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Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes

Chromosome-specific identification is a powerful technique in the study of genome structure and evolution. However, there is no reliable cytogenetic marker to unambiguously identify each of the chromosomes in sugarcane (Saccharum spp., Poaceae), which has a complex genome with a high level of ploidy...

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Autores principales: Meng, Zhuang, Zhang, Zhiliang, Yan, Tianying, Lin, Qingfang, Wang, Yu, Huang, Weiyuan, Huang, Yongji, Li, Zhanjie, Yu, Qingyi, Wang, Jianping, Wang, Kai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6232525/
https://www.ncbi.nlm.nih.gov/pubmed/30459801
http://dx.doi.org/10.3389/fpls.2018.01624
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author Meng, Zhuang
Zhang, Zhiliang
Yan, Tianying
Lin, Qingfang
Wang, Yu
Huang, Weiyuan
Huang, Yongji
Li, Zhanjie
Yu, Qingyi
Wang, Jianping
Wang, Kai
author_facet Meng, Zhuang
Zhang, Zhiliang
Yan, Tianying
Lin, Qingfang
Wang, Yu
Huang, Weiyuan
Huang, Yongji
Li, Zhanjie
Yu, Qingyi
Wang, Jianping
Wang, Kai
author_sort Meng, Zhuang
collection PubMed
description Chromosome-specific identification is a powerful technique in the study of genome structure and evolution. However, there is no reliable cytogenetic marker to unambiguously identify each of the chromosomes in sugarcane (Saccharum spp., Poaceae), which has a complex genome with a high level of ploidy and heterozygosity. In this study, we developed a set of oligonucleotide (oligo)-based probes through bioinformatic design and massive synthetization. These probes produced a clear and bright single signal in each of the chromosomes and their eight homologous chromosomes in the ancient species Saccharum spontaneum (2n = 8x = 64). Thus, they can be used as reliable markers to robustly label each of the chromosomes in S. spontaneum. We then obtained the karyotype data and established a nomenclature based on chromosomal sizes for the eight chromosomes of the octoploid S. spontaneum. In addition, we also found that the 45S and 5S rDNAs demonstrated high copy number variations among different homologous chromosomes, indicating a rapid evolution of the highly repeated sequence after polyploidization. Our fluorescence in situ hybridization (FISH) assay also demonstrated that these probes could be used as cross-species markers between or within the genera of Sorghum and Saccharum. By comparing FISH analyses, we discovered that several chromosome rearrangement events occurred in S. spontaneum, which might have contributed to the basic chromosome number reduction from 10 in sorghum to 8 in sugarcane. Consistent identification of individual chromosomes makes molecular cytogenetic study possible in sugarcane and will facilitate fine chromosomal structure and karyotype evolution of the genus Saccharum.
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spelling pubmed-62325252018-11-20 Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes Meng, Zhuang Zhang, Zhiliang Yan, Tianying Lin, Qingfang Wang, Yu Huang, Weiyuan Huang, Yongji Li, Zhanjie Yu, Qingyi Wang, Jianping Wang, Kai Front Plant Sci Plant Science Chromosome-specific identification is a powerful technique in the study of genome structure and evolution. However, there is no reliable cytogenetic marker to unambiguously identify each of the chromosomes in sugarcane (Saccharum spp., Poaceae), which has a complex genome with a high level of ploidy and heterozygosity. In this study, we developed a set of oligonucleotide (oligo)-based probes through bioinformatic design and massive synthetization. These probes produced a clear and bright single signal in each of the chromosomes and their eight homologous chromosomes in the ancient species Saccharum spontaneum (2n = 8x = 64). Thus, they can be used as reliable markers to robustly label each of the chromosomes in S. spontaneum. We then obtained the karyotype data and established a nomenclature based on chromosomal sizes for the eight chromosomes of the octoploid S. spontaneum. In addition, we also found that the 45S and 5S rDNAs demonstrated high copy number variations among different homologous chromosomes, indicating a rapid evolution of the highly repeated sequence after polyploidization. Our fluorescence in situ hybridization (FISH) assay also demonstrated that these probes could be used as cross-species markers between or within the genera of Sorghum and Saccharum. By comparing FISH analyses, we discovered that several chromosome rearrangement events occurred in S. spontaneum, which might have contributed to the basic chromosome number reduction from 10 in sorghum to 8 in sugarcane. Consistent identification of individual chromosomes makes molecular cytogenetic study possible in sugarcane and will facilitate fine chromosomal structure and karyotype evolution of the genus Saccharum. Frontiers Media S.A. 2018-11-06 /pmc/articles/PMC6232525/ /pubmed/30459801 http://dx.doi.org/10.3389/fpls.2018.01624 Text en Copyright © 2018 Meng, Zhang, Yan, Lin, Wang, Huang, Huang, Li, Yu, Wang and Wang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Meng, Zhuang
Zhang, Zhiliang
Yan, Tianying
Lin, Qingfang
Wang, Yu
Huang, Weiyuan
Huang, Yongji
Li, Zhanjie
Yu, Qingyi
Wang, Jianping
Wang, Kai
Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes
title Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes
title_full Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes
title_fullStr Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes
title_full_unstemmed Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes
title_short Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes
title_sort comprehensively characterizing the cytological features of saccharum spontaneum by the development of a complete set of chromosome-specific oligo probes
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6232525/
https://www.ncbi.nlm.nih.gov/pubmed/30459801
http://dx.doi.org/10.3389/fpls.2018.01624
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