Eggplant (Solanum melongena) and pepper (Capsicum annuum) are members of the Solanaceae, a large plant family which comprises over 3,000 species and includes the most valuable vegetable crops. The Solanaceae genomes have undergone relatively few rearrangements and duplications, share a similar gene number and show extensive synteny among them. This high level of conservation of genome organization makes this family a model to explore the common basis of phenotypic diversity. Both the pepper and eggplant genome sequences are at present available, however the rather low quality of the eggplant genome sequence, of which only about 12% was anchored, limits its use for the analysis of QTL orthology. The inheritance of agronomic traits has been extensively studied in pepper and, to a more limited extent, in eggplant. In pepper a high-density EST-based genetic map was established and SNPs associated to 96 QTL related to capsaicinoids, fruit quality and plant architecture-related traits were identified (Yarnes et al. Genome 56:61–74). We recently developed an eggplant RAD-tag (restriction associated DNA) map, which was used to locate anthocyanin and yield-related QTL (Barchi et al. PLoS One 7:e43740, Portis et al. PLoS One 9:e89499) In order to identify eggplant and pepper orthologous QTL, the eggplant RAD-tag markers and the pepper SNP markers were aligned (GMAP software) on pepper genome using GBrowse as a reference platform for QTL positioning. A total of 165 QTL of eggplant, among which 51 major QTL (PV explained ≥ 10%) affecting anthocyanin content, fruit weight and shape as well as plant and leaf morphology, were found to be orthologous with 151 QTL of pepper. In both eggplant and pepper most of the QTL affecting phenotypic traits were previously found to cluster in specific chromosomal regions, which we also detected to be orthologous in the two species. The availability in the future of a high quality eggplant genome sequence will allow to improve the resolution of our analyses.
Eggplant and pepper orthologous loci affecting traits of agronomic importance
RINALDI, RICCARDO;BARCHI, Lorenzo;PORTIS, Ezio;LANTERI, Sergio
2015-01-01
Abstract
Eggplant (Solanum melongena) and pepper (Capsicum annuum) are members of the Solanaceae, a large plant family which comprises over 3,000 species and includes the most valuable vegetable crops. The Solanaceae genomes have undergone relatively few rearrangements and duplications, share a similar gene number and show extensive synteny among them. This high level of conservation of genome organization makes this family a model to explore the common basis of phenotypic diversity. Both the pepper and eggplant genome sequences are at present available, however the rather low quality of the eggplant genome sequence, of which only about 12% was anchored, limits its use for the analysis of QTL orthology. The inheritance of agronomic traits has been extensively studied in pepper and, to a more limited extent, in eggplant. In pepper a high-density EST-based genetic map was established and SNPs associated to 96 QTL related to capsaicinoids, fruit quality and plant architecture-related traits were identified (Yarnes et al. Genome 56:61–74). We recently developed an eggplant RAD-tag (restriction associated DNA) map, which was used to locate anthocyanin and yield-related QTL (Barchi et al. PLoS One 7:e43740, Portis et al. PLoS One 9:e89499) In order to identify eggplant and pepper orthologous QTL, the eggplant RAD-tag markers and the pepper SNP markers were aligned (GMAP software) on pepper genome using GBrowse as a reference platform for QTL positioning. A total of 165 QTL of eggplant, among which 51 major QTL (PV explained ≥ 10%) affecting anthocyanin content, fruit weight and shape as well as plant and leaf morphology, were found to be orthologous with 151 QTL of pepper. In both eggplant and pepper most of the QTL affecting phenotypic traits were previously found to cluster in specific chromosomal regions, which we also detected to be orthologous in the two species. The availability in the future of a high quality eggplant genome sequence will allow to improve the resolution of our analyses.
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