Evidence of cryptic introgression in tomato (<it>Solanum lycopersicum</it> L.) based on wild tomato species alleles
<p>Abstract</p> <p>Background</p> <p>Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (<it>Solanum</it> section <it>...
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| Format: | Article |
| Language: | English |
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BMC
2012-08-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://www.biomedcentral.com/1471-2229/12/133 |
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| author | Labate Joanne A Robertson Larry D |
| author_facet | Labate Joanne A Robertson Larry D |
| author_sort | Labate Joanne A |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (<it>Solanum</it> section <it>Lycopersicon</it>) are closely related to each other and wild species genes have been extensively used for improvement of the crop, <it>Solanum lycopersicum</it> L. In addition, the lack of geographical barriers has permitted natural hybridization between <it>S. lycopersicum</it> and its closest wild relative <it>Solanum pimpinellifolium</it> in Ecuador, Peru and northern Chile. In order to better understand patterns of <it>S. lycopersicum</it> diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of <it>S. lycopersicum</it> and wild tomato species <it>S. pimpinellifolium</it>, <it>Solanum arcanum</it>, <it>Solanum peruvianum</it>, <it>Solanum pennellii</it> and <it>Solanum habrochaites</it>. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within <it>S. lycopersicum</it>, i.e., cryptic introgressions.</p> <p>Results</p> <p>Each marker was mapped with high confidence (e<1 x 10<sup>-30</sup>) 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 and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles.</p> <p>Conclusion</p> <p>Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with <it>S. pimpinellifolium</it> and were associated with primitive genotypes of <it>S. lycopersicum</it>. The positive identification of introgressed genes within crop species such as <it>S. lycopersicum</it> 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.</p> |
| first_indexed | 2024-12-18T19:21:50Z |
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| language | English |
| last_indexed | 2024-12-18T19:21:50Z |
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| spelling | doaj.art-e7f10aae9a6844dbac9dc6ae17563e692022-12-21T20:55:58ZengBMCBMC Plant Biology1471-22292012-08-0112113310.1186/1471-2229-12-133Evidence of cryptic introgression in tomato (<it>Solanum lycopersicum</it> L.) based on wild tomato species allelesLabate Joanne ARobertson Larry D<p>Abstract</p> <p>Background</p> <p>Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (<it>Solanum</it> section <it>Lycopersicon</it>) are closely related to each other and wild species genes have been extensively used for improvement of the crop, <it>Solanum lycopersicum</it> L. In addition, the lack of geographical barriers has permitted natural hybridization between <it>S. lycopersicum</it> and its closest wild relative <it>Solanum pimpinellifolium</it> in Ecuador, Peru and northern Chile. In order to better understand patterns of <it>S. lycopersicum</it> diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of <it>S. lycopersicum</it> and wild tomato species <it>S. pimpinellifolium</it>, <it>Solanum arcanum</it>, <it>Solanum peruvianum</it>, <it>Solanum pennellii</it> and <it>Solanum habrochaites</it>. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within <it>S. lycopersicum</it>, i.e., cryptic introgressions.</p> <p>Results</p> <p>Each marker was mapped with high confidence (e<1 x 10<sup>-30</sup>) 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 and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles.</p> <p>Conclusion</p> <p>Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with <it>S. pimpinellifolium</it> and were associated with primitive genotypes of <it>S. lycopersicum</it>. The positive identification of introgressed genes within crop species such as <it>S. lycopersicum</it> 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.</p>http://www.biomedcentral.com/1471-2229/12/133Cryptic introgressionLinkage dragBreedingDNA sequence<it>Solanum</it> species |
| spellingShingle | Labate Joanne A Robertson Larry D Evidence of cryptic introgression in tomato (<it>Solanum lycopersicum</it> L.) based on wild tomato species alleles BMC Plant Biology Cryptic introgression Linkage drag Breeding DNA sequence <it>Solanum</it> species |
| title | Evidence of cryptic introgression in tomato (<it>Solanum lycopersicum</it> L.) based on wild tomato species alleles |
| title_full | Evidence of cryptic introgression in tomato (<it>Solanum lycopersicum</it> L.) based on wild tomato species alleles |
| title_fullStr | Evidence of cryptic introgression in tomato (<it>Solanum lycopersicum</it> L.) based on wild tomato species alleles |
| title_full_unstemmed | Evidence of cryptic introgression in tomato (<it>Solanum lycopersicum</it> L.) based on wild tomato species alleles |
| title_short | Evidence of cryptic introgression in tomato (<it>Solanum lycopersicum</it> L.) based on wild tomato species alleles |
| title_sort | evidence of cryptic introgression in tomato it solanum lycopersicum it l based on wild tomato species alleles |
| topic | Cryptic introgression Linkage drag Breeding DNA sequence <it>Solanum</it> species |
| url | http://www.biomedcentral.com/1471-2229/12/133 |
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