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Tomaszewska P, Schwarzacher T, Heslop-Harrison JS(P. Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids. FRONTIERS IN PLANT SCIENCE 2022; 13:1026364. [PMID: 36483968 PMCID: PMC9725029 DOI: 10.3389/fpls.2022.1026364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C- into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.
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Affiliation(s)
- Paulina Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - J. S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Fominaya A, Loarce Y, González JM, Ferrer E. Cytogenetic evidence supports Avena insularis being closely related to hexaploid oats. PLoS One 2021; 16:e0257100. [PMID: 34653181 PMCID: PMC8519437 DOI: 10.1371/journal.pone.0257100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/01/2021] [Indexed: 11/19/2022] Open
Abstract
Cytogenetic observations, phylogenetic studies and genome analysis using high-density genetic markers have suggested a tetraploid Avena species carrying the C and D genomes (formerly C and A) to be the donor of all hexaploid oats (AACCDD). However, controversy surrounds which of the three extant CCDD tetraploid species—A. insularis, A. magna and A. murphyi—is most closely related to hexaploid oats. The present work describes a comparative karyotype analysis of these three CCDD tetraploid species and two hexaploid species, A. sativa and A. byzantina. This involved the use of FISH with six simple sequence repeats (SSRs) with the motifs CT, AAC, AAG, ACG, ATC and ACT, two repeated ribosomal sequences, and C genome-specific repetitive DNA. The hybridization pattern of A. insularis with oligonucleotide (AC)10 was also determined and compared with those previously published for A. sativa and A. byzantina. Significant differences in the 5S sites and SSR hybridization patterns of A. murphyi compared to the other CCDD species rule out its being directly involved in the origin of the hexaploids. In contrast, the repetitive and SSR hybridization patterns shown by the D genome chromosomes, and by most of the C genome chromosomes of A. magna and A. insularis, can be equated with the corresponding chromosomes of the hexaploids. Several chromosome hybridization signals seen for A. insularis, but not for A. magna, were shared with the hexaploid oats species, especially with A. byzantina. These diagnostic signals add weight to the idea that the extant A. insularis, or a direct ancestor of it, is the most closely related progenitor of hexaploid oats. The similarity of the chromosome hybridization patterns of the hexaploids and CCDD tetraploids was taken as being indicative of homology. A common chromosome nomenclature for CCDD species based on that of the hexaploid species is proposed.
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Affiliation(s)
- Araceli Fominaya
- Department of Biomedicine and Biotechnology, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Yolanda Loarce
- Department of Biomedicine and Biotechnology, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Juan M. González
- Department of Biomedicine and Biotechnology, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Esther Ferrer
- Department of Biomedicine and Biotechnology, University of Alcalá, Alcalá de Henares, Madrid, Spain
- * E-mail:
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Tomaszewska P, Kosina R. Cytogenetic events in the endosperm of amphiploid Avena magna × A. longiglumis. JOURNAL OF PLANT RESEARCH 2021; 134:1047-1060. [PMID: 34057611 PMCID: PMC8364899 DOI: 10.1007/s10265-021-01314-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/19/2021] [Indexed: 05/13/2023]
Abstract
This study analysed cytogenetic events occurring in the syncytial endosperm of the Avena magna H. C. Murphy & Terrell × Avena longiglumis Durieu amphiploid, which is a product of two wild species having different genomes. Selection through the elimination of chromosomes and their fragments, including those translocated, decreased the level of ploidy in the endosperm below the expected 3n, leading to the modal number close to 2n. During intergenomic translocations, fragments of the heterochromatin-rich C-genome were transferred to the D and Al genomes. Terminal and non-reciprocal exchanges dominated, whereas other types of translocations, including microexchanges, were less common. Using two probes and by counterstaining with DAPI, the A. longiglumis and the rare exchanges between the D and Al genomes were detected by GISH. The large discontinuity in the probe labelling in the C chromosomes demonstrated inequality in the distribution of repetitive sequences along the chromosome and probable intragenomic rearrangements. In the nucleus, the spatial arrangement of genomes was non-random and showed a sectorial-concentric pattern, which can vary during the cell cycle, especially in the less stable tissue like the hybrid endosperm.
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Affiliation(s)
| | - Romuald Kosina
- Institute of Environmental Biology, University of Wrocław, Przybyszewskiego 63, 51-148, Wroclaw, Poland.
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Yan H, Ren Z, Deng D, Yang K, Yang C, Zhou P, Wight CP, Ren C, Peng Y. New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum. PLoS One 2021; 16:e0240703. [PMID: 33417607 PMCID: PMC7793304 DOI: 10.1371/journal.pone.0240703] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022] Open
Abstract
The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.
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Affiliation(s)
- Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zichao Ren
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Di Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kehan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chuang Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Charlene P. Wight
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Changzhong Ren
- Baicheng Academy of Agricultural Sciences, Baicheng, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- * E-mail:
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Rodionov AV, Amosova AV, Krainova LM, Machs EM, Mikhailova YV, Gnutikov AA, Muravenko OV, Loskutov IG. Phenomenon of Multiple Mutations in the 35S rRNA Genes of the C Subgenome of Polyploid Avena L. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Peng Y, Zhou P, Zhao J, Li J, Lai S, Tinker NA, Liao S, Yan H. Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene. PLoS One 2018; 13:e0200047. [PMID: 30408035 PMCID: PMC6224039 DOI: 10.1371/journal.pone.0200047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/29/2018] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene (Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of Pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of the Pgk1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. maroccana and A. murphyi, but did not show a close relationship with any extant diploid species.
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Affiliation(s)
- Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
- Collaborative Innovation Center of Tissue Repair Material of Sichuan Province, China West Normal University, Nanchong, People’s Republic of China
| | - Jun Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Junzhuo Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Shikui Lai
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Nicholas A. Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Shu Liao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
- Collaborative Innovation Center of Tissue Repair Material of Sichuan Province, China West Normal University, Nanchong, People’s Republic of China
- * E-mail:
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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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Rodionov AV, Gnutikov AA, Kotsinyan AR, Kotseruba VV, Nosov NN, Punina EO, Rayko MP, Tyupa NB, Kim ES. ITS1–5.8S rDNA–ITS2 sequence in 35S rRNA genes as marker for reconstruction of phylogeny of grasses (Poaceae family). ACTA ACUST UNITED AC 2017. [DOI: 10.1134/s2079086417020062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Distribution of rDNA and polyploidy in Deschampsia antarctica E. Desv. in Antarctic and Patagonic populations. Polar Biol 2016. [DOI: 10.1007/s00300-016-1890-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Roa F, Guerra M. Non-Random Distribution of 5S rDNA Sites and Its Association with 45S rDNA in Plant Chromosomes. Cytogenet Genome Res 2015; 146:243-9. [PMID: 26489031 DOI: 10.1159/000440930] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
5S and 45S rDNA sites are the best mapped chromosome regions in eukaryotic chromosomes. In this work, a database was built gathering information about the position and number of 5S rDNA sites in 784 plant species, aiming to identify patterns of distribution along the chromosomes and its correlation with the position of 45S rDNA sites. Data revealed that in most karyotypes (54.5%, including polyploids) two 5S rDNA sites (a single pair) are present, with 58.7% of all sites occurring in the short arm, mainly in the proximal region. In karyotypes of angiosperms with only 1 pair of sites (single sites) they are mostly found in the proximal region (52.0%), whereas in karyotypes with multiple sites the location varies according to the average chromosome size. Karyotypes with multiple sites and small chromosomes (<3 µm) often display proximal sites, while medium-sized (between 3 and 6 µm) and large chromosomes (>6 µm) more commonly show terminal or interstitial sites. In species with holokinetic chromosomes, the modal value of sites per karyotype was also 2, but they were found mainly in a terminal position. Adjacent 5S and 45S rDNA sites were often found in the short arm, reflecting the preferential distribution of both sites in this arm. The high frequency of genera with at least 1 species with adjacent 5S and 45S sites reveals that this association appeared several times during angiosperm evolution, but it has been maintained only rarely as the dominant array in plant genera.
