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The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance

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.‎

Authors: 
Rozaimi Razali, Salim Bougouffa, Mitchell J.‎ L.‎ Morton, Damien J.‎ Lightfoot, Intikhab Alam, Magbubah Essack, Stefan T.‎ Arold, Allan A.‎ Kamau, Sandra M.‎ Schmöckel, Yveline Pailles, Mohammed Shahid, Craig T.‎ Michell, Salim Al-Babili, Yung Shwen Ho, Mark Tes
Year: 
۲۰۱۸
Publication type: 
Research Article
Publication Source: 
Frontiers
Volume/Chapter/Issue: 
۹
ISBN: 
https://doi.org/10.‎3389/fpls.‎2018.‎01402