Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato.

TLDR

Substitution mapping in tomato narrows QTL intervals by leveraging dense marker coverage and is especially useful for introgressing genes from wild relatives into domesticated species. The authors demonstrate this method by evaluating tomato lines carrying chromosomal segments from the wild species Lycopersicon chmielewskii, which is known for high soluble solids but small fruit and low yield. Field trials measured the impact of these introgressed segments on soluble solids, fruit mass, yield, and pH. Overlapping segments identified QTLs as small as 3 cM with distinct phenotypic effects, showing that trait associations often result from tightly linked QTLs rather than pleiotropy and that recombination can separate desirable loci from undesirable ones.

Abstract

Abstract Quantitative trait loci (QTLs) have been mapped to small intervals along the chromosomes of tomato (Lycopersicon esculentum), by a method we call substitution mapping. The size of the interval to which a QTL can be mapped is determined primarily by the number and spacing of previously mapped genetic markers in the region surrounding the QTL. We demonstrate the method using tomato genotypes carrying chromosomal segments from Lycopersicon chmielewskii, a wild relative of tomato with high soluble solids concentration but small fruit and low yield. Different L. chmielewskii chromosomal segments carrying a common restriction fragment length polymorphism were identified, and their regions of overlap determined using all available genetic markers. The effect of these chromosomal segments on soluble solids concentration, fruit mass, yield, and pH, was determined in the field. Many overlapping chromosomal segments had very different phenotypic effects, indicating QTLs affecting the phenotype(s) to lie in intervals of as little as 3 cM by which the segments differed. Some associations between different traits were attributed to close linkage between two or more QTLs, rather than pleiotropic effects of a single QTL: in such cases, recombination should separate desirable QTLs from genes with undesirable effects. The prominence of such trait associations in wide crosses appears partly due to infrequent reciprocal recombination between heterozygous chromosomal segments flanked by homozygous regions. Substitution mapping is particularly applicable to gene introgression from wild to domestic species, and generally useful in narrowing the gap between linkage mapping and physical mapping of QTLs.