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Title: Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

item Labate, Joanne
item Robertson, Larry

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/30/2012
Publication Date: 8/7/2012
Citation: Labate, J.A., Robertson, L.D. 2012. Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles. Biomed Central (BMC) Plant Biology. 12:133.

Interpretive Summary: Many wild plant species that are closely related to crops are conserved in gene banks and used for development of new crop varieties. This involves breeding a wild parent into a crop parent, also known as ‘introgression’. In this way many new genes have been transferred into crops for desirable traits that give wild species their hardiness, such as disease resistance or drought tolerance. Introgression inevitably includes the transfer of unfavorable genes (for example, for small and bitter fruit) into the crop alongside the favorable genes. These are then bred out of the crop through a labor intensive and time consuming process. Use of molecular markers can aid introgression breeding by helping to identify which undesirable genes came from the wild parent. In this study we used molecular markers to analyze 47 genes in tomato, nine of which we believe came from wild tomato species. We uncovered the origins of the genes and demonstrated how a deeper understanding of introgression can contribute to use of tomato stocks conserved at PGRU for more efficient crop improvement.

Technical Abstract: The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and many of the wild species have been used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. We compared DNA sequences of 47 markers ranging in length from 130 to 1200 nt (total of 24 kb) among several genotypes of S. lycopersicum versus S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum. Each marker was mapped with high confidence (e < 1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ' 2.34 %) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization networks, genomic map positions and origins of accessions were used to interpret evolutionary patterns at nine markers. Four of these markers likely involved linkage drag on chromosome 9 during introgression breeding, while the other five may be from natural hybridization with S. pimpinellifolium associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles.