compared with the rice of the first harvest, few studies on factors effecting ratoon rice yield have been conducted. Because ratoon rice is a one-season rice cultivated using axillary buds that germinate on rice stakes and generate panicles after the first crop's harvest, its production is mainly affected by the growth of axillary buds. The objectives of this study were to evaluate the sprouting mechanism of axillary buds to improve the ratoon rice yield.

RESULTS

First, we observed the differentiation and growth dynamics of axillary buds at different nodes of Shanyou 63, and found that they differentiated from bottom to top before the heading of the mother stem, and that they developed very slowly. After heading they differentiated from top to bottom, and the ones on the top, especially the top 2nd node, developed much faster than those at the other nodes. The average length and dry weight of the axillary buds were significantly greater than those at other nodes by the yellow ripe stage, and they differentiated into pistils and stamens by 6 d after the yellow ripe stage. The morphology of vegetative organs from regenerated tillers of Shanyou 63 also suggested the superior growth of the upper buds, which was regulated by hormones, in ratoon rice. Furthermore, a comprehensive proteome map of the rice axillary buds at the top 2nd node before and after the yellow ripe stage was established, and some proteins involved in steroid biosynthesis were significantly increased. Of these, four took part in brassinosteroid (BR) biosynthesis. Thus, BR signaling may play a role in the germination of axillary buds of ratoon rice.

CONCLUSIONS

The data provide insights into the molecular mechanisms underlying BR signaling, and may allow researchers to explore further the biological functions of endogenous BRs in the germination of axillary buds of ratoon rice.

Comparative co-expression network analysis extracts the SlHSP70 gene affecting to shoot elongation of tomato

Tomato is one of vegetables crops that has the highest value in the world. Thus, researchers are continually improving the agronomical traits of tomato fruits. Auxins and gibberellins regulate plant growth and development. Aux/indole-3-acetic acid 9 (SlIAA9) and the gene encoding the DELLA protein (SlDELLA) are well-known genes that regulate plant growth and development, including fruit set and enlargement by cell division and cell expansion. The absence of tomato SlIAA9 and SlDELLA results in abnormal shoot growth and leaf shape and giving rise to parthenocarpy. To investigate the key regulators that exist up- or downstream of SlIAA9 and SlDELLA signaling pathways for tomato growth and development, we performed gene co-expression network analysis by using publicly available microarray data to extract genes that are directly connected to the SlIAA9 and SlDELLA nodes, respectively. Consequently, we chose a gene in the group of heat-shock protein (HSP)70s that was connected with the SlIAA9 node and SlDELLA node in each co-expression network. To validate the extent of effect of SlHSP70-1 on tomato growth and development, overexpressing lines of the target gene were generated. We found that overexpression of the targeted SlHSP70-1 resulted in internode elongation, but the overexpressing lines did not show abnormal leaf shape, fruit set, or fruit size when compared with that of the wild type. Our study suggests that the targeted SlHSP70-1 is likely to function in shoot growth, like SlIAA9 and SlDELLA, but it does not contribute to parthenocarpy as well as fruit set. Our study also shows that only a single SlHSP70 out of 25 homologous genes could change the shoot length.

Occurrence of brassinosteroids and influence of 24-epibrassinolide with brassinazole on their content in the leaves and roots of Hordeum vulgare L. cv. Golden Promise

24-epibrassinolide overcame the inhibitory effect of brassinazole on the barley growth and the content of brassinosteroids. The present work demonstrates the occurrence of mainly castasterone, brassinolide and cathasterone and lower amounts of 24-epibrassinolide, 24-epicastasterone, 28-homobrassinolide, typhasterol, 6-deoxocastasterone and 6-deoxotyphasterol in 14-day-old de-etiolated barley (Hordeum vulgare L. cv. Golden Promise). We also investigated the endogenous level of brassinosteroids (BRs) in barley seedlings treated with 24-epibrassinolide (EBL) and/or brassinazole (Brz). To our knowledge, this is the first report related to the occurrence of BRs and application of EBL and Brz in terms of the endogenous content of BRs in barley. Brz as a specific inhibitor of BR biosynthetic reactions decreased the level of BRs in the leaves. Application of EBL showed a weak promotive effect on the BR content in Brz-treated seedlings. Brz also inhibited growth of the seedlings; however, addition of EBL overcame the inhibition. The EBL applied alone at 0.01-1 µM increased the BR level in the leaves but at 10 µM lowered the BR content. In opposition to leaves, the Brz in the concentration range from 0.1 to 1 µM did not significantly affect the content of BRs in the roots. However, application of 10 µM Brz caused BRs to decrease, but treatment of EBL concentrations overcame the inhibitory effect of Brz.

The dehydration stress of couch grass is associated with its lipid metabolism, the induction of transporters and the re-programming of development coordinated by ABA

Background

The wild relatives of crop species represent a potentially valuable source of novel genetic variation, particularly in the context of improving the crop’s level of tolerance to abiotic stress. The mechanistic basis of these tolerances remains largely unexplored. Here, the focus was to characterize the transcriptomic response of the nodes (meristematic tissue) of couch grass (a relative of barley) to dehydration stress, and to compare it to that of the barley crown formed by both a drought tolerant and a drought sensitive barley cultivar.

