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Park HW, Sevilleno SS, Ha MKTT, Cabahug-Braza RA, Yi JH, Lim KB, Cho W, Hwang YJ. The Application of Fluorescence In Situ Hybridization in the Prescreening of Veronica Hybrids. PLANTS (BASEL, SWITZERLAND) 2024; 13:1264. [PMID: 38732480 PMCID: PMC11085602 DOI: 10.3390/plants13091264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Fluorescence in situ hybridization (FISH), a molecular cytogenetic technique that enables the visualization and identification of specific DNA sequences within chromosomes, has emerged as a pivotal tool in plant breeding programs, particularly in the case of Veronica species. Veronica, a genus with a complex reproductive system, often poses challenges in accurately identifying hybrids because of its tendency to hybridize, which leads to intricate genetic variation. This study focused on the use of FISH as a prescreening method to identify true hybrids in Veronica breeding programs. FISH analysis was first performed on the parents to identify their 45S and 5S rDNA signals, along with their respective chromosome numbers. The signals were then compared with those of the twenty progenies with reference to their supposed parents. Five true hybrids, seven self-pollinated progenies, and eight false hybrids were identified through FISH. The findings highlight the significance of FISH as a screening method that contributes significantly to the efficiency of Veronica breeding programs by ensuring the preservation of desired genetic traits and minimizing the inadvertent inclusion of misidentified hybrids. To conclude, this study underscores the vital role of FISH in enhancing the precision and success of breeding programs and opens new avenues for improved breeding strategies and crop development.
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Affiliation(s)
- Hye-Wan Park
- Department of Convergence Science, Sahmyook University, Seoul 01795, Republic of Korea; (H.-W.P.); (S.S.S.)
| | - Samantha Serafin Sevilleno
- Department of Convergence Science, Sahmyook University, Seoul 01795, Republic of Korea; (H.-W.P.); (S.S.S.)
| | - My Khanh Tran Thi Ha
- Institute for Global Health Innovations, Duy Tan University, Danang 550000, Vietnam;
| | | | - Ji-Hun Yi
- Division of Garden and Plant Resources, Korea National Arboretum, Pocheon 11186, Republic of Korea;
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Wonwoo Cho
- Division of Garden and Plant Resources, Korea National Arboretum, Pocheon 11186, Republic of Korea;
| | - Yoon-Jung Hwang
- Department of Convergence Science, Sahmyook University, Seoul 01795, Republic of Korea; (H.-W.P.); (S.S.S.)
- Plant Genetics and Breeding Institute, Sahmyook University, Seoul 01795, Republic of Korea;
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Chai J, Xue L, Lei J, Yao W, Zhang M, Deng Z, Yu F. All nonhomologous chromosomes and rearrangements in Saccharum officinarum × Saccharum spontaneum allopolyploids identified by oligo-based painting. FRONTIERS IN PLANT SCIENCE 2023; 14:1176914. [PMID: 37868320 PMCID: PMC10588481 DOI: 10.3389/fpls.2023.1176914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/01/2023] [Indexed: 10/24/2023]
Abstract
Modern sugarcane cultivars (Saccharum spp., 2n = 100~120) are complex polyploids primarily derived from interspecific hybridization between S. officinarum and S. spontaneum. Nobilization is the theory of utilizing wild germplasm in sugarcane breeding, and is the foundation for utilizing S. spontaneum for stress resistance. However, the exact chromosomal transmission remains elusive due to a lack of chromosome-specific markers. Here, we applied chromosome-specific oligonucleotide (oligo)-based probes for identifying chromosomes 1-10 of the F1 hybrids between S. officinarum and S. spontaneum. Then, S. spontaneum-specific repetitive DNA probes were used to distinguish S. spontaneum in these hybrids. This oligo- fluorescence in situ hybridization (FISH) system proved to be an efficient tool for revealing individual chromosomal inheritance during nobilization. We discovered the complete doubling of S. officinarum-derived chromosomes in most F1 hybrids. Notably, we also found defective S. officinarum-derived chromosome doubling in the F1 hybrid Yacheng75-4191, which exhibited 1.5n transmission for all nonhomologous chromosomes. Altogether, these results highlight the presence of variable chromosome transmission in nobilization between S. officinarum and S. spontaneum, including 1.5n + n and 2n + n. These findings provide robust chromosome markers for in-depth studies into the molecular mechanism underlying chromosome doubling during the nobilization, as well as tracing chromosomal inheritance for sugarcane breeding.