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Badaeva ED, Shelukhina OY, Dedkova OS, Loskutov IG, Pukhalskyi VA. Comparative cytogenetic analysis of hexaploid Avena L. species. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411060068] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Peng YY, Baum BR, Ren CZ, Jiang QT, Chen GY, Zheng YL, Wei YM. The evolution pattern of rDNA ITS in Avena and phylogenetic relationship of the Avena species (Poaceae: Aveneae). Hereditas 2010; 147:183-204. [PMID: 21039456 DOI: 10.1111/j.1601-5223.2010.02172.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Ribosomal ITS sequences are commonly used for phylogenetic reconstruction because they are included in rDNA repeats, and these repeats often undergo rapid concerted evolution within and between arrays. Therefore, the rDNA ITS copies appear to be virtually identical and can sometimes be treated as a single gene. In this paper we examined ITS polymorphism within and among 13 diploid (A and C genomes), seven tetraploid (AB, AC and CC genomes) and four hexaploid (ACD genome) to infer the extent and direction of concerted evolution, and to reveal the phylogenetic and genome relationship among species of Avena. A total of 170 clones of the ITS1-5.8S-ITS2 fragment were sequenced to carry out haplotype and phylogenetic analysis. In addition, 111 Avena ITS sequences retrieved from GenBank were combined with 170 clones to construct a phylogeny and a network. We demonstrate the major divergence between the A and C genomes whereas the distinction among the A and B/D genomes was generally not possible. High affinity among the A(d) genome species A. damascena and the ACD genome species A. fatua was found, whereas the rest of the ACD genome hexaploids and the AACC tetraploids were highly affiliated with the A(l) genome diploid A. longiglumis. One of the AACC species A. murphyi showed the closest relationship with most of the hexaploid species. Both C(v) and C(p) genome species have been proposed as paternal donors of the C-genome carrying polyploids. Incomplete concerted evolution is responsible for the observed differences among different clones of a single Avena individual. The elimination of C-genome rRNA sequences and the resulting evolutionary inference of hexaploid species are discussed.
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Affiliation(s)
- Yuan-Ying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Ya'an, Sichuan, PR China
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Peng YY, Wei YM, Baum BR, Yan ZH, Lan XJ, Dai SF, Zheng YL. Phylogenetic inferences in Avena based on analysis of FL intron2 sequences. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:985-1000. [PMID: 20514475 DOI: 10.1007/s00122-010-1367-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 05/15/2010] [Indexed: 05/23/2023]
Abstract
The development and application of molecular methods in oats has been relatively slow compared with other crops. Results from the previous analyses have left many questions concerning species evolutionary relationships unanswered, especially regarding the origins of the B and D genomes, which are only known to be present in polyploid oat species. To investigate the species and genome relationships in genus Avena, among 13 diploid (A and C genomes), we used the second intron of the nuclear gene FLORICAULA/LEAFY (FL int2) in seven tetraploid (AB and AC genomes), and five hexaploid (ACD genome) species. The Avena FL int2 is rather long, and high levels of variation in length and sequence composition were found. Evidence for more than one copy of the FL int2 sequence was obtained for both the A and C genome groups, and the degree of divergence of the A genome copies was greater than that observed within the C genome sequences. Phylogenetic analysis of the FL int2 sequences resulted in topologies that contained four major groups; these groups reemphasize the major genomic divergence between the A and C genomes, and the close relationship among the A, B, and D genomes. However, the D genome in hexaploids more likely originated from a C genome diploid rather than the generally believed A genome, and the C genome diploid A. clauda may have played an important role in the origination of both the C and D genome in polyploids.
