The Solanaceae is a large plant family which comprises over 3,000 species and includes three of the most valuable vegetable crops: tomato, pepper and eggplant, which share the same chromosome number (2n=24). This plant family has experienced chromosomal changes at a modest rate compared with other families and the rates are likely conserved across different lineages. Tomato, pepper and eggplant genome sequences are at present available, however the rather low quality of the eggplant genome sequence, of which only about 12% has been anchored, limits its use for synteny studies. To better understand the structural relationships among the three species a private database browser (GMOD GBrowse) was developed as a reference platform for synteny mapping of tomato and pepper (To/Pe), eggplant and tomato (Eg/To) as well as eggplant and pepper (Eg/Pe). In order to identify eggplant and pepper conserved QTL, the eggplant RAD-tag markers and the pepper SNP markers were aligned (GMAP software) on pepper genome; furthermore, a private “Pepper Database Browser” (GMOD GBrowse) was developed as a reference platform for QTL positioning. The To/Pe mapping was based on alignment of tomato CDS on pepper sequence, otherwise Eg/To and Eg/Pe mapping was obtained by aligning an extensive eggplant RAD-tag (restriction associated DNA) map with the tomato and pepper sequences respectively. The To/Pe map confirmed the 19 inversions and 10 translocations previously reported in literature, but also highlighted 3 new translocations and 13 new inversions. Furthermore, on each chromosome, a wide number of rearrangements involving small chromosomal regions (0.5/0.7 Mbps) was identified. The Eg/To mapping confirmed the 7 translocations but only 7 of the 24 inversions previously reported, on the other hand a newly detected inversion was recognized. The Eg/Pe mapping confirmed 10 translocations and 8 inversions already detected as well as a new putative translocation. The availability in the next future of an high quality eggplant genome sequence will allow to improve the resolution of our analyses.
Synteny mapping of tomato, pepper and eggplant provides new insights on their chromosomal structural relationships
RINALDI, RICCARDO;BARCHI, Lorenzo;PORTIS, Ezio;LANTERI, Sergio
2015-01-01
Abstract
The Solanaceae is a large plant family which comprises over 3,000 species and includes three of the most valuable vegetable crops: tomato, pepper and eggplant, which share the same chromosome number (2n=24). This plant family has experienced chromosomal changes at a modest rate compared with other families and the rates are likely conserved across different lineages. Tomato, pepper and eggplant genome sequences are at present available, however the rather low quality of the eggplant genome sequence, of which only about 12% has been anchored, limits its use for synteny studies. To better understand the structural relationships among the three species a private database browser (GMOD GBrowse) was developed as a reference platform for synteny mapping of tomato and pepper (To/Pe), eggplant and tomato (Eg/To) as well as eggplant and pepper (Eg/Pe). In order to identify eggplant and pepper conserved QTL, the eggplant RAD-tag markers and the pepper SNP markers were aligned (GMAP software) on pepper genome; furthermore, a private “Pepper Database Browser” (GMOD GBrowse) was developed as a reference platform for QTL positioning. The To/Pe mapping was based on alignment of tomato CDS on pepper sequence, otherwise Eg/To and Eg/Pe mapping was obtained by aligning an extensive eggplant RAD-tag (restriction associated DNA) map with the tomato and pepper sequences respectively. The To/Pe map confirmed the 19 inversions and 10 translocations previously reported in literature, but also highlighted 3 new translocations and 13 new inversions. Furthermore, on each chromosome, a wide number of rearrangements involving small chromosomal regions (0.5/0.7 Mbps) was identified. The Eg/To mapping confirmed the 7 translocations but only 7 of the 24 inversions previously reported, on the other hand a newly detected inversion was recognized. The Eg/Pe mapping confirmed 10 translocations and 8 inversions already detected as well as a new putative translocation. The availability in the next future of an high quality eggplant genome sequence will allow to improve the resolution of our analyses.
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