Results

Many of the genes up-regulated in the nodes by the stress were homologs of genes known to be mediated by abscisic acid during the response to drought, or were linked to either development or lipid metabolism. Transporters also featured prominently, as did genes acting on root architecture. The resilience of the couch grass node arise from both their capacity to develop an altered, more effective root architecture, but also from their formation of a lipid barrier on their outer surface and their ability to modify both their lipid metabolism and transporter activity when challenged by dehydration stress.

Conclusions

Our analysis revealed the nature of dehydration stress response in couch grass. We suggested the tolerance is associated with lipid metabolism, the induction of transporters and the re-programming of development coordinated by ABA. We also proved the applicability of barley microarray for couch grass stress-response analysis.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4700-3) contains supplementary material, which is available to authorized users.

SVP-like MADS Box Genes Control Dormancy and Budbreak in Apple

The annual growth cycle of trees is the result of seasonal cues. The onset of winter triggers an endodormant state preventing bud growth and, once a chilling requirement is satisfied, these buds enter an ecodormant state and resume growing. MADS-box genes with similarity to Arabidopsis SHORT VEGETATIVE PHASE (SVP) [the SVP-like and DORMANCY ASSOCIATED MADS-BOX (DAM) genes] have been implicated in regulating flowering and growth-dormancy cycles in perennials. Here, we identified and characterized three DAM-like (MdDAMs) and two SHORT VEGETATIVE PHASE-like (MdSVPs) genes from apple (Malus × domestica 'Royal Gala'). The expression of MdDAMa and MdDAMc indicated they may play a role in triggering autumn growth cessation. In contrast, the expression of MdDAMb, MdSVPa and MdSVPb suggested a role in maintaining bud dormancy. Consistent with this, ectopic expression of MdDAMb and MdSVPa in 'Royal Gala' apple plants resulted in delayed budbreak and architecture change due to constrained lateral shoot outgrowth, but normal flower and fruit development. The association of MdSVPa and MdSVPb expression with floral bud development in the low fruiting 'Off' trees of a biennial bearing cultivar 'Sciros' suggested the SVP genes might also play a role in floral meristem identity.

QTL mapping of cucumber fruit flesh thickness by SLAF-seq

Cucumber is an agriculturally and economically important vegetable crop worldwide. Fruit flesh thickness is an important trait for cucumber and also a central determinant of yield, yet little is known about the underlying mechanism of this trait. In this study, bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) was applied to finely map the gene that underlies fruit flesh thickness in cucumber. A 0.19-Mb-long quantitative trait locus on chromosome 2 controlling fruit flesh thickness (QTL fft2.1) was identified and further confirmed by simple sequence repeat (SSR) marker-based classical QTL mapping in 138 F₂ individuals. Gene prediction of this 0.19-Mb region identified 20 genes. Quantitative RT-PCR revealed higher expression levels of Csa2 M058670.1 (SET domain protein-lysine methyltransferase) in D8 (thick fruit flesh parent) compared with that in XUE1 (thin fruit flesh parent) during fruit development. Sequence alignment analysis of Csa2M058670.1 from thick and thin fruit flesh cucumber lines revealed a 4-bp deletion mutation in the promoter region of this candidate gene, which may result in the loss of Csa2M058670.1 activation in thin fruit flesh lines. The data presented herein suggest that Csa2M058670.1 is a possible candidate gene for controlling flesh thickness in cucumber.

Brassica villosa, a system for studying non-glandular trichomes and genes in the Brassicas

Brassica villosa is a wild Brassica C genome species with very dense trichome coverage and strong resistance to many insect pests of Brassica oilseeds and vegetables. Transcriptome analysis of hairy B. villosa leaves indicated higher expression of several important trichome initiation genes compared with glabrous B. napus leaves and consistent with the Arabidopsis model of trichome development. However, transcripts of the TRY inhibitory gene in hairy B. villosa were surprisingly high relative to B. napus and relative transcript levels of SAD2, EGL3, and several XIX genes were low, suggesting potential ancillary or less important trichome-related roles for these genes in Brassica species compared with Arabidopsis. Several antioxidant, calcium, non-calcium metal and secondary metabolite genes also showed differential expression between these two species. These coincided with accumulation of two alkaloid-like compounds, high levels of calcium, and other metals in B. villosa trichomes that are correlated with the known tolerance of B. villosa to high salt and the calcium-rich natural habitat of this wild species. This first time report on the isolation of large amounts of pure B. villosa trichomes, on trichome content, and on relative gene expression differences in an exceptionally hairy Brassica species compared with a glabrous species opens doors for the scientific community to understand trichome gene function in the Brassicas and highlights the potential of B. villosa as a trichome research platform.

Tissue-specific transcriptomic profiling of Sorghum propinquum using a rice genome array

Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were expressed predominantly in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in Oryza longistaminata and S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development.