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Affiliation(s)
- Jin Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Li Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
| | - Jiawei Lei
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
| | - Zuhu Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fan Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
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Katsuoka H, Hamabe N, Kato C, Hisamatsu S, Baba F, Taneishi M, Sasaki T. Obtainment and confirmation of intergeneric hybrids between marguerite ( Argyranthemum frutescens (L.) Sch.Bip.) and two Rhodanthemum species ( R. hosmariense (Ball) B. H. Wilcox, K. Bremer & Humphries and R. catananche (Ball) B. H. Wilcox, K. Bremer & Humphries). PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:135-143. [PMID: 38250296 PMCID: PMC10797515 DOI: 10.5511/plantbiotechnology.23.0202a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/02/2023] [Indexed: 01/23/2024]
Abstract
Argyranthemum frutescens (L.) Sch.Bip. and Rhodanthemum gayanum (Coss. & Durieu) B. H. Wilcox, K. Bremer & Humphries are capable of hybridization. To expand flower color variation in this intergeneric hybrid group, we performed crosses using A. frutescens as the seed parent and R. hosmariense (Ball) B. H. Wilcox, K. Bremer & Humphries, R. catananche (Ball) B. H. Wilcox, K. Bremer & Humphries as the pollen parent. One plantlet was obtained from each cross between the white to pale pink-flowered A. frutescens and white-flowered R. hosmariense, and from a cross between the pink-flowered A. frutescens and cream to pale yellow-flowered R. catananche, via ovule culture. The cross with R. hosmariense produced an individual with white to pale pink ray florets, and the cross with R. catananche produced an individual with red ray florets. The flower and leaf shape of the progenies was intermediate between the parents, and other morphological traits were also characterized in the same manner. Morphological observations and a cleaved amplified polymorphic sequence marker-based determination, using the internal transcribed spacer region as a target for amplification and the restriction enzyme Afl II, revealed that both individuals are hybrids between A. frutescens and R. hosmariense, R. catananche. To the best of our knowledge, this is the first study to report that crossbreeding between A. frutescens (seed parent) and R. hosmariense, R. catananche (pollen parent) is possible. Moreover, further development of Argyranthemum breeding, especially that of a series of hybrid cultivars with different flower colors, is expected.
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Affiliation(s)
- Hiroyuki Katsuoka
- Izu Agricultural Research Center, Shizuoka Prefectural Research Institute of Agriculture and Forestry, 3012 Inatori, Higashiizu, Kamo, Shizuoka 413-0411, Japan
| | - Naoya Hamabe
- Izu Agricultural Research Center, Shizuoka Prefectural Research Institute of Agriculture and Forestry, 3012 Inatori, Higashiizu, Kamo, Shizuoka 413-0411, Japan
| | - Chiemi Kato
- Izu Agricultural Research Center, Shizuoka Prefectural Research Institute of Agriculture and Forestry, 3012 Inatori, Higashiizu, Kamo, Shizuoka 413-0411, Japan
| | - Susumu Hisamatsu
- Izu Agricultural Research Center, Shizuoka Prefectural Research Institute of Agriculture and Forestry, 3012 Inatori, Higashiizu, Kamo, Shizuoka 413-0411, Japan
| | - Fujio Baba
- Izu Agricultural Research Center, Shizuoka Prefectural Research Institute of Agriculture and Forestry, 3012 Inatori, Higashiizu, Kamo, Shizuoka 413-0411, Japan
| | - Motohiro Taneishi
- Izu Agricultural Research Center, Shizuoka Prefectural Research Institute of Agriculture and Forestry, 3012 Inatori, Higashiizu, Kamo, Shizuoka 413-0411, Japan
| | - Toshiyuki Sasaki
- Izu Agricultural Research Center, Shizuoka Prefectural Research Institute of Agriculture and Forestry, 3012 Inatori, Higashiizu, Kamo, Shizuoka 413-0411, Japan
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Wang L, Feng Y, Wang Y, Zhang J, Chen Q, Liu Z, Liu C, He W, Wang H, Yang S, Zhang Y, Luo Y, Tang H, Wang X. Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH. Int J Mol Sci 2022; 23:ijms232113213. [PMID: 36361999 PMCID: PMC9653872 DOI: 10.3390/ijms232113213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
A precise, rapid and straightforward approach to chromosome identification is fundamental for cytogenetics studies. However, the identification of individual chromosomes was not previously possible for Chinese cherry or other Prunus species due to the small size and similar morphology of their chromosomes. To address this issue, we designed a pool of oligonucleotides distributed across specific pseudochromosome regions of Chinese cherry. This oligonucleotide pool was amplified through multiplex PCR with specific internal primers to produce probes that could recognize specific chromosomes. External primers modified with red and green fluorescence tags could produce unique signal barcoding patterns to identify each chromosome concomitantly. The same oligonucleotide pool could also discriminate all chromosomes in other Prunus species. Additionally, the 5S/45S rDNA probes and the oligo pool were applied in two sequential rounds of fluorescence in situ hybridization (FISH) localized to chromosomes and showed different distribution patterns among Prunus species. At the same time, comparative karyotype analysis revealed high conservation among P. pseudocerasus, P. avium, and P. persica. Together, these findings establish this oligonucleotide pool as the most effective tool for chromosome identification and the analysis of genome organization and evolution in the genus Prunus.
