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Title: Chromosome-specific painting in Cucumis species using bulked oligonucleotides

Author
item HAN, YONGHUA - University Of Wisconsin
item ZHANG, TAO - University Of Wisconsin
item THAMMAPICHAI, PARADEE - University Of Wisconsin
item Weng, Yiqun
item JIANG, JIMING - University Of Wisconsin

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2015
Publication Date: 5/13/2015
Publication URL: http://handle.nal.usda.gov/10113/61124
Citation: Han, Y., Zhang, T., Thammapichai, P., Weng, Y., Jiang, J. 2015. Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics. 200(3):771-779.

Interpretive Summary: Precise and quick identification of chromosomes or chromosomal fragments is important in transfer of useful genes in crop breeding. In this study, we developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber that will be applicable in any plant species with a sequenced genome. Oligos (short DNA sequences) specific to a single cucumber chromosome were designed using a 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).

Technical Abstract: 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.