Microarray analysis of differentially expressed genes between Brassica napus strains with high- and low-oleic acid contents

An increase in oleic acid (C18:1) content is a desirable trait. Despite the critical roles of the two desaturases, FAD2 and FAD3, in the control of fatty acid desaturation, a dispute remains over whether inactivation of their genes alone is sufficient enough to generate the high-oleic trait. To address this question, we employed microarray technology to investigate the difference in gene expression profile between two different Brassica napus strains with high-C18:1 (71.71%) and low-C18:1 (55.6%) contents, respectively. Our study revealed 562 differentially expressed genes, of which 194 genes were up-regulated and 368 down-regulated. Based on the Gene Ontology classification, these genes were classified into 23 functional categories. Three of the up-regulated genes represent B. napus homologs of Arabidopsis genes encoding a cytosolic isoform of pyruvate kinase (AT3G55810), Δ9 acyl-lipid desaturase (AT1G06080, ADS1) and fatty acyl-ACP thioesterase B (AT1G08510), respectively. Conversely, the homologs of two Arabidopsis sequences encoding Δ9 acyl-lipid desaturase (AT2G31360, ADS2) and FAD3 desaturase (AT2G29980) were down-regulated in the high-oleic acid strain. Furthermore, 60 differentially expressed genes were classified as associated with relevant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, our results suggest that expressing the high-oleic acid trait may require a coordinated regulation of diverse regulatory and metabolic gene networks in addition to inactivation of the FAD2 and FAD3 genes in the oilseed. A set of the differentially expressed genes identified in this study will facilitate our efforts to tap the germplasms with the potential to express the high-oleic acid trait.

The mechanisms of brassinosteroids' action: from signal transduction to plant development

Brassinosteroids play diverse roles in plant growth and development. Plants deficient in brassinosteroid (BR) biosynthesis or defective in signal transduction show many abnormal developmental phenotypes, indicating the importance of both BR biosynthesis and the signaling pathway in regulating these biological processes. Recently, using genetics, proteomics, genomics, cell biology, and many other approaches, more components involved in the BR signaling pathway were identified. Furthermore, the physiological, cellular, and molecular mechanisms by which BRs regulate various aspects of plant development, are being discovered. These include root development, anther and pollen development and formation, stem elongation, vasculature differentiation, and cellulose biosynthesis, suggesting that the biological functions of BRs are far beyond promoting cell elongation. This review will focus on the up-to-date progresses about regulatory mechanisms of the BR signaling pathway and the physiological and molecular mechanisms whereby BRs regulate plant growth and development.

EST sequencing and gene expression profiling of cultivated peanut (Arachis hypogaea L.)

Peanut (Arachis hypogaea L.) is one of the most important oil crops in the world. However, biotechnological based improvement of peanut is far behind many other crops. It is critical and urgent to establish the biotechnological platform for peanut germplasm innovation. In this study, a peanut seed cDNA library was constructed to establish the biotechnological platform for peanut germplasm innovation. About 17,000 expressed sequence tags (ESTs) were sequenced and used for further investigation. Among which, 12.5% were annotated as metabolic related and 4.6% encoded transcription or post-transcription factors. ESTs encoding storage protein and enzymes related to protein degradation accounted for 28.8% and formed the largest group of the annotated ESTs. ESTs that encoded stress responsive proteins and pathogen-related proteins accounted for 5.6%. ESTs that encoded unknown proteins or showed no hit in the GenBank nr database accounted for 20.1% and 13.9%, respectively. A total number of 5066 EST sequences were selected to make a cDNA microarray. Expression analysis revealed that these sequences showed diverse expression patterns in peanut seeds, leaves, stems, roots, flowers, and gynophores. We also analyzed the gene expression pattern during seed development. Genes that were upregulated (≥twofold) at 15, 25, 35, and 45 days after pegging (DAP) were found and compared with 70 DAP. The potential value of these genes and their promoters in the peanut gene engineering study is discussed.

Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening

BACKGROUND

Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-methylcyclopropene.

RESULTS

To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies), we utilized both homologous and heterologous (tomato) microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated.The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database) and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato) microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening.

CONCLUSION

Our combined strategy based on microarray hybridization enabled transcriptome characterization during normal climacteric apple ripening, as well as definition of ethylene-dependent transcriptome changes. Comparison with tomato fruit maturation and ethylene responsive transcriptome activity facilitated identification of putative conserved orthologous ripening-related genes, which serve as an initial set of candidates for assessing conservation of gene activity across genomes of fruit bearing plant species.

Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

BACKGROUND

The GeneChip(R) Medicago Genome Array, developed for Medicago truncatula, is a suitable platform for transcript profiling in tetraploid alfalfa [Medicago sativa (L.) subsp. sativa]. However, previous research involving cross-species hybridization (CSH) has shown that sequence variation between two species can bias transcript profiling by decreasing sensitivity (number of expressed genes detected) and the accuracy of measuring fold-differences in gene expression.

RESULTS

Transcript profiling using the Medicago GeneChip(R) was conducted with elongating stem (ES) and post-elongation stem (PES) internodes from alfalfa genotypes 252 and 1283 that differ in stem cell wall concentrations of cellulose and lignin. A protocol was developed that masked probes targeting inter-species variable (ISV) regions of alfalfa transcripts. A probe signal intensity threshold was selected that optimized both sensitivity and accuracy. After masking for both ISV regions and previously identified single-feature polymorphisms (SFPs), the number of differentially expressed genes between the two genotypes in both ES and PES internodes was approximately 2-fold greater than the number detected prior to masking. Regulatory genes, including transcription factor and receptor kinase genes that may play a role in development of secondary xylem, were significantly over-represented among genes up-regulated in 252 PES internodes compared to 1283 PES internodes. Several cell wall-related genes were also up-regulated in genotype 252 PES internodes. Real-time quantitative RT-PCR of differentially expressed regulatory and cell wall-related genes demonstrated increased sensitivity and accuracy after masking for both ISV regions and SFPs. Over 1,000 genes that were differentially expressed in ES and PES internodes of genotypes 252 and 1283 were mapped onto putative orthologous loci on M. truncatula chromosomes. Clustering simulation analysis of the differentially expressed genes suggested co-expression of some neighbouring genes on Medicago chromosomes.