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Affiliation(s)
- Lei Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Feng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenshan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Congli Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 410100, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Shaofeng Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
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Islam MM, Deepo DM, Nasif SO, Siddique AB, Hassan O, Siddique AB, Paul NC. Cytogenetics and Consequences of Polyploidization on Different Biotic-Abiotic Stress Tolerance and the Potential Mechanisms Involved. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202684. [PMID: 36297708 PMCID: PMC9609754 DOI: 10.3390/plants11202684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 06/12/2023]
Abstract
The application of polyploidy in sustainable agriculture has already brought much appreciation among researchers. Polyploidy may occur naturally or can be induced in the laboratory using chemical or gaseous agents and results in complete chromosome nondisjunction. This comprehensive review described the potential of polyploidization on plants, especially its role in crop improvement for enhanced production and host-plant resistance development against pests and diseases. An in-depth investigation on techniques used in the induction of polyploidy, cytogenetic evaluation methods of different ploidy levels, application, and current research trends is also presented. Ongoing research has mainly aimed to bring the recurrence in polyploidy, which is usually detected by flow cytometry, chromosome counting, and cytogenetic techniques such as fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). Polyploidy can bring about positive consequences in the growth and yield attributes of crops, making them more tolerant to abiotic and biotic stresses. However, the unexpected change in chromosome set and lack of knowledge on the mechanism of stress alleviation is hindering the application of polyploidy on a large scale. Moreover, a lack of cost-benefit analysis and knowledge gaps on the socio-economic implication are predominant. Further research on polyploidy coupling with modern genomic technologies will help to bring real-world market prospects in the era of changing climate. This review on polyploidy provides a solid foundation to do next-generation research on crop improvement.
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Affiliation(s)
- Md Mazharul Islam
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
- Research and Development, Horticultural Crop Breeding, Quality Feeds Limited, Dhaka 1230, Bangladesh
| | - Deen Mohammad Deepo
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| | - Saifullah Omar Nasif
- Global Centre for Environmental Remediation (GCER), College of Engineering Science and Environment, The University of Newcastle, Newcastle, NSW 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), ATC Building, The University of Newcastle, Newcastle, NSW 2308, Australia
| | - Abu Bakar Siddique
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Oliul Hassan
- Department of Ecology and Environmental System, College of Ecology and Environmental Sciences, Kyungpook National University, Sangju 37224, Korea
| | - Abu Bakar Siddique
- Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Narayan Chandra Paul
- Kumho Life Science Laboratory, Department of Integrative Food Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea
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Karyotype Analysis, Genomic and Fluorescence In Situ Hybridization (GISH and FISH) Reveal the Ploidy and Parental Origin of Chromosomes in Paeonia Itoh Hybrids. Int J Mol Sci 2022; 23:ijms231911406. [PMID: 36232706 PMCID: PMC9570356 DOI: 10.3390/ijms231911406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
Itoh hybrids are intersectional hybrids in Paeonia L. with sect. Moutan and sect. Paeonia as paternal and maternal parents, respectively. Therefore, these hybrids have herbaceous stems with improved ornamental value introduced by the paternal parent. Although both of their parents are diploids, Itoh hybrids are triploids. Moreover, the parental origin of their chromosomes has not been extensively studied. This study systematically analyzed the genome size, ploidy, and karyotype of Itoh hybrids and compared them with their parental taxa. Although the monoploid genome size of Itoh hybrids was different, it was not significantly different from that of the parents. However, the size of varieties in the two parental taxa was significantly different from the wild species, probably due to genome rearrangements caused by artificial selection. Further karyotype analysis, correlation analysis, and hierarchical clustering could not identify the parental origin of chromosomes in Itoh hybrids. Verification through genomic and fluorescence in situ hybridization (GISH and FISH) suggested that for the three sets of chromosomes in Itoh hybrids, two were from the paternal parent, and one was from the maternal parent. One of the first two sets was from wild species, and the other from a cultivated variety. GISH could not label the chromosomes of cultivated peonies from the sect. Moutan, probably due to the huge and complex genomes compared with the wild species. Meanwhile, 5S rDNA-based FISH was first applied in Paeonia, which may be used for ploidy assessment. This work may give insights into the utilization of Itoh hybrid resources.
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Piet Q, Droc G, Marande W, Sarah G, Bocs S, Klopp C, Bourge M, Siljak-Yakovlev S, Bouchez O, Lopez-Roques C, Lepers-Andrzejewski S, Bourgois L, Zucca J, Dron M, Besse P, Grisoni M, Jourda C, Charron C. A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly. PLANT COMMUNICATIONS 2022; 3:100330. [PMID: 35617961 PMCID: PMC9482989 DOI: 10.1016/j.xplc.2022.100330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 04/10/2022] [Accepted: 04/27/2022] [Indexed: 06/02/2023]
Abstract
Vanilla planifolia, the species cultivated to produce one of the world's most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.
