Physical map of quantitative metabolic loci from a wild species tomato (Solanum pennellii)

KAMENETZKY L.; ASIS R.; BASSI S.; FERNIE A. R.; GIOVANNONI J.; VREVALOB J.; ROSSI M.; CARRARI F.

Búzios, Brasil

Simposio; II Simpósio Brasileiro de Genética Molecular de Plantas; 2009

The wild tomato species Solanum pennellii has contributed with an important portion of the allelicvariance in revealingquantitative trait loci (QTL) but its genomic sequence information is still poor. As a part of alarger project to determine metabolic determinant of tomato fruit quality we constructed a physical map of 5 genomicregions of S. pennellii associated to metabolic QTL and Yield Associated Loci (YAL) with agronomic interest (BIN 1C,2B, 4I, 7H and 11C). The physical map, consisting of 381 anchored BAC/COS clones was built by double screeningovergo hybridization and BAC/COS-end sequence information. The number of anchored clones by cM rangebetween 2.1 to 10.3. 519 end sequences with an average length of 693 pb encompassing 359667 pb, were usedto the physical maps construction. After contig assembling, sequence marker searching and comparison against S.lycopersicum orthologous regions, 89 (23%) of the clones resulted informative in terms of identity with markers and/ore S. lycopersicum clones. The integration of anchoring with both, hybridization and in silico experiments showedS. pennellii map topology colinear with the S. lycopersicum genome used as target. Almost all informative clonesanchored to S lycopersicum clones with similar map position of the S. pennellii anchored clone. Differences in mapposition between hybridization and computational anchoring range from 0 to 15 cM with an average value of 8.8cM. Although 49 out of 104 markers anchored similar number of clones in both species, 35 markers anchored onlyS. pennellii clones and 11 markers anchored only S. lycoersicum clones. These differences could be attributed to atleast two reasons: 1) differences in genomic libraries composition and; 2) differences in genomic sequence betweenboth species. Due to the high number of markers anchored only one of the two species could be interesting to furtheranalyze clones anchored only in S. pennellii genome to get in deep of drastically differences in sequences betweenrelated tomato species, also this results could assist long-range assembly of whole genome shotgun sequencescaffolds and to anchor the physical map to the tomato genome sequence. A total of 435 sequences includingsingletons and contigs from BAC and COS libraries and comprising 310981pb were subjected to gene sequenceannotation by MapMan software. 21 gene categories were found, sequences annotated range from 28 to 84% in the5 BINs under study. The largest gene density was found in BIN 4I and the most abundant number of gene classesin BIN 7H. The results obtained here allow the identification of wild alleles potentially involved in the tomato fruitquality determination.