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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS APPROACHES FOR IMPROVING NUTRITIONAL QUALITY OF FOOD CROP SPECIES Title: Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits

Authors
item Kamenetzky, Laura -
item Asis, Ramon -
item Bassi, Sebastian -
item DE Godoy, Fabiana -
item Bermudez, Luisa -
item Fernie, Alisdair -
item Vrebalov, Julia -
item Giovannoni, James
item Rossi, Magdalena -
item Carrari, Fernando -

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 26, 2010
Publication Date: January 29, 2010
Citation: Kamenetzky, L., Asis, R., Bassi, S., De Godoy, F., Bermudez, L., Fernie, A., Vrebalov, J., Giovannoni, J.J., Rossi, M., Carrari, F. 2010. Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits. Plant Physiology. 152:1772-1786.

Interpretive Summary: Tomato fruits constitute one of the most important sources of minerals, vitamins, fibers and antioxidants in human diets. Genomic approaches focused on the genetic determinants regulating the pathways for the production of these nutrients could provide important information concerning the genes operating in these processes. Here we describe a large scale analysis of the wild tomato species S. pennellii and its genome and a comparison with the cultivated tomato S. lycopersicum. Five genomic regions associated with fruit carbon primary metabolism were chosen. These regions include allelic variation impacting fruit color, volatile content and yield traits linked to chemical metabolite variation found previously in the fruits of these lines. The physical map, built by anchoring 374 clones from BAC (bacterial artificial chromosome) and cosmid S. pennellii genomic libraries to the tomato genetic map, revealed a consistent pattern of co-aligning regions suggesting that both genomes can be considered largely collinear. Targeted sequencing allowed the annotation of 408 genes and uncovered a high degree of micro-synteny between these two Solanum species and to a lesser extent with the Arabidopsis thaliana genomes (as would be expected). Finally, the time of divergence between species was assessed in 2.7 MYA (million years ago). The large dataset presented here constitute a useful tool for trait fine mapping and rapid screening of target genes in map-based cloning approaches.

Technical Abstract: With the aim to determine the genetic basis of key points regulating tomato fruit metabolism, a detailed physical map of genomic regions spanning metabolic quantitative trait loci, previously detected in a Solanum pennellii introgression line population, was constructed representing one of the few such maps of an undomesticated plant species. Two genomic libraries from S. pennellii were screened with 104 co-located markers from five selected genomic regions and a total of 614 BAC/cosmid clones were identified. Integration of clones end sequence data, with genetic and physical maps, allowed the anchoring of 374 BAC/cosmid clones representing approximately 10 % of the selected regions and 1 % of the wild tomato genome. The physical map showed that the S. pennellii genome is largely collinear with the domesticated tomato. A total of 1,238,705 nt from both BAC/cosmid ends and nine large insert clones, were sequenced, annotated and functionally categorized. The sequence data facilitated polymorphism analysis between the wild and cultivated tomatoes. Micro-synteny analysis allowed us to estimate the divergence date between S. pennellii and S. lycopersicum as 2.7 MYA. These results serve as a reference for comparative studies at both the macro- and micro-synteny levels within the genus and provide a valuable tool for QTL fine mapping leading to a better understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition.

Last Modified: 11/24/2014
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