Resequencing at ≥ 40-fold depth of the parental genomes of a Solanum lycopersicum × S. pimpinellifolium recombinant inbred line population and characterisation of frame-shift InDels that are highly likely to perturb protein function

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dc.contributor.authorKevei, Zoltan
dc.contributor.authorKing, Robert C.
dc.contributor.authorMohareb, Fady R.
dc.contributor.authorSergeant, Martin J.
dc.contributor.authorAwan, Sajjad Z.
dc.contributor.authorThompson, Andrew J.
dc.date.accessioned2016-02-23T14:09:54Z
dc.date.available2016-02-23T14:09:54Z
dc.date.issued2015-03-24
dc.description.abstractA recombinant in-bred line population derived from a cross between Solanum lycopersicum var. cerasiforme (E9) and S. pimpinellifolium (L5) has been used extensively to discover quantitative trait loci (QTL), including those that act via rootstock genotype, however, high-resolution single-nucleotide polymorphism genotyping data for this population are not yet publically available. Next-generation resequencing of parental lines allows the vast majority of polymorphisms to be characterized and used to progress from QTL to causative gene. We sequenced E9 and L5 genomes to 40- and 44-fold depth, respectively, and reads were mapped to the reference Heinz 1706 genome. In L5 there were three clear regions on chromosome 1, chromosome 4, and chromosome 8 with increased rates of polymorphism. Two other regions were highly polymorphic when we compared Heinz 1706 with both E9 and L5 on chromosome 1 and chromosome 10, suggesting that the reference sequence contains a divergent introgression in these locations. We also identified a region on chromosome 4 consistent with an introgression from S. pimpinellifolium into Heinz 1706. A large dataset of polymorphisms for the use in fine-mapping QTL in a specific tomato recombinant in-bred line population was created, including a high density of InDels validated as simple size-based polymerase chain reaction markers. By careful filtering and interpreting the SnpEff prediction tool, we have created a list of genes that are predicted to have highly perturbed protein functions in the E9 and L5 parental lines.en_UK
dc.identifier.citationKevei Z, King RC, Mohareb F, Sergeant MJ, Awan SZ, Thompson AJ. Resequencing at ≥ 40-fold depth of the parental genomes of a Solanum lycopersicum × S. pimpinellifolium recombinant inbred line population and characterisation of frame-shift InDels that are highly likely to perturb protein function. G3, May 1 2015, vol. 5, no. 5, pp971-981en_UK
dc.identifier.issn2160-1836
dc.identifier.urihttp://dx.doi.org/10.1534/g3.114.016121
dc.identifier.urihttp://dspace.lib.cranfield.ac.uk/handle/1826/9728
dc.language.isoenen_UK
dc.publisherGenetics Society of Americaen_UK
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (CC:BY 3.0)(http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.subjectSolanum lycopersicumen_UK
dc.subjectS. pimpinellifoliumen_UK
dc.subjectSL2.50en_UK
dc.subjectSNPen_UK
dc.subjectInDelen_UK
dc.subjectintrogressionen_UK
dc.subjectlarge effect polymorphismsen_UK
dc.subjectrecombinant inbred linesen_UK
dc.titleResequencing at ≥ 40-fold depth of the parental genomes of a Solanum lycopersicum × S. pimpinellifolium recombinant inbred line population and characterisation of frame-shift InDels that are highly likely to perturb protein functionen_UK
dc.typeArticleen_UK

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