150+ Tomato resequencing project

150 Tomato Genome ReSequencing project

Two factors are essential for continued improvement of crop species by plant breeding: tools to identify adequate genetic variation, and technology to efficiently (re)combine useful alleles in new breeding lines. Material from wild relatives, ancestors and landraces held in germplasm collections of crop species contains an underexploited wealth of genetic variation, and will therefore offer a useful gene pool to cope with existing and new breeding challenges.

Exploiting wild and early domesticated resources has the potential to genetically enrich extant crops with alleles that can improve traits that have recently become important in the face of new challenges and requirements regarding climate change, sustainable production and a growing demand for more and better food. Once adequate genetic variation has been identified, the efficiency and success rate of breeding programs that make use of it can be greatly increased by DNA based selection of lines and markers associated with traits of interest.

Aim

The aim of the 150 Tomato Genome ReSequencing project is to reveal and explore the genetic variation available in tomato. Tomato has been selected as target crop because it is economically one of the most important crop species for the Dutch breeding industry, and is one the most important vegetables globally. However, since the tomato shows only limited genetic diversity in commercial breeding lines, valuable alleles will be available in wild tomato relatives. Since breeding and selection was targeted at only a narrow range of desirable agricultural traits, also old breeding material could be source of interesting alleles that have been lost during domestication.

Accessions

In order to identify the sequence diversity within tomato, 83 genotypes including 10 old varieties, 43 land races and 30 wild accessions will be seqeunced. Ten accessions of S. lycopersicum var. lycopersicum and S. lycopersicum var. cerasiforme will be selected that represent the maximum range of expected genetic variation. Forty three landraces will be selected based upon the analysis performed within the EU-SOL project, or made available by the industrial parties. The selection will include cherry, beef, round, momotaro (pink tomato) and heirloom types. A further thirty accessions will be selected from 10 Solanum section Lycopersicon species besides S. lycopersicum. These wild tomato species represent the full range of expected genetic variation around S. lycopersicum that can still be used as potential breeding material. From three wild species new reference genomes will be composed. Finally, 60 F₈ individuals will be selected from an S. pimpinellifolium RIL population for low depth sequencing. This set of sequenced individuals provides a first step in tomato research to develop tools and pipelines for “genotyping-by-sequencing” approaches, and to study recombination events at the sequence level.

Citation

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Aflitos S., Schijlen E., de Jong H., de Ridder D., Smit S., Finkers R., Wang J., Zhang G., Li N., Mao L., Bakker F., Dirks R., Breit T., Gravendeel B., Huits H., Struss D., Swanson-Wagner R., van Leeuwen H., van Ham RC., Fito L., Guignier L., Sevilla M., Ellul P., Ganko E., Kapur A., Reclus E., de Geus B., van de Geest H., Te Lintel Hekkert B., van Haarst J., Smits L., Koops A., Sanchez-Perez G., van Heusden AW., Visser R., Quan Z., Min J., Liao L., Wang X., Wang G., Yue Z., Yang X., Xu N., Schranz E., Smets E., Vos R., Rauwerda J., Ursem R., Schuit C., Kerns M., van den Berg J., Vriezen W., Janssen A., Datema E., Jahrman T., Moquet F., Bonnet J., Peters S. Plant J. 80(1): 136-148 (2014 Oct)

Data Availability

All data has been submitted to the European nucleotide archive