Academic journal article Genetics

A Transgenomic Cytogenetic Sorghum (Sorghum Propinquum) Bacterial Artificial Chromosome Fluorescence in Situ Hybridization Map of Maize (Zea Mays L.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

Academic journal article Genetics

A Transgenomic Cytogenetic Sorghum (Sorghum Propinquum) Bacterial Artificial Chromosome Fluorescence in Situ Hybridization Map of Maize (Zea Mays L.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

Article excerpt

ABSTRACT

A cytogenetic FISH map of maize pachytene-stage chromosome 9 was produced with 32 maize marker-selected sorghum BACs as probes. The genetically mapped markers used are distributed along the linkage maps at an average spacing of 5 cM. Each locus was mapped by means of multicolor direct FISH with a fluorescently labeled probe mix containing a whole-chromosome paint, a single sorghum BAC clone, and the centromeric sequence, CentC. A maize-chromosome-addition line of oat was used for bright unambiguous identification of the maize 9 fiber within pachytene chromosome spreads. The locations of the sorghum BAC-FISH signals were determined, and each new cytogenetic locus was assigned a centiMcClintock position on the short (9S) or long (9L) arm. Nearly all of the markers appeared in the same order on linkage and cytogenetic maps but at different relative positions on the two. The CentC FISH signal was localized between cdo17 (at 9L.03) and tda66 (at 9S.03). Several regions of genome hyperexpansion on maize chromosome 9 were found by comparative analysis of relative marker spacing in maize and sorghum. This transgenomic cytogenetic FISH map creates anchors between various maps of maize and sorghum and creates additional tools and information for understanding the structure and evolution of the maize genome.

THE genome of maize (Zea mays L.) has been studied as a model for eukaryotic genetics, cereal crops, and monocot genome evolution (Chandler and Brendel 2002), but its size and organizational complexity complicate resolution of its structure. The presence of large gene-poor areas, segmental duplications, abundant retrotransposons, and microvariation among lines of maize all confound efforts to develop a fully assembled physical map of the entire maize genome (KUMAR and BENNETZEN 1999; GAUT et al. 2000; MEYERS et al. 2001; YUAN et al. 2003; MESSING et al. 2004; SWIGONOVA et al. 2004; PATERSON et al. 2005). Despite these complexities, several different kinds of maps have been developed to characterize its structure and function at the DNA and chromosome levels. Many linkage maps have been developed, including those based on mutant phenotypes (EMERSON et al. 1935) and more recently those that include thousands of additional molecular markers such as restriction fragment length polymorphisms (RFLPs), simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs), and insertion- deletion polymorphisms (indels) (HELENTJARIS et al. 1986; COE et al. 1987; BURR et al. 1988; CAUSSE et al. 1996; SENIOR and HEUN 1993; TARAMINO and TINGEY 1996; HARUSHIMA et al. 1998; DAVIS et al. 1999; LEE et al. 2002; SHAROPOVA et al. 2002; BOWERS et al. 2003; FU et al. 2006). Physical maps of overlapping clones have been produced and anchored to the linkage map by means of molecular probes (DE JONG et al. 1999; BENNETZEN et al. 2001; CHANDLER and BRENDEL 2002; GARDINER et al. 2004; MESSING et al. 2004; BOWERS et al. 2005; SONG et al. 2005; HASS-JACOBUS et al. 2006). Another type of physical map is the cytological map produced by direct microscopic inspection of the chromosomes that make up the nuclear genome. Cytogenetic maps are valuable because they can place genetic loci directly within the entire chromosome, the ultimate contig, providing information on the location, order, and distribution of DNA sequences in relation to other genetic markers along the chromosomes (SADDER et al. 2000; ANDERSON et al. 2004; KIM et al. 2005a,b). In contrast to those of the well-developed linkage maps and clone- or sequence-based physical maps, the construction of high-density cytogenetic maps is nascent and relatively underdeveloped.

Cytological analysis of maize meiotic chromosomes provided fundamental insights into transmission genetics and the dynamic nature of the maize genome. The early insights included the physical basis of genetic recombination, the discovery of transposable DNA elements, the capping properties of telomeres, and evidence in support of the chromosome theory of inheritance (CREIGHTON and MCCLINTOCK 1931; RHOADES and McCLINTOCK 1935; McCLINTOCK 1941, 1978; RHOADES 1950; and reviewed by CARLSON 1988). …

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