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Affiliation(s)
- Yuan-Ying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu City, 611130, Sichuan, People's Republic of China
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Phylogenetic Relationships of Tetraploid AB-Genome Avena Species Evaluated by Means of Cytogenetic (C-Banding and FISH) and RAPD Analyses. ACTA ACUST UNITED AC 2010. [DOI: 10.1155/2010/742307] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tetraploid oat species Avena abyssinica, A. vaviloviana, A. barbata, and A. agadiriana were studied using C-banding technique, in situ hybridization with the 45S and 5S rDNA probes, and RAPD analysis in comparison with the diploid species carrying different types of the A-genome (A. wiestii, As; A. longiglumis, Al; A. canariensis, Ac; A. damascena, Ad, A. prostrata, Ap). The investigation confirmed that all four tetraploids belong to the same AB-genome group; however A. agadiriana occupies distinct position among others. The C-banding, FISH, and RAPD analyses showed that Avena abyssinica, A. vaviloviana, and A. barbata are very similar; most probably they originated from a common tetraploid ancestor as a result of minor translocations and alterations of C-banding polymorphism system. AB-genome species are closely related with the A-genome diploids, and an As-genome species may be regarded as the most probable donor of their A-genome. Although their second diploid progenitor has not been identified, it seems unlikely that it belongs to the As-genome group. The exact diploid progenitors of A. agadiriana have not been determined; however our results suggest that at least one of them could be related to A. damascena.
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Badaeva ED, Shelukhina OY, Diederichsen A, Loskutov IG, Pukhalskiy VA. Comparative cytogenetic analysis of Avena macrostachya and diploid C-genome Avena species. Genome 2010; 53:125-37. [DOI: 10.1139/g09-089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The chromosome set of Avena macrostachya Balansa ex Coss. et Durieu was analyzed using C-banding and fluorescence in situ hybridization with 5S and 18S-5.8S-26S rRNA gene probes, and the results were compared with the C-genome diploid Avena L. species. The location of major nucleolar organizer regions and 5S rDNA sites on different chromosomes confirmed the affiliation of A. macrostachya with the C-genome group. However, the symmetric karyotype, the absence of “diffuse heterochromatin”, and the location of large C-band complexes in proximal chromosome regions pointed to an isolated position of A. macrostachya from other Avena species. Based on the distribution of rDNA loci on the C-genome chromosomes of diploid and polyploid Avena species, we propose a model of the chromosome alterations that occurred during the evolution of oat species.
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Affiliation(s)
- Ekaterina D. Badaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow 119991, Russia
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- N.I. Vavilov Institute of Plant Industry, Russian Academy of Agricultural Sciences, 44 Bolshaya Morskaya Street, St. Petersburg, Russia
| | - Olga Yu. Shelukhina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow 119991, Russia
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- N.I. Vavilov Institute of Plant Industry, Russian Academy of Agricultural Sciences, 44 Bolshaya Morskaya Street, St. Petersburg, Russia
| | - Axel Diederichsen
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow 119991, Russia
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- N.I. Vavilov Institute of Plant Industry, Russian Academy of Agricultural Sciences, 44 Bolshaya Morskaya Street, St. Petersburg, Russia
| | - Igor G. Loskutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow 119991, Russia
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- N.I. Vavilov Institute of Plant Industry, Russian Academy of Agricultural Sciences, 44 Bolshaya Morskaya Street, St. Petersburg, Russia
| | - Vitaly A. Pukhalskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow 119991, Russia
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- N.I. Vavilov Institute of Plant Industry, Russian Academy of Agricultural Sciences, 44 Bolshaya Morskaya Street, St. Petersburg, Russia
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Luan L, Wang X, Long WB, Liu YH, Tu SB, Xiao XY, Kong FL. A comparative cytogenetic study of the rice (Oryza sativa L.) autotetraploid restorers and hybrids. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409090087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shelukhina OY, Badaeva ED, Brezhneva TA, Loskutov IG, Pukhalsky VA. Comparative analysis of diploid species of Avena L. Using cytogenetic and biochemical markers: Avena pilosa M. B. and A. clauda Dur. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408090111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Nikoloudakis N, Katsiotis A. The origin of the C-genome and cytoplasm of Avena polyploids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:273-81. [PMID: 18463841 DOI: 10.1007/s00122-008-0772-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 04/09/2008] [Indexed: 05/23/2023]
Abstract
The contribution of C-genome diploid species to the evolution of polyploid oats was studied using C-genome ITS-specific primers. SCAR analysis among Avena accessions confirmed the presence of C-genome ITS1-5.8S-ITS2 sequences in the genome of AACC and AACCDD polyploids. In situ hybridization and screening of more than a thousand rRNA clones in Avena polyploid species containing the C-genome revealed substantial C-genome rRNA sequence elimination. C-genome clones sequenced and Maximum Likelihood Parsimony analysis revealed close proximity to Avena ventricosa ITS1-5.8S-ITS2 sequences, providing strong evidence of the latter's active role in the evolution of tetraploid and hexaploid oats. In addition, cloning and sequencing of the chloroplastic trnL intron among the most representative Avena species verified the maternal origin of A-genome for the AACC interspecific hybrid formation, which was the genetic bridge for the establishment of cultivated hexaploid oats.
