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Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides

Yonghua Han, Tao Zhang, Paradee Thammapichai, Yiqun Weng, Jiming Jiang
Genetics 2015 v.200 no.3 pp. 771-779
Cucumis hystrix, Cucumis sativus, bioinformatics, biotin, chromosome mapping, chromosomes, cucumbers, digoxigenin, fluorescence in situ hybridization, genome, hybrids, meiosis, oligonucleotides, wild relatives
Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a single chromosome of cucumber were identified using a newly developed bioinformatic pipeline and then massively synthesized de novo in parallel. The synthesized oligos were amplified and labeled with biotin or digoxigenin for use in fluorescence in situ hybridization. We developed three different probes with each containing 23,000-27,000 oligos. These probes hybridized specifically to a single cucumber chromosome and were used to paint homoeologous chromosomes in other Cucumis species which have diverged from cucumber for up to 12 million years. The bulked oligo probes can be used to effectively paint and track a single chromosome in early meiosis and were used to precisely map the pairing of a single pair of homoeologous chromosomes in a hybrid between cucumber and its wild relative Cucumis hystrix.