Colorado State University

University of Hohenheim

Florida State University

University of California

Integrating genetic linkage maps with pachytene chromosome structure in maize

--Anderson, LK, Salameh, N, Bass HW, Harper LC, Cande WZ, Weber G, Stack SM

Integrating genetic linkage maps with chromosome structure has been an important objective ever since it was demonstrated that genes occur in a fixed order on chromosomes. Linkage maps are defined by the percentage of recombination between markers [as expressed in centiMorgans (cM)] and reveal the linear order of markers. However, they do not contain in (positions on chromosomes) or as a physical length (number of formation on the actual physical distance between markers, whether that distance is expressed as a cytological length DNA base pairs). This is because crossing over is not evenly distributed along chromosomes. Crossing over is suppressed in heterochromatin and centromeres, and crossing over is variable even in euchromatin where most crossing over occurs. As a result, linkage maps cannot be simply overlaid on chromosomes to determine the physical position of genes. One way to integrate linkage maps with chromosome structure is to utilize high-resolution cytological markers of crossing over, such as recombination nodules (RNs). RNs are proteinaceous, multi-component, ellipsoids approximately 100 nm in diameter, which are found in the central region of synaptonemal complexes (SCs) between homologous chromosomes (bivalents) at pachytene. Evidence that RNs mark crossover sites include the close correspondence between the frequency and distribution of RNs compared to chiasmata, the presence of an essential crossover protein (MLH1p) in RNs, and the presence of MLH1p/RNs at chiasma sites. Because RNs can be observed only by electron microscopy of SCs in elongate pachytene bivalents, RNs represent the highest resolution markers available for determining the chromosomal location of crossing over. Each RN represents one crossover between two homologous non-sister chromatids, which yields two recombinant and two parental chromosomes that is, by definition, equivalent to 50 cM on a linkage map. On this basis, the frequency of RNs can be converted to cM and used to prepare a detailed map of recombination along the physical length of each of the ten pachytene chromosomes/SCs in maize. Because RN maps relate the amount of recombination to cytological position along pachytene chromosomes and linkage maps report the amount of recombination relative to genes or other markers, it is now possible to combine these two approaches to directly relate genetically-mapped markers to cytological position. We have used this procedure to predict the physical position of genetically mapped core bin markers on each of the ten chromosomes of maize. 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 the predicted and observed locations was very strong (r2 = 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 work has been accepted for publication in Genetics.

Acknowledgements. This work was supported by the National Science Foundation (MCB-9728673 to SMS, MCB-0314644 to LKA, and DBI-9813365 to ZC and LH), the Consortium for Plant Biotechnology Research, Inc. (DOE OR22072-102) and the Florida State University Research Foundation (to HB), and Eiselenstiftung, Ulm, Germany (to GW).