Comparison of changes in fruit gene expression in tomato introgression lines provides evidence of genome-wide transcriptional changes and reveals links to mapped QTLs and described traits. J Exp Bot

Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
Journal of Experimental Botany (Impact Factor: 5.53). 07/2005; 56(416):1591-604. DOI: 10.1093/jxb/eri154
Source: PubMed


Total soluble solids content is a key determinant of tomato fruit quality for processing. Several tomato lines carrying defined introgressions from S. pennellii in a S. lycopersicum background produce fruit with elevated Brix, a refractive index measure of soluble solids. The genetic basis for this trait can be determined by fine-mapping each QTL to a single gene, but this is time-consuming and technically demanding. As an alternative, high-throughput analytical technologies can be used to provide useful information that helps characterize molecular changes in the introgression lines. This paper presents a study of transcriptomic changes in six introgression lines with increased fruit Brix. Each line also showed altered patterns of fruit carbohydrate accumulation. Transcriptomic changes in fruit at 20 d after anthesis (DAA) were assessed using a 12 000-element EST microarray and significant changes analysed by SAM (significance analysis of microarrays). Each non-overlapping introgression resulted in a unique set of transcriptomic changes with 78% of significant changes being unique to a single line. Principal components analysis allowed a clear separation of the six lines, but also revealed evidence of common changes; lines with quantitatively similar increases in Brix clustered together. A detailed examination of genes encoding enzymes of primary carbon metabolism demonstrated that few of the known introgressed alleles were altered in expression at the 20 DAA time point. However, the expression of other metabolic genes did change. Particularly striking was the co-ordinated up-regulation of enzymes of sucrose mobilization and respiration that occurred only in the two lines with the highest Brix increase. These common downstream changes suggest a similar mechanism is responsible for large Brix increases.

  • Source
    • "In fact, the molecular basis underlying allelic variation at QTLs is similar to the identified variation for simple Mendelian loci, namely, alterations in gene expression or protein function (Paran and Zamir 2003). Expression gene profiling could be carried out between contrasting QTL genotypes (Wayne and McIntyre 2002; Hazen et al. 2005; Baxter et al. 2005; Steiner et al. 2009) or between each individual of a segregating population (Damerval et al. 1994; Jansen and Nap 2001; Liu et al. 2011). In this latter case, gene expression data can be analyzed in combination with molecular marker data, making possible the use of QTL analysis for the identification of influential genes and gene products (expression QTL or eQTL). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple. Although major scab resistance genes (R gene) have been widely studied, little is known about the molecular mechanisms underlying partial resistance, thought to be more durable. We used a candidate gene approach to decipher the genetic determinism of the durable partial resistance in ‘Président Roulin’, an old Belgian apple cultivar. Pathological tests using monoconidial isolates of V. inaequalis on F1 ‘Gala’ x ‘Président Roulin’ progeny suggested that partial resistance was broad spectrum but resulted from the combination of several race-specific interactions and was governed by at least five R genes. From an earlier transcript profiling study, we selected 13 pathogen-regulated genes in ‘Président Roulin’ with a known role in plant defense and characterized their expression over a time-course experiment. These candidate defense genes (CDGs) were regulated between 6 and 120 h after inoculation. Most were significantly up- or downregulated in incompatible interactions only or were induced earlier compared with compatible interactions. Among them, eight were mapped in silico within chromosomal regions containing disease resistance factors (R gene analogues, major scab R genes or quantitative trait loci). We also investigated the extent of the correlation between CDG expression data and phenotypic variation in the progeny. We estimated that the induction of nine out of 10 CDGs accounted for up to 46 % of the phenotypic variance. Our study has improved the understanding of partial apple scab resistance and could be used in developing functional molecular markers for breeding new ‘spray-free’ cultivars with durable scab resistance.
    Full-text · Article · Dec 2015 · Tree Genetics & Genomes
  • Source
    • "Among available methods for high-throughput analysis the microarray is a powerful tool for large-scale gene expression studies in many plant species with whole genome sequenced: potato [5,6], tomato [7,8], soybean [9,10], wheat [11], barley [12,13] maize [14,15], grape [16], pine [17], Arabidopsis [18-20]. The main advantage of microarray analyses is to evaluate the expression of large number of genes in different genotypes, organs, tissues, treatments, using the same set of genes. "
    [Show abstract] [Hide abstract]
    ABSTRACT: A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes. Plants have evolved complex mechanisms to recognize such attacks, and to trigger a defense response. To understand the transcriptional basis of this response, we compare gene expression profiles of two coffee genotypes, susceptible and resistant to leaf miner (Leucoptera coffella). A total of 22000 EST sequences from the Coffee Genome Database were selected for a microarray analysis. Fluorescence probes were synthesized using mRNA from the infested and non-infested coffee plants. Array hybridization, scanning and data normalization were performed using Nimble Scan(R) e ArrayStar(R) platforms. Genes with foldchange values +/-2 were considered differentially expressed. A validation of 18 differentially expressed genes was performed in infected plants using qRT-PCR approach. The microarray analysis indicated that resistant plants differ in gene expression profile. We identified relevant transcriptional changes in defense strategies before insect attack. Expression changes (>2.00-fold) were found in resistant plants for 2137 genes (1266 up-regulated and 873 down-regulated). Up-regulated genes include those responsible for defense mechanisms, hypersensitive response and genes involved with cellular function and maintenance. Also, our analyses indicated that differential expression profiles between resistant and susceptible genotypes are observed in the absence of leaf-miner, indicating that defense is already build up in resistant plants, as a priming mechanism. Validation of selected genes pointed to four selected genes as suitable candidates for markers in assisted-selection of novel cultivars. Our results show evidences that coffee defense responses against leaf-miner attack are balanced with other cellular functions. Also analyses suggest a major metabolic reconfiguration that highlights the complexity of this response.
    Full-text · Article · Jan 2014 · BMC Genomics
  • Source
    • "TSS reflects dry matter content and is inversely proportionate to fruit size. TSS in large beefsteak tomatoes ranges from 3 to 5%, in medium-sized fruit from 5 to 7% and cherry tomato fruit from 9 to 15% (Baxter et al., 2005; Gautier et al., 2010; Georgelis et al., 2004; Luengwilai et al., 2010b; Rick, 1974). TSI is used to indicate sweetness. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Although a large component of tomato fruit taste is sugars, the choice of tomato cultivar and the postharvest practices implemented by industry are designed to reduce crop loss and lengthen shelf-life and do not prioritize sweetness. However, because there is a growing recognition that taste and flavor are key components of tomato marketability, greater emphasis is now being placed on improving traits like sugar content. In this review the factors, both pre-, post and at harvest that influence sugar content in fruits sold at market are broadly outlined. Lines of investigation that may maximise the outcome of current practices and lead, long-term, to enhanced postharvest fruit sugar contents are suggested.
    Full-text · Article · Jan 2012 · Postharvest Biology and Technology
Show more