High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice

Large-scale physical mapping has been a major challenge for plant geneticis ts due to the lack of techniques that are widely affordable and can be appl ied to different species. Here we present a physical map of rice chromosome 10 developed by fluorescence in situ hybridization (FISH) mapping of bacte rial artificial chromosome (BAC) clones on meiotic pachytene chromosomes. T his physical map is fully integrated with a genetic linkage map of rice chr omosome 10 because each BAC clone is anchored hr a genetically mapped restr iction fragment length polymorphism marker. The pachytene chromosome-based FISH mapping shows a superior resolving power compared to the somatic metap hase chromosome-based FISH mapping shows a superior resolving power compare d to the somatic metaphase chromosome-based methods. The telomere-centromer e orientation of DNA clones separated by 40 kb can be resolved on early pac hytene chromosomes. Genetic recombination is generally evenly distributed a long rice chromosome 10. However. the highly heterochromatic short arm show s a lower recombination frequency than the largely euchromatic long arm. Su ppression of recombination was found in the centromeric region, but the aff ected region is far smaller than those reported in wheat and barley. Our FI SH mapping effort also revealed the precise genetic position of the centrom ere on chromosome 10.