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Affiliation(s)
- Quentin Piet
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France
| | - Gaetan Droc
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France.
| | | | - Gautier Sarah
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France; AGAP, Univ. Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France
| | - Christophe Klopp
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Mickael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sonja Siljak-Yakovlev
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution (ESE), 91190 Gif-sur-Yvette, France
| | | | | | | | | | - Joseph Zucca
- Département Biotechnologie, V. Mane Fils, 06620 Le Bar Sur Loup, France
| | - Michel Dron
- Université Paris-Saclay, CNRS, INRAE, Univ. Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
| | - Pascale Besse
- Université de la Réunion, UMR PVBMT, Saint-Pierre, La Réunion, France
| | | | - Cyril Jourda
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France.
| | - Carine Charron
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France
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Molecular Karyotyping on Populus simonii × P. nigra and the Derived Doubled Haploid. Int J Mol Sci 2021; 22:ijms222111424. [PMID: 34768855 PMCID: PMC8584087 DOI: 10.3390/ijms222111424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The molecular karyotype could represent the basic genetic make-up in a cell nucleus of an organism or species. A doubled haploid (DH) is a genotype formed from the chromosome doubling of haploid cells. In the present study, molecular karyotype analysis of the poplar hybrid Populus simonii × P. nigra (P. xiaohei) and the derived doubled haploids was carried out with labeled telomeres, rDNA, and two newly repetitive sequences as probes by fluorescence in situ hybridization (FISH). The tandem repeats, pPC349_XHY and pPD284_XHY, with high-sequence homology were used, and the results showed that they presented the colocalized distribution signal in chromosomes. For P. xiaohei, pPD284_XHY produced hybridizations in chromosomes 1, 5, 8, and 9 in the hybrid. The combination of pPD284_XHY, 45S rDNA, and 5S rDNA distinctly distinguished six pairs of chromosomes, and the three pairs of chromosomes showed a significant difference in the hybridization between homologous chromosomes. The repeat probes used produced similar FISH hybridizations in the DH; nevertheless, pPD284_XHY generated an additional hybridization site in the telomere region of chromosome 14. Moreover, two pairs of chromosomes showed differential hybridization distributions between homologous chromosomes. Comparisons of the distinguished chromosomes between hybrid and DH poplar showed that three pairs of chromosomes in the DH presented hybridization patterns that varied from those of the hybrid. The No. 8 chromosome in DH and one of the homologous chromosomes in P. xiaohei shared highly similar FISH patterns, which suggested the possibility of intact or mostly partial transfer of the chromosome between the hybrid and DH. Our study will contribute to understanding the genetic mechanism of chromosomal variation in P. xiaohei and derived DH plants.
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Ramzan F, Kim HT, Younis A, Ramzan Y, Lim KB. Genetic assessment of the effects of self-fertilization in a Lilium L. hybrids using molecular cytogenetic methods (FISH and ISSR). Saudi J Biol Sci 2020; 28:1770-1778. [PMID: 33732061 PMCID: PMC7938132 DOI: 10.1016/j.sjbs.2020.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 11/28/2022] Open
Abstract
Self-fertilization (also termed selfing) is a mode of reproduction that occurs in hermaphrodites and has evolved several times in various plant and animal species. A transition from outbreeding to selfing in hermaphroditic flowers is typically associated with changes in flower morphology and functionality. This study aimed to identify genetic effects of selfing in the F2 progeny of F1 hybrid developed by crossing Lilium lancifolium with the Asiatic Lilium hybrid ‘Dreamland.’ Fluorescence in situ hybridization (FISH) and inter-simple sequence repeats (ISSR) techniques were used to detect genetic variations in plants produced by selfing. The FISH results showed that F1 hybrid were similar to the female parent (L. lancifolium) regarding the 45S loci, but F2 individuals showed variation in the number and location of the respective loci. In F2 progeny, F2-2, F2-3, F2-4, F2-5, and F2-8 hybrids expressed two strong and one weak 5S signal on chromosome 3, whereas F2-7 and F2-9 individuals expressed one strong and two weak signals. Only two strong 5S signals were detected in an F2-1 plant. The ISSR results showed a maximum similarity value of 0.6269 between the female parent and the F2-2 hybrid. Regarding similarity to the male parent, a maximum value of 0.6119 was found in the F2-1 and F2-2 hybrids. The highest genetic distance from L. lancifolium and the Asiatic Lilium hybrid ‘Dreamland’ was observed in the F2-4 progeny (0.6352 and 0.7547, respectively). Phylogenetic relationships showed that the F2 progeny were closer to the male parent than to the female parent. Self-fertilization showed effects on variation among the F2 progeny, and effects on the genome were confirmed using FISH and ISSR analyses.
