The genome sequence of the wild tomatoSolanum pimpinellifoliumprovides insights into salinity tolerance [article]

Rozaimi Razali, Salim Bougouffa, Mitchell J. L. Morton, Damien J. Lightfoot, Intikhab Alam, Magbubah Essack, Stefan T. Arold, Allan Kamau, Sandra M. Schmöckel, Yveline Pailles, Mohammed Shahid, Craig T. Michell (+5 others)
<span title="2017-11-08">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Solanum pimpinellifolium, a wild relative of cultivated tomato, offers a wealth of breeding potential for several desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome and annotation ofS. pimpinellifoliumLA0480. The LA0480 genome 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
more &raquo; ... 0 protein-coding genes. Additionally, we used DEAP to compare protein function betweenS. pimpinellifoliumand cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses. Moreover, we present phenotypic data from one field experiment that demonstrate a greater salinity tolerance for fruit- and yield-related traits inS. pimpinellifoliumcompared with cultivated tomato. To understand the genomic basis for these differences inS. pimpinellifoliumandS. lycopersicum, we analyzed 15 genes that have previously been shown to mediate salinity tolerance in plants. We show thatS. pimpinellifoliumhas 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 ofS. pimpinellifolium, and to discover the genomic basis underlying its environmental robustness.
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