Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
Abstract
Genetic variation in the tomato clade was explored by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups. We present a reconstruction of three new reference genomes in support of our comparative genome analyses. Sequence diversity in commercial breeding lines appears extremely low, indicating the dramatic genetic erosion of crop tomatoes. This is reflected by the SNP count in wild species which can exceed 10 million i.e. 20 fold higher than in crop accessions. Comparative sequence alignment reveals group, species, and accession specific polymorphisms, which explain characteristic fruit traits and growth habits in tomato accessions. Using gene models from the annotated Heinz reference genome, we observe a bias in dN/dS ratio in fruit and growth diversification genes compared to a random set of genes, which probably is the result of a positive selection. We detected highly divergent segments in wild S. lycopersicum species, and footprints of introgressions in crop accessions originating from a common donor accession. Phylogenetic relationships of fruit diversification and growth specific genes from crop accessions show incomplete resolution and are dependent on the introgression donor. In contrast, whole genome SNP information has sufficient power to resolve the phylogenetic placement of each accession in the four main groups in the Lycopersicon clade using Maximum Likelihood analyses. Phylogenetic relationships appear correlated with habitat and mating type and point to the occurrence of geographical races within these groups and thus are of practical importance for introgressive hybridization breeding. Our study illustrates the need for multiple reference genomes in support of tomato comparative genomics and Solanum genome evolution studies.
Keywords
Cite
@article{arxiv.1504.05610,
title = {Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing},
author = {Saulo A. Aflitos and Elio Schijlen and Richard Finkers and Sandra Smit and Jun Wang and Gengyun Zhang and Ning Li and Likai Mao and Hans de Jong and Freek Bakker and Barbara Gravendeel and Timo Breit and Rob Dirks and Henk Huits and Darush Struss and Ruth Wagner and Hans van Leeuwen and Roeland van Ham and Laia Fito and Laëtitia Guigner and Myrna Sevilla and Philippe Ellul and Eric W. Ganko and Arvind Kapur and Emmanuel Reclus and Bernard de Geus and Henri van de Geest and Bas te Lintel Hekkert and Jan C. Van Haarst and Lars Smits and Andries Koops and Gabino Sanchez Perez and Dick de Ridder and Sjaak van Heusden and Richard Visser and Zhiwu Quan and Jiumeng Min and Li Liao and Xiaoli Wang and Guangbiao Wang and Zhen Yue and Xinhua Yang and Na Xu and Eric Schranz and Eric F. Smets and Rutger A. Vos and Han Rauwerda and Remco Ursem and Cees Schuit and Mike Kerns and Jan van den Berg and Wim H. Vriezen and Antoine Janssen and Torben Jahrman and Frederic Moquet and Julien Bonnet and Sander A. Peters},
journal= {arXiv preprint arXiv:1504.05610},
year = {2015}
}
Comments
4 Figure, 10 Supplementary Figures, 2 Supplementary Figures This is the pre-peer reviewed version of the following article: The Plant Journal 80.1 (2014): 136-148, which has been published in final form at http://doi.org/10.1111/tpj.12616