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Affiliation(s)
- Fahad Ramzan
- Deptartment of Horticulture, Kyungpook National University, Daegu 41566, South Korea
| | - Hyoung Tae Kim
- Deptartment of Horticulture, Kyungpook National University, Daegu 41566, South Korea
| | - Adnan Younis
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Yasir Ramzan
- Wheat Research Institute, AARI, Faisalabad, Pakistan
| | - Ki-Byung Lim
- Deptartment of Horticulture, Kyungpook National University, Daegu 41566, South Korea
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10
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Yu HL, Li ZY, Ren WJ, Han FQ, Yang LM, Zhuang M, Lv HH, Liu YM, Fang ZY, Zhang YY. Creation of fertility-restored materials for Ogura CMS in Brassica oleracea by introducing Rfo gene from Brassica napus via an allotriploid strategy. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2825-2837. [PMID: 32613264 PMCID: PMC7497352 DOI: 10.1007/s00122-020-03635-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/09/2020] [Indexed: 05/14/2023]
Abstract
Ogura CMS fertility-restored materials, with 18 chromosomes, normal seed setting, stable fertility and closer genetic background to the parent Chinese kale, were successfully developed in B. oleracea via a triploid strategy for the first time. Ogura cytoplasmic male sterility (CMS) is the most widely used sterile type in seed production for commercial hybrids of Brassica oleracea vegetables. However, the natural Ogura CMS restorer line has not been found in B. oleracea crops. In this study, the triploid strategy was used with the aim to create euploid B. oleracea progenies with the Rfo gene. The allotriploid AAC hybrid YL2 was used as a male parent to backcross with Ogura CMS Chinese kale. After successive backcrosses, the BC2 Rfo-positive individual 16CMSF2-11 and its BC3 progenies, with 18 chromosomes, were developed, which were morphologically identical to the parent Chinese kale. Compared with F1 and BC1 plants, it showed stable fertility performance, and regular meiosis behavior and could produce seeds normally under natural pollination. The genomic composition analysis of Rfo-positive progenies by using molecular markers showed that more than 87% of the C-genome components of BC3 Rfo-progenies recovered to the parent Chinese kale, while most or all of the An-genome segments were lost in 16CMSF2-11 and its progenies. The results suggested that the genetic background of Rfo-positive individuals was closer to that of the parent Chinese kale along with backcrossing. Hereof, the Ogura CMS fertility-restored materials of Chinese kale were successfully created via triploid strategy for the first time, providing a bridge for utilizing the Ogura CMS B. oleracea germplasm in the future. Moreover, our study indicates that the triploid strategy is effective for transferring genes from B. napus into B. oleracea.
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Affiliation(s)
- Hai-Long Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China
| | - Zhi-Yuan Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China
| | - Wen-Jing Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China
| | - Feng-Qing Han
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China
| | - Li-Mei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China
| | - Hong-Hao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China
| | - Yu-Mei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China
| | - Zhi-Yuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China.
| | - Yang-Yong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing, 100081, People's Republic of China.
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11
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Shahsavand Hassani H, R Blattner F, Houben A, Bӧrner A. Production and First Assessment of Iranian Secondary Tritipyrum Genotypes by GISH and AFLP Markers. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 17:e1796. [PMID: 32671119 PMCID: PMC7357698 DOI: 10.30498/ijb.2019.91760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Non-Iranian Primary Tritipyrum (2n=6x=42, AABBEbEb) set seed after Triticale (2n=6x=42, AABBRR) and Tritordeum (2n=6x=42, AABBHcHc) but, due to a few undesirable agronomic traits, it cannot fulfil the commercial expectations of farming. Objectives To remove these deficiencies, six hexaploid Tritipyrum lines were crossed with four Iranian bread wheat cultivars which led to the production of 107 (F1), 479 (F2), 768 (F3), and 1539 (F4) Iranian Secondary Tritipyrum Genotypes (ISTG) seeds. This study was carried out for selecting the plants potentially carry the 5Eb chromosome/s and are good candidates for salt tolerant by GISH and RFLP markers. Materials and Methods The procedure involved extracting the total DNA content of 209 plants, including non-Iranian primary Tritipyrum lines, Iranian wheat cultivars, Chinese Spring addition, and substitution lines for 5Eb and Iranian secondary Tritipyrum genotypes (ISTG: F1, F2, F3, F4). Genomic in situ Hybridization (GISH) on mitotic spreads of fertile new Iranian secondary Tritipyrum genotypes (ISTG) was carried out to demonstrate the feasibility of single Eb chromosomes. There were three trials of 18 Fragment Length Polymorphism (AFLP) EcoRI/MseI primers to identify the presence of the 5Eb chromosome in 105 ISTG plants, along with four wheat addition lines and substitution lines for the 5Eb chromosome. Results GISH on mitotic spreads demonstrated the feasibility of producing 75 plants out of 105 fertile new Iranian secondary Tritipyrum genotypes (ISTG) with 0-14 single Eb chromosomes. Among the mentioned markers, only the E36/M59 marker showed 43, 50, 30 and 47 identical bands, respectively, in contrast to 53 expected bands in all plants with the 5Eb chromosome which indicated 21, 33, 9 and 6 out of 75 ISTG plants, respectively, with the 5Eb chromosome. Conclusion This study indicated that 69 ISTG Tritipyrum plants were potentially carry the 5Eb chromosome/s and are good candidates for salt tolerant tests in comparison with Iranian modern bread wheat cultivars.
