| Abstract Detail
Conference Wide Fukuoka, Hiroyuki [1], Miyatake, Koji [1], Nunome, Tsukasa [1], Negoro, Satomi [1], Kono, Izumi [2], Kanamori, Hiroyuki [2], Yamaguchi, Hirotaka [1]. Comprehensive analysis of expressed sequence tags in eggplant and their application for DNA marker development by comparative sequence analysis in Solanaceae. MORE than 31,000 cDNA clones of eggplant (Solanum melongena L.) randomly picked up from sixteen libraries derived from various tissues under various conditions were sequenced from both ends. The data were processed by a FASTA-based clustering program and 11,146 independent sequences (unigenes) were identified comprising 3,692 clusters and 7,454 singlets. The unigenes were compared against three plant gene data sets, namely, Arabidopsis hypothetical ORFs, the plant division of DDBJ records and the 26k tomato (Solanum lycopersicum) unigenes. Among the eggplant 11k unigenes, 65% of them (7,188 unigenes) shared significantly high similarity (E < 1e-10) with the sequences registered in all of the three data sets indicating that these sequences were widely common for higher plants. Out of the rest, 1,538 unigenes were matched with tomato unigenes only and no corresponding sequences were found in the other two databases, suggesting that the 1,538 sequences could be Solanum-specific. The unigenes which showed no homology to all of the three databases were 1,877 (17%). These sequences in part might be eggplant-specific, but most of them would be the genes that were common to Solanum species not identified as tomato ESTs. Tomato EST data were mainly collected from late maturing fruits and mature leaves and therefore, the data could be biased to some extent. In order to develop gene-based DNA markers, the 11k eggplant unigene, the 26k tomato unigenes and the Arabidopsis ORFs were reciprocally compared each other by Smith-Waterman algorism (SSEARCH) and 1,388 eggplant unigene sequences were selected as conserved orthologous genes among the three species. Out of these, some primer sets were designed for 781 unigenes to amplify intron-containing genome sequences. Polymorphisms among cultivars were screened by PCR-based direct sequencing and developed SNPs-based markers were mapped using intra-specific F2 population. Comparative analysis with tomato maps is also in progress.
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1 - National Institute of Vegetable and Tea Science (NIVTS), Laboratory of Breeding Technology, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
2 - Society for Techno-Innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsu, Ibaraki, 305-0854, JAPAN
Keywords:
eggplant
EST
linkage map
comparative genomics.
Session: Poster-109
Location: Ballroom CD/Monona Terrace
Date: Tuesday, July 25th, 2006
Time: 8:00 AM
Abstract ID:196 |
