Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis

Plant breeding is enhanced by the availability of molecular markers for rapid screening and selection in populations. Identifi cation of polymorphic loci in cultivated tomato (Solanum lycopersicum L.) has been hampered by limited genome sampling across cultivated types. Whole transcriptome sequencing of six accessions that span cultivated market classes was performed using sequencing by synthesis. A total of 291,915,037 quality fi ltered reads representing 17 Gb of sequence were generated. Assembly of the reads resulted in 30.6 to 34.9 Mb of sequence for each of the six accessions and provided representation of 55.3 to 59.6% of the predicted tomato gene set with a wide range of molecular function Gene Ontologies (GOs) represented. A computational pipeline was developed to identify single nucleotide polymorphisms (SNPs). When coupled with two Sanger-derived expressed sequence tag datasets and a reference genome, 62,576 nonredundant putative SNPs in tomato were identifi ed. The SNPs within the contigs were present within all of the GO molecular function categories. The computational pipeline had validation rates in SNP genotyping assays that ranged from 95 to 100%, and the utility of these SNPs for assessing genetic variation within cultivated and wild populations was demonstrated. Collectively, the transcript sequences and the annotated SNPs provide a resource to facilitate tomato genetics and breeding efforts. TOMATO (Solanum lycopersicum L.) has undergone intensive selection through domestication and breeding (Miller and Tanksley, 1990). Although selection generally narrows genetic diversity relative to founding populations, there has been a long tradition of intraspecifi c hybridization in tomato breeding. Th is approach has contributed to higher coeffi cients of genetic distance and greater allelic richness in contemporary cultivated varieties relative to landraces and vintage varieties (Park et al., 2004; Sim et al., 2009, 2011; Williams and St. Clair, 1993). In addition, breeding for market specialization with a strong emphasis on distinct plant architecture and fruit characteristics has led to genetic diff erentiation within contemporary lineages (Sim et al., 2011). Measures of genetic polymorphism, genetic distance, and population diff erentiation are important to the management of germplasm resources, crop improvement programs, and the success of association mapping. Tomato has provided a strong model for identifying genes that distinguish domestic and wild plants but has been explored less from the perspective of post-domestication selection. Mapping in wide crosses and the characterization of genes that aff ect specifi c traits have produced substantial understanding into the mechanisms of disease resistance (e.g., Jones et al., 1994; Martin et al., 1993), plant and fruit Published in The Plant Genome 5:17–29. doi: 10.3835/plantgenome2011.12.0033 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. J.P. Hamilton and C.R. Buell, Michigan State Univ., Dep. of Plant Biology, East Lansing, MI 48824; S. Sim and D.M. Francis, The Ohio State Univ., OARDC, Dep. of Horticulture and Crop Science, Wooster, OH 44691; K. Stoffel and A.V. Deynze, Univ. of California, Seed Biotechnology Center, Davis, CA 95616. Received 16 Dec. 2011. *Corresponding author ([email protected]). Abbreviations: EST, expressed sequence tag; Fst, the proportion of total genetic variance in a subpopulation relative to the total variance; GA2, Genome Analyzer II; GO, Gene Ontology; GOSlim, Gene Ontology Slim; NPGS, National Plant Germplasm System; PC, principal component; PCA, principal component analysis; RNA, ribonucleic acid; SNP, single nucleotide polymorphism; TAIR, The Arabidopsis Information Resource; TGI, Tomato Genome Initiative. Published March 2012