Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum x Solanum pennellii introgression lines

摘要

Marker-trait association studies in tomato haveprogressed rapidly due to the availability of several populationsdeveloped between wild species and domesticatedtomato. However, in the absence of whole genomesequences for each wild species, molecular marker methodsfor whole genome comparisons and Wne mapping arerequired. We describe the development and validation of adiversity arrays technology (DArT) platform for tomatousing an introgression line (IL) population consisting ofwild Solanum pennellii introgressed into Solanum lycopersicum(cv. M82). A tomato diversity array consisting of6,912 clones from domesticated tomato and twelve wildtomato/Solanaceous species was constructed. We successfullybin-mapped 990 polymorphic DArT markers togetherwith 108 RFLP markers across the IL population, increasingthe number of markers available for each S. pennelliiintrogression by tenfold on average. A subset of DArTmarkers from ILs previously associated with increased levelsof lycopene and carotene were sequenced, and 44%matched protein coding genes. The bin-map position andorder of sequenced DArT markers correlated well withtheir physical position on scaVolds of the draft tomatogenome sequence (SL2.40). The utility of sequenced DArTmarkers was illustrated by converting several markers inboth the S. pennellii and S. lycopersicum phases to cleavedampliWed polymorphic sequence (CAPS) markers. Genotypescores from the CAPS markers conWrmed the genotypescores from the DArT hybridizations used to constructthe bin map. The tomato diversity array provides additional“sequence-characterized” markers for Wne mapping ofQTLs in S. pennellii ILs and wild tomato species.