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Chromosome painting and its applications in cultivated and wild rice

Hou, Lili, Xu, Meng, Zhang, Tao, Xu, Zhihao, Wang, Weiyun, Zhang, Jianxiang, Yu, Meimei, Ji, Wen, Zhu, Cenwen, Gong, Zhiyun, Gu, Minghong, Jiang, Jiming, Yu, Hengxiu
BMC plant biology 2018 v.18 no.1 pp. 110
Oryza sativa, aneuploidy, chromosome painting, chromosome translocation, chromosomes, mammals, nucleotide sequences, oligonucleotides, wild rice
BACKGROUND: 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 opportunity to establish chromosome-specific probes in plants. However, never before has whole chromosome painting been performed in rice. RESULTS: 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 L., AA, 2n = 2× = 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 a wild rice (Oryza eichingeri A. Peter, CC, 2n = 2× = 24). CONCLUSION: The study reveals that a pool of oligos specific to a chromosome is a useful tool for chromosome painting in rice.