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Affiliation(s)
- Hossein Shahsavand Hassani
- Department of Agronomy and Plant breeding, College of Agriculture, Shahid Bahonar University of Kerman (SBUK), Kerman, Iran.,Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Frank R Blattner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns str. 3, D-06466, Gatersleben, Germany
| | - Andreas Houben
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns str. 3, D-06466, Gatersleben, Germany
| | - Andreas Bӧrner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns str. 3, D-06466, Gatersleben, Germany
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12
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Contreras R, van den Brink L, Burgos B, González M, Gacitúa S. Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9060744. [PMID: 32545703 PMCID: PMC7355918 DOI: 10.3390/plants9060744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/31/2020] [Accepted: 06/11/2020] [Indexed: 05/25/2023]
Abstract
The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.
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Affiliation(s)
- Roberto Contreras
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Av. Copayapu 485, 1530000 Copiapó, Chile
| | - Liesbeth van den Brink
- Department of Evolution and Ecology, Plant Ecology Group, Universität Tübingen, 72076 Tübingen, Germany;
| | - Boris Burgos
- Corporación Nacional Forestal (CONAF), Región de Atacama, Juan Martínez 55, 1530000 Copiapó, Chile;
| | - Marlene González
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
| | - Sandra Gacitúa
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
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13
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Souza RCD, Marques DDA, de Carvalho Filho MM, Oliveira ARDS, Siqueira WJ, Benko-Iseppon AM, Brasileiro-Vidal AC. Genome composition and pollen viability of Jatropha (Euphorbiaceae) interspecific hybrids by Genomic In Situ Hybridization (GISH). Genet Mol Biol 2020; 42:e20190112. [PMID: 32059051 PMCID: PMC7198012 DOI: 10.1590/1678-4685-gmb-2019-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/10/2019] [Indexed: 11/24/2022] Open
Abstract
Interspecific hybridization is required for the development of Jatropha
curcas L. improved cultivars, due to its narrow genetic basis. The
present study aimed to analyze the parental genomic composition of F1
and BC1F1 generations derived from interspecific crosses
(J. curcas/J. integerrima and J. curcas/J.
multifida) by GISH (Genomic In Situ
Hybridization), and the meiotic index and pollen viability of F1
hybrids. In F1 cells from both hybrids, 11 chromosomes of each
parental was observed, as expected, but chromosome rearrangement events could be
detected using rDNA chromosome markers, suggesting unbalanced cells. In the
BC1F1, both hybrids had 22 chromosomes, suggesting
that only n = 11 gametes were viable in the next generation.
However, GISH allowed the identification of three and two alien chromosomes in
J. curcas//J. integerrima and J. curcas//J.
multifida BC1F1 hybrids, respectively,
suggesting a preferential transmission of J. curcas chromosomes
for both hybrids. Pollen viability in F1 hybrids derived from
J. curcas/J. integerrima crosses were higher (82-83%) than
those found for J. curcas/J. multifida (68%), showing
post-meiotic problems in these last hybrids, with dyads, triads, polyads, and
micronuclei as post-meiosis results. The here presented cytogenetic
characterization of interspecific hybrids and their backcross progenies can
contribute to the selection of the best genotypes for future assisted breeding
of J. curcas.
