Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses with Tomato

By Iovene, Marina; Wielgus, Susan M. et al. | Genetics, November 2008 | Go to article overview

Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses with Tomato


Iovene, Marina, Wielgus, Susan M., Simon, Philipp W., Buell, C. Robin, Jiang, Jiming, Genetics


ABSTRACT

Potato (Solanum tuberosum) has the densest genetic linkage map and one of the earliest established cytogenetic maps among all plant species. However, there has been limited effort to integrate these maps. Here, we report fluorescence in situ hybridization (FISH) mapping of 30 genetic marker-anchored bacterial artificial chromosome (BAC) clones on the pachytene chromosome 6 of potato. The FISH mapping results allowed us to define the genetic positions of the centromere and the pericentromeric heterochromatin and to relate chromatin structure to the distribution of recombination along the chromosome. A drastic reduction of recombination was associated with the pericentromeric heterochromatin that accounts for ~28% of the physical length of the pachytene chromosome. The pachytene chromosomes 6 of potato and tomato (S. lycopersicum) share a similar morphology. However, distinct differences of heterochromatin distribution were observed between the two chromosomes. FISH mapping of several potato BACs on tomato pachytene chromosome 6 revealed an overall colinearity between the two chromosomes. A chromosome inversion was observed in the euchromatic region of the short arms. These results show that the potato and tomato genomes contain more chromosomal rearrangements than those reported previously on the basis of comparative genetic linkage mapping.

POTATO (Solanum tuberosum, 2n = 4x = 48) is the fourth most important food crop in the world, surpassed only by rice, wheat, and maize. Genetic research of potato has been long hampered by the autotetraploidy and highly heterozygous nature of the potato genome. This challenge, however, has been overcome by the advent of modern molecular marker technology. Several molecular marker-based genetic linkage maps of diploid potato were developed (Bonierbale et al. 1988; Gebhardt et al. 1989, 1991; Tanksley et al. 1992; Jacobs et al. 1995), including a 10,000-marker ultradensemapthat represents oneof the densest genetic maps in any eukaryote (van Os et al. 2006). Other resources for genomics research have also been developed, including expressed sequence tags (ESTs) (Ronning et al. 2003; Flinn et al. 2005), bacterial artificial chromosome (BAC) libraries (Song et al. 2000; Zhang et al. 2003; Chen et al. 2004), and BAC end sequences (Zhu et al. 2008). An international potato genome sequencing consortium has been established recently(http://potatogenome.net) that will make potato one of few major crop species whose genome will be sequenced using a BAC-by-BAC-based approach.

Despite the development of several potato genetic linkage maps, there has been limited effort to integrate the linkage maps with cytogenetic maps (Dong et al. 2000; Song et al. 2000). The chromosomal positions of the molecular makers used in linkage mapping are largely unknown. Furthermore, it is not known if the DNA markers are uniformly distributed along the individual chromosomes. The international potato genome sequencing project will be based on a BAC physical map anchored by the amplified fragment length polymorphism (AFLP) markers used in the development of the ultradense potato linkage map (van Os et al. 2006). The genomewide saturation of these AFLPmarkers over the entire length of the chromosomes will be a key measure for the success of the sequencing project. The potato chromosomes have been well known to consist of cytologically distinct pericentromeric heterochromatin and distal euchromatin (Yeh and Peloquin 1965). Thus, integration of the genetic linkage map with the cytogenetic map will reveal the euchromatic or heterochromatic locations of the genetic markers.

Fluorescence in situ hybridization (FISH) has become the most common approach to map DNA markers to specific chromosomal domains ( Jiang and Gill 1994, 2006). Meiotic pachytene chromosomes are superior to somatic metaphase chromosomes for FISH mapping resolution (Cheng et al. 2002). Integration of genetic linkage maps with pachytene chromosome-based cytogenetic maps has been reported in several plant species (Chenget al. …

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Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses with Tomato
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