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Affiliation(s)
- N Nikoloudakis
- Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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Peng YY, Wei YM, Baum BR, Zheng YL. Molecular diversity of the 5S rRNA gene and genomic relationships in the genus Avena (Poaceae: Aveneae). Genome 2008; 51:137-54. [PMID: 18356948 DOI: 10.1139/g07-111] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The molecular diversity of the rDNA sequences (5S rDNA units) in 71 accessions from 26 taxa of Avena was evaluated. The analyses, based on 553 sequenced clones, indicated that there were 6 unit classes, named according to the haplomes (genomes) they putatively represent, namely the long A1, long B1, long M1, short C1, short D1, and short M1 unit classes. The long and short M1 unit classes were found in the tetraploid A. macrostachya, the only perennial species. The long M1 unit class was closely related to the short C1 unit class, while the short M1 unit class was closely related to the long A1 and long B1 unit classes. However, the short D1 unit class was more divergent from the other unit classes. There was only one unit class per haplome in Avena, whereas haplomes in the Triticeae often have two. Most of the sequences captured belonged to the long A1 unit class. Sequences identified as the long B1 unit class were found in the tetraploids A. abyssinica and A. vaviloviana and the diploids A. atlantica and A. longiglumis. The short C1 unit class was found in the diploid species carrying the C genome, i.e., A. clauda, A. eriantha, and A. ventricosa, and also in the diploid A. longiglumis, the tetraploids A. insularis and A. maroccana, and all the hexaploid species. The short D1 unit class was found in all the hexaploid species and two clones of A. clauda. It is noteworthy that in previous studies the B genome was found only in tetraploid species and the D genome only in hexaploid species. Unexpectedly, we found that various diploid Avena species contained the B1 and D1 units. The long B1 unit class was found in 3 accessions of the diploid A. atlantica (CN25849, CN25864, and CN25887) collected in Morocco and in 2 accessions of A. longiglumis (CIav9087 and CIav9089) collected in Algeria and Libya, respectively, whereas only 1 clone of A. clauda (CN21378) had the short D1 unit. Thus there might be a clue as to where to search for diploids carrying the B and D genomes. Avena longiglumis was found to be the most diverse species, possibly harboring the A, B, and C haplomes. The long M1 and short M1 are the unit classes typical of A. macrostachya. These results could explain the roles of A. clauda, A. longiglumis, and A. atlantica in the evolution of the genus Avena. Furthermore, one clone of the tetraploid A. murphyi was found to have sequences belonging to the short D1 unit class, which could indicate that A. murphyi might have been the progenitor of hexaploid oats and not, as postulated earlier, A. insularis. The evolution of Avena did not follow the molecular clock. The path inferred is that the C genome is more ancient than the A and B genomes and closer to the genome of A. macrostachya, the only existing perennial, which is presumed to be the most ancestral species in the genus.
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Affiliation(s)
- Yuan-Ying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Yaan 625014, Sichuan, People's Republic of China
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