Academic journal article Genetics

Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome 1

Academic journal article Genetics

Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome 1

Article excerpt

ABSTRACT

Predicting the chromosomal location of mapped markers has been difficult because linkage maps do not reveal differences in crossover frequencies along the physical structure of chromosomes. Here we combine a physical crossover map based on the distribution of recombination nodules (RNs) on Solanum lycopersicum (tomato) synaptonemal complex 1 with a molecular genetic linkage map from the interspecific hybrid S. lycopersicum × S. pennellii to predict the physical locations of 17 mapped loci on tomato pachytene chromosome 1. Except for one marker located in heterochromatin, the predicted locations agree well with the observed locations determined by fluorescence in situ hybridization. One advantage of this approach is that once the RN distribution has been determined, the chromosomal location of any mapped locus (current or future) can be predicted with a high level of confidence.

WHILE linkage maps accurately describe gene order and the amount of crossing over between genes, they are less useful for predicting the physical locations of genes on chromosomes. This is because the frequency of crossing over along the length of chromosomes is not uniform, and as a result loci that are physically far apart on chromosomes can be nearby on linkage maps and vice versa (Sturtevant and Beadle 1939; Khush and Rick 1968; Sherman and Stack 1995; Zhong et al. 1999; Islam-Faridi et al. 2002; Budiman et al. 2004). Such discrepancies are impediments to applying linkage maps to guide genome sequence assembly or for gene discovery by chromosome walking (Budiman et al. 2004).

A variety of cytogenetic techniques have been used to determine the position of genes on chromosomes without relying on linkage maps. Widely used techniques include (1) cytogenetic analysis of chromosome duplications, deletions, and rearrangements (Khush and Rick 1968; Berger 2004); (2) genetic analysis of radiation hybrids whereby genes are assigned to particular chromosomal fragments on the basis of presence vs. absence tests (Hudson et al. 2001; Kynast et al. 2004); and (3) fluorescence in situ hybridization (FISH) involving hybridization of labeled DNA fragments to intact chromosomes to show the positions of complementary sequences (Fransz et al. 1996; De Jong et al. 1999; Jackson et al. 2000). While these techniques have been used to localizemany genes on chromosomes, they are limited by special requirements, and they are not high throughput.

Recently, Anderson et al. (2004) reported a new approach for locating mapped loci on maize pachytene chromosomes. This technique depends on first mapping the frequency and location of recombination nodules (RNs) on synaptonemal complexes (SCs, pachytene bivalents). Assuming that eachRN represents a crossover (Carpenter 1975; Herickhoff et al. 1993; Sherman and Stack 1995; Pigozzi and Solari 1999; Marcon and Moens 2003), variation in the frequency and distribution of RNs on SCs represents the variation in recombination rates along pachytene chromosomes. RN distributions can be converted to centimorgan (cM) distributions, thereby creating an RN-cM recombination map for each pachytene chromosome (Anderson et al. 2004). By relating crossover frequency to chromosome structure, the RN-cM map provides a means to predict the positions of mapped loci on pachytene chromosomes. While this approach also has special requirements, the advantage is that once the RN-cM map is made, the chromosomal positions of all mapped loci can be predicted easily, along with any additional markers placed on the genetic map in the future. The accuracy of this approach for maize was tested for markers on chromosome 9 by comparing the predicted chromosomal locations of loci from the UMC98 linkage map (Davis et al. 1999) with their observed physical locations determined independently by FISH. The correlation between the predicted and observed chromosomal locations was very strong (r2 = 0.996), indicating that most, if not all, loci on the linkage map can be positioned accurately on maize SCs using the RN-cM map [see the Morgan2McClintock Translator (http://www. …

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