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

• Published in: Journal of experimental botany 2005-06, Vol.56 (416), p.1591-1604
• Main Authors: Baxter, Charles J, Sabar, Mohammed, Quick, W. Paul, Sweetlove, Lee J
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; Brix; Carbohydrate Metabolism; chromosome mapping; crop yield; Dehydrogenases; Enzymes; Fruit - metabolism; Fruits; fruits (plant anatomy); Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant - physiology; Genes; Genes. Genome; interspecific hybridization; introgression; linkage (genetics); Lycopersicon esculentum; Lycopersicon esculentum - genetics; Lycopersicon esculentum - metabolism; messenger RNA; microarray technology; Molecular and cellular biology; Molecular genetics; Plants; quantitative trait loci; Quantitative Trait Loci - genetics; Quantitative Trait Loci - physiology; Research Papers; RNA; Solanum lycopersicum var. lycopersicum; Solanum pennellii var. pennellii; Starches; tomato microarray; tomatoes; transcription (genetics); Transcription, Genetic; Transcriptomics; vegetable crops; yield
• ISSN: 0022-0957; 1460-2431
• DOI: 10.1093/jxb/eri154

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.