Advanced cytogenetics in Oryzeae

Abstract

Cytogenetic research in rice has lagged considerably behind that in other cereal species, including maize and wheat. However, the advent of new molecular techniques has facilitated work in rice cytology. Rice pachytene chromosomes are ideal for fluorescence in situ hybridization (FISH) mapping. The rice genome contains less repetitive DNA than that of many other cereal species. Even though there are repetitive DNA sequences in most rice bacterial artificial chromosomes (BACs), it is possible to map these BAC clones on rice chromosomes and DNA fibers by preannealing the probes to rice Cot-1 DNA. Thus, rice genomic DNA clones are suitable for fiber-FISH mapping and FISH on extended DNA fibers. We found that DNA clones separated by about 100 kb of DNA can be resolved on rice pachytene chromosomes. This is a much higher resolution than metaphase chromosomes, where adjacent BACs would have to be separated by several megabases to resolve their order. We recently developed a set of BACs that can be used to mark all 24 rice chromosome arms. This is a valuable tool for future cytogenetic mapping in rice. Using fiber-FISH, several rice BACs have been mapped to determine the size of the gaps in BAC contigs that are set to be sequenced. Several rice BACs have also been mapped in related species within the Oryzeae to determine the physical conservation of genomic architecture. Based on the fiber-FISH mapping of rice BACs in American wild rice (Zizania palustris), it appeared that over this evolutionary distance there has been an accumulation of intergenic DNA that is not conserved between these two species. Although the comparative genetic map of wild rice and rice is more than 80% colinear, the physical conservation of rice BACs in wild rice appears to be interrupted by DNA sequences that are not shared between these two species.