Kevei, Zoltan, King, Robert C., Mohareb, Fady, Sergeant, Martin J., Awan, Sajjad Zahoor and Thompson, Andrew J. (2015) Resequencing at >=40-fold depth of the parental genomes of a Solanum Lycopersicum x S. pimpinellifolium recombinant inbred line population and characterization of frame-shift indels that are highly likely to perturb protein function. G3 : genes, genomes, genetics, 5 (5). pp. 971-981. doi:10.1534/g3.114.016121 ISSN 2160-1836.

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Abstract

A 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.

Item Type:	Journal Article
Subjects:	S Agriculture > SB Plant culture
Divisions:	Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	Tomatoes -- Genetics
Journal or Publication Title:	G3 : genes, genomes, genetics
Publisher:	Genetics Society of America
ISSN:	2160-1836
Official Date:	1 May 2015
Dates:	Date Event 1 May 2015 Published 24 March 2015 Available 22 March 2015 Accepted 10 December 2014 Submitted
Volume:	5
Number:	5
Number of Pages:	11
Page Range:	pp. 971-981
DOI:	10.1534/g3.114.016121
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access (Creative Commons)
Date of first compliant deposit:	29 December 2015
Date of first compliant Open Access:	29 December 2015
Funder:	Seventh Framework Programme (European Commission) (FP7)
Grant number:	289365 (FP7)

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