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Affiliation(s)
- Rosilda Cintra de Souza
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.,Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, Pernambuco, Brazil
| | | | | | | | | | | | - Ana Christina Brasileiro-Vidal
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.,Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, Pernambuco, Brazil
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14
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Sevilleno SS, Ju YH, Kim JS, Mancia FH, Byeon EJ, Cabahug RA, Hwang YJ. Cytogenetic analysis of Bienertia sinuspersici Akhani as the first step in genome sequencing. Genes Genomics 2020; 42:337-345. [PMID: 31902107 DOI: 10.1007/s13258-019-00908-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/18/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND C4 plants are efficient in suppressing photorespiration and enhancing carbon gain as compared to C3 plants. Bienertia sinuspersici Akhani is one of the few species in the family Amaranthaceae that can perform C4 photosynthesis within individual chlorenchyma cells, without the conventional Kranz anatomy in its leaf. This plant is salt-tolerant and is well-adapted to thrive in hot and humid climates. To date, there have been no reported cytogenetic analyses yet on this species. OBJECTIVE This study aims to provide a cytogenetic analysis of B. sinuspersici as the first step in genome sequencing. METHODS Fluorescence in situ hybridization (FISH) karyotype analysis was conducted using the metaphase chromosomes of B. sinuspersici probed with 5S and 45S rDNA and Arabidopsis-type telomeric repeats. RESULTS Results of the cytogenetic analysis confirmed that B. sinuspersici has 2n = 2x = 18 consisting of nine pairs of metacentric chromosomes. Two loci of 45S rDNA were found on the distal regions of the short arm of chromosome 7. Nine loci of 5S rDNA were found in the pericentromeric regions of chromosomes 1, 3, 4, 6, and 8, which also colocalized with Arabidopsis-type telomeric repeats; while four loci in the interstitial regions of chromosome 5 and 8 can be observed. The single locus of 5S rDNA that was found in chromosome 8 appears to be hemizygous. CONCLUSION The FISH karyotype analysis, based on the combination of rDNAs, telomeric tandem repeat markers and C0t DNA chromosome landmarks, allowed efficient chromosome identification and provided useful information in characterizing the genome of B. sinuspersici.
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Affiliation(s)
| | - Yoon Ha Ju
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jung Sun Kim
- Genetics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Franklin Hinosa Mancia
- Department of Environmental Horticulture, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Eun Ju Byeon
- Genetics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Raisa Aone Cabahug
- Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Yoon-Jung Hwang
- Department of Convergence Science, Sahmyook University, Seoul, 01795, Republic of Korea.
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15
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Identification of ribosomal sites and karyotype analysis in Festuca ulochaeta Steud. and Festuca fimbriata Ness., grasses native to Brazil. Mol Biol Rep 2019; 47:261-267. [PMID: 31621017 DOI: 10.1007/s11033-019-05126-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
Festuca L. has more than 600 perennial species described, which makes it the largest genus within the family Poaceae. In Brazil, only two native species of Festuca have been described, for which cytogenetic studies need to be strengthened: Festuca ulochaeta and Festuca fimbriata. The aim of this study was to characterize the karyotypes of F. ulochaeta and F. fimbriata based on the mapping of rDNA sites. The FISH was performed with 35S and 5S rDNA probes. Both species have 42 chromosomes, of which 36 were metacentric and six were submetacentric. Festuca fimbriata has two pairs of 35S rDNA sites, one located on the metacentric pair 4, in an interstitial position, and one at the submetacentric pair 14 in the proximal position. Festuca ulochaeta has one pair of 35S rDNA in interstitial-proximal position in the metacentric pair 3. Both species showed 5S rDNA sites only on chromosome pair 21 in the terminal position of the short arm. The analysis of the chromosomal characteristics indicates that these species have a symmetrical karyotype and allopolyploid origin.
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16
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Mandáková T, Zozomová-Lihová J, Kudoh H, Zhao Y, Lysak MA, Marhold K. The story of promiscuous crucifers: origin and genome evolution of an invasive species, Cardamine occulta (Brassicaceae), and its relatives. ANNALS OF BOTANY 2019; 124:209-220. [PMID: 30868165 PMCID: PMC6758578 DOI: 10.1093/aob/mcz019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/24/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Cardamine occulta (Brassicaceae) is an octoploid weedy species (2n = 8x = 64) originated in Eastern Asia. It has been introduced to other continents including Europe and considered to be an invasive species. Despite its wide distribution, the polyploid origin of C. occulta remained unexplored. The feasibility of comparative chromosome painting (CCP) in crucifers allowed us to elucidate the origin and genome evolution in Cardamine species. We aimed to investigate the genome structure of C. occulta in comparison with its tetraploid (2n = 4x = 32, C. kokaiensis and C. scutata) and octoploid (2n = 8x = 64, C. dentipetala) relatives. METHODS Genomic in situ hybridization (GISH) and large-scale CCP were applied to uncover the parental genomes and chromosome composition of the investigated Cardamine species. KEY RESULTS All investigated species descended from a common ancestral Cardamine genome (n = 8), structurally resembling the Ancestral Crucifer Karyotype (n = 8), but differentiated by a translocation between chromosomes AK6 and AK8. Allotetraploid C. scutata originated by hybridization between two diploid species, C. parviflora and C. amara (2n = 2x = 16). By contrast, C. kokaiensis has an autotetraploid origin from a parental genome related to C. parviflora. Interestingly, octoploid C. occulta probably originated through hybridization between the tetraploids C. scutata and C. kokaiensis. The octoploid genome of C. dentipetala probably originated from C. scutata via autopolyploidization. Except for five species-specific centromere repositionings and one pericentric inversion post-dating the polyploidization events, the parental subgenomes remained stable in the tetra- and octoploids. CONCLUSIONS Comparative genome structure, origin and evolutionary history was reconstructed in C. occulta and related species. For the first time, whole-genome cytogenomic maps were established for octoploid plants. Post-polyploid evolution in Asian Cardamine polyploids has not been associated with descending dysploidy and intergenomic rearrangements. The combination of different parental (sub)genomes adapted to distinct habitats provides an evolutionary advantage to newly formed polyploids by occupying new ecological niches.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics research group, CEITEC – Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Judita Zozomová-Lihová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano, Japan
| | - Yunpeng Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Centre for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, China
| | - Martin A Lysak
- Plant Cytogenomics research group, CEITEC – Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Karol Marhold
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovak Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
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17
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Abstract
The long linear chromosomes of eukaryotic organisms are tightly packed into the nucleus of the cell. Beyond a first organization into nucleosomes and higher-order chromatin fibers, the positioning of nuclear DNA within the three-dimensional space of the nucleus plays a critical role in genome function and gene expression. Different techniques have been developed to assess nanoscale chromatin organization, nuclear position of genomic regions or specific chromatin features and binding proteins as well as higher-order chromatin organization. Here, I present an overview of imaging and molecular techniques applied to study nuclear architecture in plants, with special attention to the related protocols published in the "Plant Chromatin Dynamics" edition from Methods in Molecular Biology.