CONCLUSIONS

The problems associated with transcript profiling in alfalfa stems using the Medicago GeneChip as a CSH platform were mitigated by masking probes targeting ISV regions and SFPs. Using this masking protocol resulted in the identification of numerous candidate genes that may contribute to differences in cell wall concentration and composition of stems of two alfalfa genotypes.

Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes

BACKGROUND

Common bean (Phaseolus vulgaris L.) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip(R) Soybean Genome Array (soybean GeneChip) may be used for gene expression studies using common bean.

RESULTS

To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and accuracy of measuring differential gene expression in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and accuracy of measuring differential gene expression. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR (qRT-PCR) analysis of 20 randomly selected genes and purine-ureide pathway genes demonstrated an increased accuracy of measuring differential gene expression after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The sequence divergence pattern analysis suggested that the genes for basic cellular functions and metabolism were highly conserved between soybean and common bean. Additionally, our results show that some classes of genes, particularly those associated with environmental adaptation, are highly divergent.

CONCLUSIONS

The soybean GeneChip is a suitable cross-species platform for transcript profiling in common bean when used in combination with the masking protocol described. In addition to transcript profiling, CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.

Genomics for weed science

Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and evolutionary processes of weedy plants. Genomics-based tools such as extensive EST databases and microarrays have been developed for a limited number of weedy species, although application of information and resources developed for model plants and crops are possible and have been exploited. These tools have just begun to provide insights into the response of these weeds to herbivore and pathogen attack, survival of extreme environmental conditions, and interaction with crops. The potential of these tools to illuminate mechanisms controlling the traits that allow weeds to invade novel habitats, survive extreme environments, and that make weeds difficult to eradicate have potential for both improving crops and developing novel methods to control weeds.

Regulation of gene expression by chromosome 5A during cold hardening in wheat

Cold hardening is necessary to achieve the genetically determined maximum freezing tolerance and to reduce yield losses in winter cereals. The aim of the present study was to determine a set of genes with an important role in this process, by comparing of chromosome 5A substitution lines with different levels of freezing tolerance, since chromosome 5A is a major regulator of this trait. During 21 days of treatment at 2 degrees C, 303 genes were up-regulated, while 222 were down-regulated at most sampling points, and 156 at around half of them (out of the 10,297 unigenes studied). The freezing-tolerant substitution line exhibited 1.5 times as many differentially expressed genes than the sensitive one. The transcription of 78 genes (39 up-regulated) proved to be chromosome 5A-dependent. These genes encoded proteins involved in transcriptional regulation, defence processes and carbohydrate metabolism. Three of the chromosome 5A-related genes, coding for a cold-responsive, a Ca-binding and an embryo and meristem-related protein, were genetically mapped and characterized in further detail. The present experimental system was appropriate for the selection of chromosome 5A-related genes involved in short- and long-term cold acclimation in wheat. By modifying the expression of these genes it may be possible to improve freezing tolerance.

Interspecific profiling of gene expression informed by comparative genomic hybridization: A review and a novel approach in African cichlid fishes

Modern genomic approaches have facilitated great progress in our understanding of the molecular and genetic underpinnings of ecological and evolutionary processes. Analysis of gene expression through heterologous hybridization in particular has enabled genome-scale studies in many ecologically and evolutionarily interesting species. However, these studies have been hampered by the difficulty of comparing-on a common array platform-gene-expression profiles across species due to sequence divergence altering the dynamics of hybridization. All too often, comparisons of expression profiles across species were limited to contrasting lists of gene or even of just functional categories. Here we review these issues and propose a novel solution. Exploiting the diverse cichlid lineages of East Africa as our model-system, we then present results from an experimental case study that compares the neural gene-expression profiles of males and females of two species that differ in mating system. Using a single microarray platform that contains genes from one species, Astatotilapia burtoni, we conducted a total of 16 direct comparisons for neural gene-expression level between individual males and females from a pair of sister species, the polygynous Enantiopus melanogenys and the monogamous Xenotilapia flavipinnis. Next, we conducted a meta-analysis with previously published data from two different intra-specific expression studies to determine whether sex-specific neural gene expression is more closely associated with behavioral phenotype than it is with gonadal sex. Our results indicate that the gene expression profiles are species-specific to a large extent, as relatively few genes show conserved expression patterns associated with either sex. Finally, we describe how competitive genomic DNA hybridizations between the two focal species allow us to assess the degree to which divergence of sequences biases the results. We propose a masking technique that correlates interspecific expression ratios obtained with cDNA with hybridization ratios obtained with genomic DNA for the same set of species and determines threshold sequence divergence to reduce false positives. Our approach should be applicable to a wide range of interesting questions related to the evolution and ecology of gene expression.

Comparative transcriptomics in the Triticeae

Background

Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes.

Results

We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring). For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex) using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups", has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip.

Conclusion

While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because given small evolutionary distance between the two species it is widely expected, but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able to distinguish contributions from individual homoeologs. Furthermore, the comparison between the two species leads us to conclude that the conservation of both gene sequence as well as gene expression is positively correlated with absolute expression levels, presumably reflecting increased selection pressure on genes coding for proteins present at high levels. In addition, the results indicate the presence of a correlation between sequence and expression conservation within the Triticeae.

