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.

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    • "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. "
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    BMC Genomics 01/2014; 15(1):66. DOI:10.1186/1471-2164-15-66 · 3.99 Impact Factor
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    • "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. "
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    • "For example, the genomic region denominated by IL-4-4 contains three positive enzyme activity QTLs for the enzymes in the glycolysis/gluconeogenesis pathway (NAD-GAPDH, UGP, and FruK). For two of these enzymes, Baxter et al. (2005) reported increased levels of the corresponding transcripts (NAD-GAPDH, fructokinase). Furthermore, Schauer et al. (2006) described positive metabolite QTLs at this same locus for Fru, Suc, Glc, Fru-6-P, glycerate-3- phosphate, citrate, isocitrate, Asp, Glu, and succinate, including metabolites that are direct substrates or products of NAD-GAPDH, UGP, and FruK or metabolites farther upstream or downstream in the glycolysis/gluconeogenesis pathway. "
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