Abstract
Integrated cytogenetic pachytene fluorescence in situ hybridization (FISH) maps were developed for chromosomes 1, 3, 4, 5, 6, and 8 of maize using restriction fragment length polymorphism marker-selected Sorghum propinquum bacterial artificial chromosomes (BACs) for 19 core bin markers and 4 additional genetic framework loci. Using transgenomic BAC FISH mapping on maize chromosome addition lines of oats, we found that the relative locus position along the pachytene chromosome did not change as a function of total arm length, indicative of uniform axial contraction along the fibers during mid-prophase for tested loci on chromosomes 4 and 5. Additionally, we cytogenetically FISH mapped six loci from chromosome 9 onto their duplicated syntenic regions on chromosomes 1 and 6, which have varying amounts of sequence divergence, using sorghum BACs homologous to the chromosome 9 loci. We found that successful FISH mapping was possible even when the chromosome 9 selective marker had no counterpart in the syntenic block. In total, these 29 FISH-mapped loci were used to create the most extensive pachytene FISH maps to date for these six maize chromosomes. The FISH-mapped loci were then merged into one composite karyotype for direct comparative analysis with the recombination nodule-predicted cytogenetic, genetic linkage, and genomic physical maps using the relative marker positions of the loci on all the maps. Marker colinearity was observed between all pair-wise map comparisons, although marker distribution patterns varied widely in some cases. As expected, we found that the recombination nodule-based predictions most closely resembled the cytogenetic map positions overall. Cytogenetic and linkage map comparisons agreed with previous studies showing a decrease in marker spacing in the peri-centromeric heterochromatin region on the genetic linkage maps. In fact, there was a general trend with most loci mapping closer towards the telomere on the linkage maps than on the cytogenetic maps, regardless of chromosome number or maize inbred line source, with just some of the telomeric loci exempted. Finally and somewhat surprisingly, we observed considerable variation between the relative arm positions of loci when comparing our cytogenetic FISH map to the B73 genomic physical maps, even where comparisons were to a B73-derived cytogenetic map. This variation is more evident between different chromosome arms, but less so within a given arm, ruling out any type of inbred-line dependent global features of linear deoxyribonucleic acid compared with the meiotic fiber organization. This study provides a means for analyzing the maize genome structure by producing new connections for integrating the cytogenetic, linkage, and physical maps of maize.Electronic supplementary materialThe online version of this article (doi:10.1007/s10577-012-9281-4) contains supplementary material, which is available to authorized users.
Highlights
Maize (Zea mays L. spp. mays) is a well-studied cereal crop species with extensive genetic diversity (Chandler and Brendel 2002; Fu and Dooner 2002; Buckler et al 2009; Flint-Garcia et al 2009a, b; Schnable et al 2009; Springer et al 2009)
This study provides a means for analyzing the maize genome structure by producing new connections for integrating the cytogenetic, linkage, and physical maps of maize
Maize chromosome arm ratios in oat addition lines are consistent with those previously reported for maize
Summary
Maize (Zea mays L. spp. mays) is a well-studied cereal crop species with extensive genetic diversity (Chandler and Brendel 2002; Fu and Dooner 2002; Buckler et al 2009; Flint-Garcia et al 2009a, b; Schnable et al 2009; Springer et al 2009). Mays) is a well-studied cereal crop species with extensive genetic diversity (Chandler and Brendel 2002; Fu and Dooner 2002; Buckler et al 2009; Flint-Garcia et al 2009a, b; Schnable et al 2009; Springer et al 2009). The maize maps share genetic markers whose colinearity is derived from the linear structure of the chromosomes themselves, but they differ greatly in method of production, units, and the ways they are viewed and used in genetics, genomics, and selective breeding. Integrating different map types with shared markers provides a comprehensive view of genome structure while consolidating the most useful features of the various maps as such, production and integration of maps for model species, such as maize, are an active and long-term endeavor spanning many decades
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