A molecular approach to understanding plant-plant interactions in the context of invasion biology

Competition is a major determinant of plant community structure, and can influence the size and reproductive fitness of a species. Therefore, competitive responses may arise from alterations in gene expression and plant function when an individual is confronted with new competitors. This study explored competition at the level of gene expression by hybridising transcripts from Centaurea maculosa Lam., one of North America's most invasive exotic plant species, to an Arabidopsis thaliana (L.) Heynh microarray chip. Centaurea was grown in competition with Festuca idahoensis Elmer, a native species that generally has weak competitive effects against Centaurea; Gaillardia aristata Pursh, a native species that tends to be a much stronger competitor against Centaurea; and alone (control). Some transcripts were induced or repressed to a similar extent regardless of the plant neighbour grown with Centaurea. Other transcripts showed differential expression that was specific to the competitor species, possibly indicating a species-specific aspect of the competitive response of Centaurea. These results are the first to identify genes in an invasive plant that are induced or repressed by plant neighbours and provide a new avenue of insight into the molecular aspects of plant competitive ability.

Identification of plant defence genes in canola using Arabidopsis cDNA microarrays

We report the identification of novel defence genes in canola by using a cDNA microarray from Arabidopsis. We examined changes that occur in the abundance of transcripts corresponding to 2375 Arabidopsis expressed sequence tags (selected for defence gene identification) following inoculation of canola plants with the fungal necrotrophic leaf pathogen, Alternaria brassicicola. Microarray data obtained from this cross-hybridisation experiment were compared to expression profiles previously obtained from the equivalent Arabidopsis experiment. Homology searches using a canola expressed sequence tag database with approximately 6000 unique clones led to identification of canola defence genes. Pathogen-responsive transcripts included those associated to known defence genes, reactive oxygen species metabolism, disease resistance and regulatory genes, and cell maintenance/metabolism genes. Using specific primers for quantitative real-time reverse transcriptase PCR, gene expression profiles in canola were obtained that demonstrated coordinated defence responses, including systemic responses in distal tissue and salicylic acid- and methyl jasmonate-mediated signalling against A. brassicicola.

Analysis of gene expression profiles in response to Sclerotinia sclerotiorum in Brassica napus

Sclerotinia sclerotiorum is a necrotrophic plant pathogen which causes serious disease in agronomically important crop species. The molecular basis of plant defense to this pathogen is poorly understood. We investigated gene expression changes associated with S. sclerotiorum infection in a partially resistant and a susceptible genotype of oilseed Brassica napus using a whole genome microarray from Arabidopsis. A total of 686 and 1,547 genes were found to be differentially expressed after infection in the resistant and susceptible genotypes, respectively. The number of differentially expressed genes increased over infection time with the majority being up-regulated in both genotypes. The putative functions of the differentially expressed genes included pathogenesis-related (PR) proteins, proteins involved in the oxidative burst, protein kinase, molecule transporters, cell maintenance and development, abiotic stress, as well as proteins with unknown functions. The gene regulation patterns indicated that a large part of the defense response exhibited as a temporal and quantitative difference between the two genotypes. Genes associated with jasmonic acid (JA) and ethylene signal transduction pathways were induced, but no salicylic acid (SA) responsive genes were identified. Candidate defense genes were identified by integration of the early response genes in the partially resistant line with previously mapped quantitative trait loci (QTL). Expression levels of these genes were verified by Northern blot analyses. These results indicate that genes encoding various proteins involved in diverse roles, particularly WRKY transcription factors and plant cell wall related proteins may play an important role in the defense response to S. sclerotiorum disease.

Comparative expression profiling in meristems of inbred-hybrid triplets of maize based on morphological investigations of heterosis for plant height

Heterosis, the superior performance of hybrids as compared to their parental mean is an agronomically important phenomenon well-described morphologically. However, little is known about its molecular basis. We investigated four genetically unrelated maize (Zea mays L.) inbred lines and their F(1) crosses both at the phenotype and transcriptome level, focusing on plant height (PHT) component traits. Substantial mid-parent heterosis (MPH) was found for all parent-hybrid triplets for PHT in the range of 37.9-56.4% in the field and 11.1-39.5% under controlled greenhouse conditions. Analyses of heterosis for number and length of internodes showed two to three times higher MPH in the field as compared to the greenhouse. All three traits exhibited high heritabilities, highest for PHT 95-98%. Two methods for gene expression quantification were applied. High-density cDNA uni-gene microarrays containing 11,827 ESTs were utilized for the selection of differentially expressed genes related to heterosis for PHT. For the four triplets with eight possible parent-hybrid comparisons we identified 434 consistently differentially expressed genes with a p < or = 0.05. Microarray results were used to verify the dominance/overdominance hypothesis. In our study, more than 50% genes showed overdominance, 26% partial dominance, 12.6% complete dominance and 10.2% additive gene action. Moreover, more consistently differentially expressed genes were detected in related triplets, sharing one parent, than in unrelated triplets. Quantitative RT-PCR was applied in order to validate microarray results. The role of the differentially expressed genes in relation to heterosis for PHT is discussed.

