Chromosome-specific painting in cultivated and wild rice using bulked oligonucleotides

【摘要】：The chromosome-specific probe is a fundamental tool of chromosome painting and has been commonly applied in mammalian species.The technology,however,has not been widely applied in plants due to a lack of methodologies for probe development.Identification and labeling of a large number of oligonucleotides(oligos) specific to a single chromosome offers us an pportunity to establish chromosomespecific probes in plants.However,never before has whole chromosome painting been performed in rice.We developed a pooled chromosome 9-specific probe in rice,which contains 25,000 oligos based on the genome sequence of a japonica rice(Oryza sativa,AA,2 n=2 x=24).Chromosome 9 was easily identified in both japonica and indica rice using this chromosome 9-painting probe.The probe was also successfully used to identify and characterize chromosome 9 in additional lines of O.sativa,a translocation line,two new aneuploids associated with chromosome 9 and sever wild rice with different genomes.This indicates that sequence similarity exists in chromosome 9 between O.sativa and wild rice with different genomes and a pool of oligos specific to a single chromosome is a useful tool for chromosome painting in rice.However,the FISH signal of chromosome 9 specific probe on chromosome 9 of O.eichingeri was much weaker than that in O.sativa,indicating that some differentiation has been occurred between O.eichingeri and O.sativa.