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Affiliation(s)
- Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001, Clermont-Ferrand, France.
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18
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Abstract
High-quality chromosome images of mitotic and meiotic cell divisions in plant tissues are inextricably connected with the technical control of cell spread preparations. Superb chromosome slides are the best for studying chromosome morphology and making karyotypes; they also are the best start for a successful fluorescent in situ hybridization experiment. In this study, we describe the essentials for fixation, enzymatic digestion, squash, spread, and dropping protocols for clean and well-differentiated nuclei and chromosome complements. In addition, we focus on the use of standard whole image processing for best sharpness, brightness and contrast adjustments, differentiation of heterochromatin/euchromatin, and high dynamic range imaging of big chromosomes. We also explain how to combine transparent layers or spot channels of different fluorescent images for making publication quality, full color photos.
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19
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Ramzan F, Younis A, Lim KB. Application of Genomic In Situ Hybridization in Horticultural Science. Int J Genomics 2017; 2017:7561909. [PMID: 28459054 PMCID: PMC5387808 DOI: 10.1155/2017/7561909] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/25/2017] [Accepted: 02/28/2017] [Indexed: 11/17/2022] Open
Abstract
Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such as Clivia, Rhododendron, and Lycoris ornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH) techniques in horticultural plants.
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Affiliation(s)
- Fahad Ramzan
- Department of Horticulture, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Adnan Younis
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Ki-Byung Lim
- Department of Horticulture, Kyungpook National University, Daegu 41566, Republic of Korea
- Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea
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20
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Lan H, Chen CL, Miao Y, Yu CX, Guo WW, Xu Q, Deng XX. Fragile Sites of 'Valencia' Sweet Orange (Citrus sinensis) Chromosomes Are Related with Active 45s rDNA. PLoS One 2016; 11:e0151512. [PMID: 26977938 PMCID: PMC4792391 DOI: 10.1371/journal.pone.0151512] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/29/2016] [Indexed: 12/12/2022] Open
Abstract
Citrus sinensis chromosomes present a morphological differentiation of bands after staining by the fluorochromes CMA and DAPI, but there is still little information on its chromosomal characteristics. In this study, the chromosomes in 'Valencia' C. sinensis were analyzed by fluorescence in situ hybridization (FISH) using telomere DNA and the 45S rDNA gene as probes combining CMA/DAPI staining, which showed that there were two fragile sites in sweet orange chromosomes co-localizing at distended 45S rDNA regions, one proximally locating on B-type chromosome and the other subterminally locating on D-type chromosome. While the chromosomal CMA banding and 45S rDNA FISH mapping in the doubled haploid line of 'Valencia' C. sinensis indicated six 45S rDNA regions, four were identified as fragile sites as doubled comparing its parental line, which confirmed the cytological heterozygosity and chromosomal heteromorphisms in sweet orange. Furthermore, Ag-NOR identified two distended 45S rDNA regions to be active nucleolar organizing regions (NORs) in diploid 'Valencia' C. sinensis. The occurrence of quadrivalent in meiosis of pollen mother cells (PMCs) in 'Valencia' sweet orange further confirmed it was a chromosomal reciprocal translocation line. We speculated this chromosome translocation was probably related to fragile sites. Our data provide insights into the chromosomal characteristics of the fragile sites in 'Valencia' sweet orange and are expected to facilitate the further investigation of the possible functions of fragile sites.
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Affiliation(s)
- Hong Lan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Li Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yin Miao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang-Xiu Yu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiu-Xin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
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