Senescence-associated genes induced during compatible viral interactions with grapevine and Arabidopsis

The senescence process is the last stage in leaf development and is characterized by dramatic changes in cellular metabolism and the degeneration of cellular structures. Several reports of senescence-associated genes (SAGs) have appeared, and an overlap in some of the genes induced during senescence and pathogen infections has been observed. For example, the enhanced expression of SAGs in response to diseases caused by fungi, bacteria, and viruses that trigger the hypersensitive response (HR) or during infections induced by virulent fungi and bacteria that elicit necrotic symptoms has been observed. The present work broadens the search for SAGs induced during compatible viral interactions with both the model plant Arabidopsis thaliana and a commercially important grapevine cultivar. The transcript profiles of Arabidopsis ecotype Uk-4 infected with tobacco mosaic virus strain Cg (TMV-Cg) and Vitis vinifera cv. Carménère infected with grapevine leafroll-associated virus strain 3 (GLRaV-3) were analysed using microarray slides of the reference species Arabidopsis. A large number of SAGs exhibited altered expression during these two compatible interactions. Among the SAGs were genes that encode proteins such as proteases, lipases, proteins involved in the mobilization of nutrients and minerals, transporters, transcription factors, proteins related to translation and antioxidant enzymes, among others. Thus, part of the plant's response to virus infection appears to be the activation of the senescence programme. Finally, it was demonstrated that several virus-induced genes are also expressed at elevated levels during natural senescence in healthy plants.

Can plant biochemistry contribute to understanding of invasion ecology?

Ecologists have long searched for an explanation as to why some plant invaders become much more dominant in their naturalized range than in their native range, and, accordingly, several non-exclusive ecological hypotheses have been proposed. Recently, a biochemical explanation was proposed--the "novel weapons hypothesis"--based on findings that Centaurea diffusa and Centaurea maculosa produce bioactive compounds (weapons) that are more active against naïve plant species in the introduced range than against co-evolved species in the native range. In this Opinion article, we revise and expand this biochemical hypothesis and discuss experimental and conceptual advances and limitations.

The Affymetrix Medicago GeneChip® array is applicable for transcript analysis of alfalfa (Medicago sativa)

The recently released Affymetrix GeneChip^® Medicago Genome Array contains approximately 52 700 probe sets representing genes in both the model legume Medicago truncatula Gaertn. and the closely related crop species Medicago sativa L. (alfalfa). We evaluated the utility of the Medicago GeneChip^® for monitoring genome-wide expression of M. truncatula and alfalfa seedlings grown to the first trifoliate leaf stage. We found that approximately 40-54% of the Medicago probes were detected in leaf or root samples of alfalfa or M. truncatula. Approximately 45-59% of the detected Medicago probes were called 'present' in all replicate GeneChips of Medicago species, indicating a considerable overlap in the number and type of Medicago probes detected between root and leaf organs. Nevertheless, gene expression differences between roots and leaf organs accounted for approximately 17% of the total variation, regardless of the Medicago species from which the samples were harvested. The result shows that the Medicago GeneChip^® is applicable for transcript analysis for both alfalfa and M. truncatula.

Comparative transcriptome analyses of barley and rice under salt stress

Although barley and rice belong to the same family Poaceae, they differ in their ability to tolerate salt stress. In an attempt to understand the molecular bases of such differences, we compared changes in transcriptome between barley and rice in response to salt stress using barley cDNA microarrays. At 1 and 24 h after salt stress, many genes were up-regulated in barley, but not in rice. Leaf water potential declined in the first 10 h of stress in both species, but recovered in the period 24-48 h only in barley. In addition, we found that barley partitioned Na+ to the roots and away from the shoots more efficiently than rice. These differences in physiological responses were correlated with the differences in the steady-state abundance of transcripts for the genes related to adaptive functions. Transcripts for plasma membrane protein 3 and inorganic pyrophosphatase were up-regulated in both species, but only transiently in rice. This indicates that adaptive mechanisms for regulating ion homeostasis are partly conserved in the two species, but it seems that rice cannot sustain cellular ion homeostasis for a long time like barley. These results imply that genetic modification of regulatory controls of early salt-responsive genes might lead to development of the salt tolerance trait in rice.

Primary metabolic pathways and signal transduction in sunflower (Helianthus annuus L.): comparison of transcriptional profiling in leaves and immature embryos using cDNA microarrays

The early stage of embryo development is a critical step in plant production. To identify genes with potential roles in the early sunflower seed development, a cDNA microarray approach was employed. We developed a thematic cDNA microarray containing clones representing high sequence similarities with known or predicted Arabidopsis genes implicated in different metabolic and signal transduction pathways. This 800-element cDNA array was used to compare the expression patterns in leaves and immature embryos (2 mm and 6 mm). Statistical analysis, using two-step ANOVA, revealed that 143 cDNA clones can be considered as differentially expressed. Of these, 62 clones were found to be up-regulated in leaves, 81 in embryos whereas only seven clones displayed increased level of mRNA in the 6 mm embryos when compared with 2 mm embryos. The differentially expressed clones are distributed among many metabolic and signal transduction pathways. For example, genes related to fatty acid metabolism and amino acid biosynthesis exhibited preferential expression patterns in immature embryos. Also, clones potentially encoding enzymes involved in the metabolism of ascorbate and aldarate, pyruvate, propanoate and inositol, and citrate cycle were found to be up-regulated in embryos. In contrast, cDNA clones putatively involved in energy metabolism were more abundant in leaves than embryos. Clones encoding potential signal transduction components including receptors, protein kinases, protein phosphatases, and transcription factors were also identified, with preferential expression profiles in immature embryos. The expression patterns derived from this study provide initial characterization of metabolic pathways and signalling transduction networks occurring in the early stage of sunflower seed development.

