A 105-kilobase bacterial artificial chromosome (BAC) clone from the ovate- containing region of tomato chromosome 2 was sequenced and annotated. The tomato BAC sequence was then compared, gene by gene, with the sequenced portions of the Arabidopsis thaliana genome. Rather than matching a single portion of the Arabidopsis genome, the tomato clone shows conservation of gene content and order with four different segments of Arabidopsis chromosomes 2–5. The gene order and content of these individual Arabidopsis segments indicate that they derived from a common ancestral segment through two or more rounds of large-scale genome duplication events—possibly polyploidy. One of these duplication events is ancient and may predate the divergence of the Arabidopsis and tomato lineages. The other is more recent and is estimated to have occurred after the divergence of tomato and Arabidopsis ≈112 million years ago. Together, these data suggest that, on the scale of BAC-sized segments of DNA, chromosomal rearrangements (e.g., inversions and translocations) have been only a minor factor in the divergence of genome organization among plants. Rather, the dominating factors have been repeated rounds of large-scale genome duplication followed by selective gene loss. We hypothesize that these processes have led to the network of synteny revealed between tomato and Arabidopsis and predict that such networks of synteny will be common when making comparisons among higher plant taxa (e.g., families).

Although tomato has been the subject of extensive quantitative trait loci (QTLs) mapping experiments, most of this work has been conducted on transient populations (e.g., F₂or backcross) and few homozygous, permanent mapping populations are available. To help remedy this situation, we have developed a set of inbred backcross lines (IBLs) from the interspecific cross between Lycopersicon esculentum cv. E6203 and L. pimpinellifolium (LA1589). A total of 170 BC₂F₁plants were selfed for five generations to create a set of homozygous BC₂F₆lines by single-seed descent. These lines were then genotyped for 127 marker loci covering the entire tomato genome. These IBLs were evaluated for 22 quantitative traits. In all, 71 significant QTLs were identified, 15% (11/71) of which mapped to the same chromosomal positions as QTLs identified in earlier studies using the same cross. For 48% (34/71) of the detected QTLs, the wild allele was associated with improved agronomic performance. A number of new QTLs were identified including several of significant agronomic importance for tomato production: fruit shape, firmness, fruit color, scar size, seed and flower number, leaf curliness, plant growth, fertility, and flowering time. To improve the utility of the IBL population, a subset of 100 lines giving the most uniform genome coverage and map resolution was selected using a randomized greedy algorithm as implemented in the software package MapPop (http://www.bio.unc.edu/faculty/vision/lab/mappop/). The map, phenotypic data, and seeds for the IBL population are publicly available (http://soldb.cit.cornell.edu) and will provide tomato geneticists and breeders with a genetic resource for mapping, gene discovery, and breeding.Key words: tomato, Lycopersicon esculentum, IBLs, QTL, mapping.