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Amosova AV, Gnutikov AA, Rodionov AV, Loskutov IG, Nosov NN, Yurkevich OY, Samatadze TE, Zoshchuk SA, Muravenko OV. Genome Variability in Artificial Allopolyploid Hybrids of Avena sativa L. and Avena macrostachya Balansa ex Coss. et Durieu Based on Marker Sequences of Satellite DNA and the ITS1-5.8S rDNA Region. Int J Mol Sci 2024; 25:5534. [PMID: 38791572 PMCID: PMC11122565 DOI: 10.3390/ijms25105534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Artificial hybrids between cultivated Avena species and wild Avena macrostachya that possess genes for resistance to biotic and abiotic stresses can be important for oat breeding. For the first time, a comprehensive study of genomes of artificial fertile hybrids Avena sativa × Avena macrostachya and their parental species was carried out based on the chromosome FISH mapping of satellite DNA sequences (satDNAs) and also analysis of intragenomic polymorphism in the 18S-ITS1-5.8S rDNA region, using NGS data. Chromosome distribution patterns of marker satDNAs allowed us to identify all chromosomes in the studied karyotypes, determine their subgenomic affiliation, and detect several chromosome rearrangements. Based on the obtained cytogenomic data, we revealed differences between two A. macrostachya subgenomes and demonstrated that only one of them was inherited in the studied octoploid hybrids. Ribotype analyses showed that the second major ribotype of A. macrostachya was species-specific and was not represented in rDNA pools of the octoploids, which could be related to the allopolyploid origin of this species. Our results indicate that the use of marker satDNAs in cytogenomic studies can provide important data on genomic relationships within Avena allopolyploid species and hybrids, and also expand the potential for interspecific crosses for breeding.
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Affiliation(s)
- Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander A. Gnutikov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
| | - Alexander V. Rodionov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Igor G. Loskutov
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
| | - Nikolai N. Nosov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Svyatoslav A. Zoshchuk
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
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The Divergence of Chromosome Structures and 45S Ribosomal DNA Organization in Cucumis debilis Inferred by Comparative Molecular Cytogenetic Mapping. PLANTS 2022; 11:plants11151960. [PMID: 35956438 PMCID: PMC9370355 DOI: 10.3390/plants11151960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/09/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
Cucumis debilis W.J.de Wilde & Duyfjes is an annual and monoecious plant. This species is endemic to Southeast Asia, particularly Vietnam. However, C. debilis is rarely studied, and no detailed information is available regarding its basic chromosome number, 45S ribosomal DNA (rDNA) status, and divergence among other Cucumis species. In this study, we characterized the morphological characters and determined and investigated the basic chromosome number and chromosomal distribution of 45S rDNA of C. debilis using the fluorescent in situ hybridization (FISH) technique. A maximum likelihood tree was constructed by combining the chloroplast and internal transcribed spacer of 45S rDNAs to infer its relationship within Cucumis. C. debilis had an oval fruit shape, green fruit peel, and protrusion-like white spots during the immature fruit stage. FISH analysis using 45S rDNA probe showed three pairs of 45S rDNA loci located at the terminal region in C. debilis, similar to C. hystrix. Meanwhile, two, two, and five pairs of 45S rDNA loci were observed for C. melo, C. metuliferus, and C. sativus, respectively. One melon (P90) and cucumber accessions exhibited different chromosomal localizations compared with other members of Cucumis. The majority of Cucumis species showed the terminal location of 45S rDNA, but melon P90 and cucumber exhibited terminal–interstitial and all interstitial orientations of 45S rDNA loci. Based on molecular cytogenetics and phylogenetic evidence, C. debilis is more closely related to cucumber than melon. Therefore, C. debilis may serve as a potential parental accession for genetic improvement of cucumber through interspecific hybridization.