Transcriptional profiling of imbibed Brassica napus seed

Using an Arabidopsis microarray, we compared gene expression between germinating Brassica napus seeds and seeds in which germination was inhibited either by polyethylene glycol (PEG) or by the abscisic acid (ABA) analog PBI429, which produces stronger and longer lasting ABA-like effects. A total of 40 genes were induced relative to the germinating control by both treatments. Conspicuous among these were genes associated with late seed development. We identified 36 genes that were downregulated by both PEG and PBI429. Functions of these genes included carbohydrate metabolism, cell wall-related processes, detoxification of reactive oxygen, and triacylglycerol breakdown. The PBI429 treatment produced an increase in endogenous ABA and increased ABA catabolism. However, PEG treatment did not result in similar effects. The transcription factor ABI5 was consistently upregulated by both treatments and PKL was downregulated. These results suggest a greater importance of ABA signaling and reduced importance of GA signaling in nongerminating seeds.

Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability

Regulation of mRNA turnover is an important cellular strategy for posttranscriptional control of gene expression, mediated by the interplay of cis-acting sequences and associated trans-acting factors. Pub1p, an ELAV-like yeast RNA-binding protein with homology to T-cell internal antigen 1 (TIA-1)/TIA-1-related protein (TIAR), is an important modulator of the decay of two known classes of mRNA. Our goal in this study was to determine the range of mRNAs whose stability is dependent on Pub1p, as well as to identify specific transcripts that directly bind to this protein. We have examined global mRNA turnover in isogenic PUB1 and pub1delta strains through gene expression analysis and demonstrate that 573 genes exhibit a significant reduction in half-life in a pub1delta strain. We also examine the binding specificity of Pub1p using affinity purification followed by microarray analysis to comprehensively distinguish between direct and indirect targets and find that Pub1p significantly binds to 368 cellular transcripts. Among the Pub1p-associated mRNAs, 53 transcripts encoding proteins involved in ribosomal biogenesis and cellular metabolism are selectively destabilized in the pub1delta strain. In contrast, genes involved in transporter activity demonstrate association with Pub1p but display no measurable changes in transcript stability. Characterization of two candidate genes, SEC53 and RPS16B, demonstrate that both Pub1p-dependent regulation of stability and Pub1p binding require 3' untranslated regions, which harbor distinct sequence motifs. These results suggest that Pub1p binds to discrete subsets of cellular transcripts and posttranscriptionally regulates their expression at multiple levels.

Dynamics of leaf and root growth: endogenous control versus environmental impact

AIMS

Production of biomass and yield in natural and agronomic conditions depend on the endogenous growth capacity of plants and on the environmental conditions constraining it. Sink growth drives the competition for carbon, nutrients and water within the plant, and determines the structure of leaves and roots that supply resources to the plant later on. For their outstanding importance, analyses of internal growth mechanisms and of environmental impact on plant growth are long-standing topics in plant sciences.

SCOPE

Recent technological developments have made it feasible to study the dynamics of plant growth in temporal and spatial scales that are relevant to link macroscopic growth with molecular control. These developments provided first insights into the truly dynamic interaction between environment and endogenous control of plant growth.

CONCLUSIONS

Evidence is presented in this paper that the relative importance of endogenous control versus the impact of the dynamics of the environment depends on the frequency pattern of the environmental conditions to which the tissue is exposed. It can further be speculated that this is not only relevant within individual plants (hence leaves versus roots), but also crucial for the adaptation of plant species to the various dynamics of their environments. The following are discussed: mechanisms linking growth and concentrations of primary metabolites, and differences and homologies between spatial and temporal patterns of root and leaf growth with metabolite patterns.

Identification of Transcripts Involved in Resistance Responses to Leaf Spot Disease Caused by Cercosporidium personatum in Peanut (Arachis hypogaea)

ABSTRACT Late leaf spot disease caused by Cercosporidium personatum is one of the most destructive foliar diseases of peanut (Arachis hypogaea) worldwide. The objective of this research was to identify resistance genes in response to leaf spot disease using microarray and real-time polymerase chain reaction (PCR). To identify transcripts involved in disease resistance, we studied the gene expression profiles in two peanut genotypes, resistant or susceptible to leaf spot disease, using cDNA microarray containing 384 unigenes selected from two expressed sequenced tag (EST) cDNA libraries challenged by abiotic and biotic stresses. A total of 112 spots representing 56 genes in several functional categories were detected as up-regulated genes (log(2) ratio > 1). Seventeen of the top 20 genes, each matching gene with known function in GenBank, were selected for validation of their expression levels using real-time PCR. The two peanut genotypes were also used to study the functional analysis of these genes and the possible link of these genes to the disease resistance trait. Microarray technology and real-time PCR were used for comparison of gene expression. The selected genes identified by microarray analysis were validated by real-time PCR. These genes were more greatly expressed in the resistant genotype as a result of response to the challenge of C. personatum than in the susceptible genotype. Further investigations are needed to characterize each of these genes in disease resistance. Gene probes could then be developed for application in breeding programs for marker-assisted selection.

Plant defence responses: conservation between models and crops

Diseases of plants are a major problem for agriculture world wide. Understanding the mechanisms employed by plants to defend themselves against pathogens may lead to novel strategies to enhance disease resistance in crop plants. Much of the research in this area has been conducted with Arabidopsis as a model system, and this review focuses on how relevant the knowledge generated from this model system will be for increasing resistance in crop plants. In addition, the progress made using other model plant species is discussed. While there appears to be substantial similarity between the defence responses of Arabidopsis and other plants, there are also areas where significant differences are evident. For this reason it is also necessary to increase our understanding of the specific aspects of the defence response that cannot be studied using Arabidopsis as a model.

Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies

A functional genomics project has been initiated to approach the molecular characterization of the main biological and agronomical traits of citrus. As a key part of this project, a citrus EST collection has been generated from 25 cDNA libraries covering different tissues, developmental stages and stress conditions. The collection includes a total of 22,635 high-quality ESTs, grouped in 11,836 putative unigenes, which represent at least one third of the estimated number of genes in the citrus genome. Functional annotation of unigenes which have Arabidopsis orthologues (68% of all unigenes) revealed gene representation in every major functional category, suggesting that a genome-wide EST collection was obtained. A Citrus clementina Hort. ex Tan. cv. Clemenules genomic library, that will contribute to further characterization of relevant genes, has also been constructed. To initiate the analysis of citrus transcriptome, we have developed a cDNA microarray containing 12,672 probes corresponding to 6875 putative unigenes of the collection. Technical characterization of the microarray showed high intra- and inter-array reproducibility, as well as a good range of sensitivity. We have also validated gene expression data achieved with this microarray through an independent technique such as RNA gel blot analysis.

An EST resource for cassava and other species of Euphorbiaceae

Cassava (Manihot esculenta) is a major food staple for nearly 600 million people in Africa, Asia, and Latin America. Major losses in yield result from biotic and abiotic stresses that include diseases such as Cassava Mosaic Disease (CMD) and Cassava Bacterial Blight (CBB), drought, and acid soils. Additional losses also occur from deterioration during the post-harvest storage of roots. To help cassava breeders overcome these obstacles, the scientific community has turned to modern genomics approaches to identify key genetic characteristics associated with resistance to these yield-limiting factors. One approach for developing a genomics program requires the development of ESTs (expressed sequence tags). To date, nearly 23,000 ESTs have been developed from various cassava tissues, and genotypes. Preliminary analysis indicates existing EST resources contain at least 6000-7000 unigenes. Data presented in this report indicate that the cassava ESTs will be a valuable resource for the study of genetic diversity, stress resistance, and growth and development, not only in cassava, but also other members of the Euphorbiaceae family.

ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development

Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit.

Weed genomics: new tools to understand weed biology

In spite of the large yield losses that weeds inflict on crops, we know little about the genomics of economically important weed species. Comparative genomics between plant model species and weeds, map-based approaches, genomic sequencing and functional genomics can play vital roles in understanding and dissecting weedy traits of agronomically important weed species that damage crops. Weed genomics research should increase our understanding of the evolution of herbicide resistance and of the basic genetics underlying traits that make weeds a successful group of plants. Here, we propose specific weed candidates as genomic models, including economically important plants that have evolved herbicide resistance on several occasions and weeds with good comparative genomic qualities that can be anchored to the genomics of Arabidopsis and Oryza sativa.

Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

BACKGROUND

To cancel experimental variations, microarray data must be normalized prior to analysis. Where an appropriate model for statistical data distribution is available, a parametric method can normalize a group of data sets that have common distributions. Although such models have been proposed for microarray data, they have not always fit the distribution of real data and thus have been inappropriate for normalization. Consequently, microarray data in most cases have been normalized with non-parametric methods that adjust data in a pair-wise manner. However, data analysis and the integration of resultant knowledge among experiments have been difficult, since such normalization concepts lack a universal standard.

RESULTS

A three-parameter lognormal distribution model was tested on over 300 sets of microarray data. The model treats the hybridization background, which is difficult to identify from images of hybridization, as one of the parameters. A rigorous coincidence of the model to data sets was found, proving the model's appropriateness for microarray data. In fact, a closer fitting to Northern analysis was obtained. The model showed inconsistency only at very strong or weak data intensities. Measurement of z-scores as well as calculated ratios was reproducible only among data in the model-consistent intensity range; also, the ratios were independent of signal intensity at the corresponding range.

CONCLUSION

The model could provide a universal standard for data, simplifying data analysis and knowledge integration. It was deduced that the ranges of inconsistency were caused by experimental errors or additive noise in the data; therefore, excluding the data corresponding to those marginal ranges will prevent misleading analytical conclusions.

Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species

Synthetic oligonucleotides (oligos) represent an attractive alternative to cDNA amplicons for spotted microarray analysis in a number of model organisms, including Arabidopsis, C. elegans, Drosophila, human, mouse and yeast. However, little is known about the relative effectiveness of 60-70-mer oligos and cDNAs for detecting gene expression changes. Using 192 pairs of Arabidopsis thaliana cDNAs and corresponding 70-mer oligos, we performed three sets of dye-swap experiments and used analysis of variance (anova) to compare sources of variation and sensitivities for detecting gene expression changes in A. thaliana, A. arenosa and Brassica oleracea. Our major findings were: (1) variation among different RNA preparations from the same tissue was small, but large variation among dye-labellings and slides indicates the need to replicate these factors; (2) sources of variation were similar for experiments with all three species, suggesting these feature types are effective for analysing gene expression in related species; (3) oligo and cDNA features had similar sensitivities for detecting expression changes and they identified a common subset of significant genes, but results from quantitative RT-PCR did not support the use of one over the other. These findings indicate that spotted oligos are at least as effective as cDNAs for microarray analyses of gene expression. We are using oligos designed from approximately 26,000 annotated genes of A. thaliana to study gene expression changes in Arabidopsis and Brassica polyploids.