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Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis.
Plant J. 2020 04; 102(1):178-186.PJ

Abstract

Chromosome painting is a powerful technique for chromosome and genome studies. We developed a flexible chromosome painting technique based on multiplex PCR of a synthetic oligonucleotide (oligo) library in cucumber (Cucumis sativus L., 2n = 14). Each oligo in the library was associated with a universal as well as nested specific primers for amplification, which allow the generation of different probes from the same oligo library. We were also able to generate double-stranded labelled oligos, which produced much stronger signals than single-stranded labelled oligos, by amplification using fluorophore-conjugated primer pairs. Oligos covering cucumber chromosome 1 (Chr1) and chromosome 4 (Chr4) consisting of eight segments were synthesized in one library. Different oligo probes generated from the library painted the corresponding chromosomes/segments unambiguously, especially on pachytene chromosomes. This technique was then applied to study the homoeologous relationships among cucumber, C. hystrix and C. melo chromosomes based on cross-species chromosome painting using Chr4 probes. We demonstrated that the probe was feasible to detect interspecies chromosome homoeologous relationships and chromosomal rearrangement events. Based on its advantages and great convenience, we anticipate that this flexible oligo-painting technique has great potential for the studies of the structure, organization, and evolution of chromosomes in any species with a sequenced genome.

Authors+Show Affiliations

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

31692131

Citation

Bi, Yunfei, et al. "Flexible Chromosome Painting Based On Multiplex PCR of Oligonucleotides and Its Application for Comparative Chromosome Analyses in Cucumis." The Plant Journal : for Cell and Molecular Biology, vol. 102, no. 1, 2020, pp. 178-186.
Bi Y, Zhao Q, Yan W, et al. Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis. Plant J. 2020;102(1):178-186.
Bi, Y., Zhao, Q., Yan, W., Li, M., Liu, Y., Cheng, C., Zhang, L., Yu, X., Li, J., Qian, C., Wu, Y., Chen, J., & Lou, Q. (2020). Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis. The Plant Journal : for Cell and Molecular Biology, 102(1), 178-186. https://doi.org/10.1111/tpj.14600
Bi Y, et al. Flexible Chromosome Painting Based On Multiplex PCR of Oligonucleotides and Its Application for Comparative Chromosome Analyses in Cucumis. Plant J. 2020;102(1):178-186. PubMed PMID: 31692131.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis. AU - Bi,Yunfei, AU - Zhao,Qinzheng, AU - Yan,Wenkai, AU - Li,Mengxue, AU - Liu,Yuxi, AU - Cheng,Chunyan, AU - Zhang,Lu, AU - Yu,Xiaqing, AU - Li,Ji, AU - Qian,Chuntao, AU - Wu,Yufeng, AU - Chen,Jinfeng, AU - Lou,Qunfeng, Y1 - 2019/12/08/ PY - 2019/05/18/received PY - 2019/10/09/revised PY - 2019/10/21/accepted PY - 2019/11/7/pubmed PY - 2021/1/26/medline PY - 2019/11/7/entrez KW - Cucumis KW - chromosome painting KW - homoeologous relationship KW - multiplex PCR KW - oligonucleotides KW - technical advance SP - 178 EP - 186 JF - The Plant journal : for cell and molecular biology JO - Plant J VL - 102 IS - 1 N2 - Chromosome painting is a powerful technique for chromosome and genome studies. We developed a flexible chromosome painting technique based on multiplex PCR of a synthetic oligonucleotide (oligo) library in cucumber (Cucumis sativus L., 2n = 14). Each oligo in the library was associated with a universal as well as nested specific primers for amplification, which allow the generation of different probes from the same oligo library. We were also able to generate double-stranded labelled oligos, which produced much stronger signals than single-stranded labelled oligos, by amplification using fluorophore-conjugated primer pairs. Oligos covering cucumber chromosome 1 (Chr1) and chromosome 4 (Chr4) consisting of eight segments were synthesized in one library. Different oligo probes generated from the library painted the corresponding chromosomes/segments unambiguously, especially on pachytene chromosomes. This technique was then applied to study the homoeologous relationships among cucumber, C. hystrix and C. melo chromosomes based on cross-species chromosome painting using Chr4 probes. We demonstrated that the probe was feasible to detect interspecies chromosome homoeologous relationships and chromosomal rearrangement events. Based on its advantages and great convenience, we anticipate that this flexible oligo-painting technique has great potential for the studies of the structure, organization, and evolution of chromosomes in any species with a sequenced genome. SN - 1365-313X UR - https://www.unboundmedicine.com/medline/citation/31692131/Flexible_chromosome_painting_based_on_multiplex_PCR_of_oligonucleotides_and_its_application_for_comparative_chromosome_analyses_in_Cucumis_ L2 - https://doi.org/10.1111/tpj.14600 DB - PRIME DP - Unbound Medicine ER -