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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Plant Sci. | doi: 10.3389/fpls.2018.01402

The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance

  • 1Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Saudi Arabia
  • 2RSRC, King Abdullah University of Science and Technology, Saudi Arabia
  • 3BESE, King Abdullah University of Science and Technology, Saudi Arabia
  • 4Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology, Saudi Arabia
  • 5International Center for Biosaline Agriculture, United Arab Emirates
  • 6University of Eastern Finland, Finland

Solanum pimpinellifolium, a wild relative of cultivated tomato, offers a wealth of breeding potential for desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome assembly and annotation of S. pimpinellifolium ‘LA0480’. Moreover, we present phenotypic data from one field experiment that demonstrate a greater salinity tolerance for fruit- and yield-related traits in S. pimpinellifolium compared with cultivated tomato. The ‘LA0480’ genome assembly size (811 Mb) and the number of annotated genes (25,970) are within the range observed for other sequenced tomato species. We developed and utilized the Dragon Eukaryotic Analyses Platform (DEAP) to functionally annotate the ‘LA0480’ protein-coding genes. Additionally, we used DEAP to compare protein function between S. pimpinellifolium and cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses. To understand the genomic basis for these differences in S. pimpinellifolium and S. lycopersicum, we analyzed 15 genes that have previously been shown to mediate salinity tolerance in plants. We show that S. pimpinellifolium has a higher copy number of the inositol-3-phosphate synthase and phosphatase genes, which are both key enzymes in the production of inositol and its derivatives. Moreover, our analysis indicates that changes occurring in the inositol phosphate pathway may contribute to the observed higher salinity tolerance in ‘LA0480’. Altogether, our work provides essential resources to understand and unlock the genetic and breeding potential of S. pimpinellifolium, and to discover the genomic basis underlying its environmental robustness.

Keywords: Wild tomato, Solanum pimpinellifolium, genome analysis, salinity tolerance, inositol 3-phosphate synthase

Received: 29 Apr 2018; Accepted: 04 Sep 2018.

Edited by:

Henry T. Nguyen, University of Missouri, United States

Reviewed by:

Aureliano Bombarely, Virginia Tech, United States
Marina Tucci, Consiglio Nazionale Delle Ricerche (CNR), Italy  

Copyright: © 2018 Razali, Bougouffa, Morton, Lightfoot, Alam, Essack, Arold, Kamau, Schmöckel, Pailles, Shahid, Michell, Al-Babili, Ho, Tester, Bajic and Negrao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Prof. Vladimir B. Bajic, King Abdullah University of Science and Technology, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia, vladimir.bajic@kaust.edu.sa
PhD. Sonia Negrao, King Abdullah University of Science and Technology, BESE, Thuwal, Saudi Arabia, sonia.negrao@ucd.ie