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Amosova AV, Zoshchuk SA, Rodionov AV, Ghukasyan L, Samatadze TE, Punina EO, Loskutov IG, Yurkevich OY, Muravenko OV. Molecular cytogenetics of valuable Arctic and sub-Arctic pasture grass species from the Aveneae/Poeae tribe complex (Poaceae). BMC Genet 2019; 20:92. [PMID: 31801460 PMCID: PMC6894191 DOI: 10.1186/s12863-019-0792-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/22/2019] [Indexed: 12/25/2022] Open
Abstract
Abstract Background Grasslands in the Arctic tundra undergo irreversible degradation due to climatic changes and also over-exploitation and depletion of scarce resources. Comprehensive investigations of cytogenomic structures of valuable Arctic and sub-Arctic grassland species is essential for clarifying their genetic peculiarities and phylogenetic relationships, and also successful developing new forage grass cultivars with high levels of adaptation, stable productivity and longevity. We performed molecular cytogenetic characterization of insufficiently studied pasture grass species (Poaceae) from related genera representing two neighboring clades: 1) Deschampsia and Holcus; 2) Alopecurus, Arctagrostis and Beckmannia, which are the primary fodder resources in the Arctic tundra. Results We constructed the integrated schematic maps of distribution of these species in the northern, central and eastern parts of Eurasia based on the currently available data as only scattered data on their occurrence is currently available. The species karyotypes were examined with the use of DAPI-banding, multicolour FISH with 35S rDNA, 5S rDNA and the (GTT)9 microsatellite motif and also sequential rapid multocolour GISH with genomic DNAs of Deschampsia sukatschewii, Deschampsia flexuosa and Holcus lanatus belonging to one of the studied clades. Cytogenomic structures of the species were specified; peculiarities and common features of their genomes were revealed. Different chromosomal rearrangements were detected in Beckmannia syzigachne, Deschampsia cespitosa and D. flexuosa; B chromosomes with distinct DAPI-bands were observed in karyotypes of D. cespitosa and H. lanatus. Conclusions The peculiarities of distribution patterns of the examined chromosomal markers and also presence of common homologous DNA repeats in karyotypes of the studies species allowed us to verify their relationships. The obtained unique data on distribution areas and cytogenomic structures of the valuable Arctic and sub-Arctic pasture species are important for further genetic and biotechnological studies and also plant breeding progress.
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Affiliation(s)
- Alexandra V Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation.
| | - Svyatoslav A Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander V Rodionov
- Komarov Botanical Institute, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Lilit Ghukasyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana E Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Elizaveta O Punina
- Komarov Botanical Institute, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Igor G Loskutov
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Olga Yu Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga V Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
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Abstract
Cultivated hexaploid oat has three different sets of nuclear genomes (A, C, D), but its evolutionary history remains elusive. A multiplexed shotgun sequencing procedure was explored to acquire maternal phylogenetic signals from chloroplast and mitochondria genomes of 25 Avena species. Phylogenetic analyses of the acquired organelle SNP data revealed a new maternal pathway towards hexaploids of oat genome evolution involving three diploid species (A. ventricosa, A. canariensis and A. longiglumis) and two tetraploid species (A. insularis and A. agadiriana). Cultivated hexaploid A. sativa acquired its maternal genome from an AC genome tetraploid close to A. insularis. Both AC genome A. insularis and AB genome A. agadiriana obtained a maternal genome from an ancient A, not C, genome diploid close to A. longiglumis. Divergence dating showed the major divergences of C genome species 19.9–21.2 million years ago (Mya), of the oldest A genome A. canariensis 13–15 Mya, and of the clade with hexaploids 8.5–9.5 Mya. These findings not only advance our knowledge on oat genome evolution, but also have implications for oat germplasm conservation and utilization in breeding.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N, 0X2, Canada.
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Luo X, Tinker NA, Zhou Y, Wight CP, Liu J, Wan W, Chen L, Peng Y. Genomic relationships among sixteen species of Avena based on (ACT)6 trinucleotide repeat FISH. Genome 2018; 61:63-70. [DOI: 10.1139/gen-2017-0132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Knowledge of the locations of repeat elements could be very important in the assembly of genome sequences and their assignment to physical chromosomes. Genomic and species relationships among 16 species were investigated using fluorescence in situ hybridization (FISH) with the Am1 and (ACT)6 probes. The Am1 oligonucleotide probe was particularly enriched in the C genomes, whereas the (ACT)6 trinucleotide repeat probe showed a diverse distribution of hybridization patterns in the A, AB, C, AC, and ACD genomes but might not be present in the B and D genomes. The hybridization pattern of Avena sativa was very similar to that of A. insularis, indicating that this species most likely originated from A. insularis as a tetraploid ancestor. Although the two FISH probes failed to identify relationships of more species, this proof-of-concept approach opens the way to the use of FISH probes in assigning other signature elements from genomic sequence to physical chromosomes.
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Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Nick A. Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, KW Neatby Bldg., Central Experimental Farm, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Charlene P. Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, KW Neatby Bldg., Central Experimental Farm, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Juncheng Liu
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Wenlin Wan
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Liang Chen
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
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