Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize

Abstract

Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1) all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2) each RN corresponds to one crossover, and (3) the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r 2 ϭ 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well. INTEGRATING genetic linkage maps with chromoorganized meiotic chromosomes. This is an important point because the observed location of a gene on a some structure has been an important objective ever since it was demonstrated that genes occur in a fixed chromosome (relative to the centromere) can be different on mitotic compared to meiotic chromosomes, as order on chromosomes (Sutton 1903; Bridges 1916).demonstrated by Froenicke et al. (2002) for mouse Linkage maps are defined by the percentage of recombichromosomes. Related observations indicate that differnation between markers [as expressed in centimorgans ences in mitotic and meiotic chromosomes may affect (cM)] and reveal the linear order of markers. However, the relative cytological distance between markers in they do not contain information on the actual physical plants as well (Stack 1984). In this regard, Drosophila distance between markers, whether that distance is exmelanogaster has the best integration of cytological (chropressed as a cytological length (positions on chromomosome), genetic (recombination), and physical (DNA somes) or as a physical length (number of DNA base sequence) aspects of the genome, but this integration pairs). This is because crossing over is not evenly distribis based on somatic polytene chromosomes (http://fly uted along chromosomes. Crossing over is suppressed base.bio.indiana.edu/), not on meiotic chromosomes in heterochromatin and centromeres, and crossing over where crossing over actually occurs. For these reasons, is variable even in euchromatin where most crossing the position of individual genes along meiotic chromoover occurs (Sherman and Stack 1995; Harper and somes and the relation of gene position to meiotic reCande 2000; Anderson et al. 2003). As a result, linkage combination are understood o...

Retroelement Genome Painting: Cytological Visualization of Retroelement Expansions in the Genera Zea and Tripsacum

“…Advances in FISH techniques have allowed specific maize loci to be detected, anchoring the genetic map to a physical location (Koumbaris and Bass 2003;Anderson et al 2004;Kato et al 2006;Wang et al 2006). In the related Sorghum species, the use of BACs has allowed detailed cytogenetic maps to be developed (Zwick et al 1998;Islam-Faridi et al 2002;Kim et al 2002), opening up the possibility of cytogenetic examination of chromosomal rearrangements among species in this genus.…”

“…Improvements in chromosome spreading procedures, development of a collection of DNA elements that can be used as fluorescence in situ hybridization (FISH) probes to identify each chromosome (Kato et al 2004), and detection of specific genetic loci on chromosomes (Koumbaris and Bass 2003;Anderson et al 2004;Kato et al 2006) have expanded the number of cytological tools available to maize researchers.…”

Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome1

“…Because the total EXPEN 2000 map length for chromosome 1 differs from the corresponding RN-cM map length (Table 1), the EXPEN 2000 map positions were adjusted proportionally for each arm to fit the length of the RN-cM map following the procedures described by Anderson et al (2004). These adjusted values are now termed the RN-cM values for each marker (Table 1).…”

“…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 each RN 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.…”