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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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2
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Jiang W, Jiang C, Yuan W, Zhang M, Fang Z, Li Y, Li G, Jia J, Yang Z. A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era. BMC PLANT BIOLOGY 2021; 21:213. [PMID: 33980176 PMCID: PMC8114715 DOI: 10.1186/s12870-021-02999-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/28/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromosomes are often contradictory. A universal karyotyping nomenclature system for precise chromosome identification and comparative evolutionary studies would be essential for genus Avena based on the recently released genome sequences of hexaploid and diploid Avena species. RESULTS Tandem repetitive sequences were predicted and physically located on chromosomal regions of the released Avena sativa OT3098 genome assembly v1. Eight new oligonucleotide (oligo) probes for sequential fluorescence in situ hybridization (FISH) were designed and then applied for chromosome karyotyping on mitotic metaphase spreads of A. brevis, A. nuda, A. wiestii, A. ventricosa, A. fatua, and A. sativa species. We established a high-resolution standard karyotype of A. sativa based on the distinct FISH signals of multiple oligo probes. FISH painting with bulked oligos, based on wheat-barley collinear regions, was used to validate the linkage group assignment for individual A. sativa chromosomes. We integrated our new Oligo-FISH based karyotype system with earlier karyotype nomenclatures through sequential C-banding and FISH methods, then subsequently determined the precise breakage points of some chromosome translocations in A. sativa. CONCLUSIONS This new universal chromosome identification system will be a powerful tool for describing the genetic diversity, chromosomal rearrangements and evolutionary relationships among Avena species by comparative cytogenetic and genomic approaches.
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Affiliation(s)
- Wenxi Jiang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China
| | - Chengzhi Jiang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China
| | - Weiguang Yuan
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China
| | - Meijun Zhang
- College of Agronomy, Shanxi Agricultural University, 030801, Taigu, China
| | - Zijie Fang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China
| | - Yang Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China
| | - Juqing Jia
- College of Agronomy, Shanxi Agricultural University, 030801, Taigu, China.
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China.
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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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Maughan PJ, Lee R, Walstead R, Vickerstaff RJ, Fogarty MC, Brouwer CR, Reid RR, Jay JJ, Bekele WA, Jackson EW, Tinker NA, Langdon T, Schlueter JA, Jellen EN. Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biol 2019; 17:92. [PMID: 31757219 PMCID: PMC6874827 DOI: 10.1186/s12915-019-0712-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat's adaptive and food quality characteristics. RESULTS The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species-including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species. CONCLUSIONS The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.
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Affiliation(s)
- Peter J Maughan
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA.
| | - Rebekah Lee
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Rachel Walstead
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | - Melissa C Fogarty
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Cory R Brouwer
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Robert R Reid
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jeremy J Jay
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | | | | | - Tim Langdon
- IBERS, Aberystwyth University, Aberystwyth, Wales, UK
| | | | - Eric N Jellen
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
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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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Fominaya A, Loarce Y, Montes A, Ferrer E. Chromosomal distribution patterns of the (AC) 10 microsatellite and other repetitive sequences, and their use in chromosome rearrangement analysis of species of the genus Avena. Genome 2016; 60:216-227. [PMID: 28156137 DOI: 10.1139/gen-2016-0146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fluorescence in situ hybridization (FISH) was used to determine the physical location of the (AC)10 microsatellite in metaphase chromosomes of six diploid species (AA or CC genomes), two tetraploid species (AACC genome), and five cultivars of two hexaploid species (AACCDD genome) of the genus Avena, a genus in which genomic relationships remain obscure. A preferential distribution of the (AC)10 microsatellite in the pericentromeric and interstitial regions was seen in both the A- and D-genome chromosomes, while in C-genome chromosomes the majority of signals were located in the pericentromeric heterochromatic regions. New large chromosome rearrangements were detected in two polyploid species: an intergenomic translocation involving chromosomes 17AL and 21DS in Avena sativa 'Araceli' and another involving chromosomes 4CL and 21DS in the analyzed cultivars of Avena byzantina. The latter 4CL-21DS intergenomic translocation differentiates clearly between A. sativa and A. byzantina. Searches for common hybridization patterns on the chromosomes of different species revealed chromosome 10A of Avena magna and 21D of hexaploid oats to be very similar in terms of the distribution of 45S and Am1 sequences. This suggests a common origin for these chromosomes and supports a CCDD rather than an AACC genomic designation for this species.
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Affiliation(s)
- Araceli Fominaya
- Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain.,Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain
| | - Yolanda Loarce
- Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain.,Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain
| | - Alexander Montes
- Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain.,Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain
| | - Esther Ferrer
- Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain.,Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain
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7
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Luo X, Zhang H, Kang H, Fan X, Wang Y, Sha L, Zhou Y. Exploring the origin of the D genome of oat by fluorescence in situ hybridization. Genome 2014; 57:469-72. [DOI: 10.1139/gen-2014-0048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Further understanding of the origin of cultivated oat would accelerate its genetic improvement. In particular, it would be useful to clarify which diploid progenitor contributed the D genome of this allohexaploid species. In this study, we demonstrate that the landmarks produced by fluorescence in situ hybridization (FISH) of species of Avena using probes derived from Avena sativa can be used to explore the origin of the D genome. Selected sets of probes were hybridized in several sequential experiments performed on exactly the same chromosome spreads, with multiple probes of cytological preparations. Probes pITS and A3-19 showed there might be a similar distribution of pITS between the Ac and D genomes. These results indicated that the Ac genome is closely related to the D genome, and that Avena canariensis (AcAc) could be the D-genome donor of cultivated oat.
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Affiliation(s)
- Xiaomei Luo
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
- College of Forestry, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Haiqin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Lina Sha
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
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Linares C, González J, Ferrer E, Fominaya A. The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S-5.8S-26S rDNA and a C genome specific DNA sequence in the genus Avena. Genome 2012; 39:535-42. [PMID: 18469914 DOI: 10.1139/g96-068] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S-5.8S-26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A-C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C-A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S-5.8S-26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.
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Sanz MJ, Loarce Y, Ferrer E, Fominaya A. Use of tyramide-fluorescence in situ hybridization and chromosome microdissection for ascertaining homology relationships and chromosome linkage group associations in oats. Cytogenet Genome Res 2012; 136:145-56. [PMID: 22285909 DOI: 10.1159/000335641] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2011] [Indexed: 01/11/2023] Open
Abstract
The physical mapping of single locus sequences by tyramide-fluorescence in situ hybridization (Tyr-FISH) and the analysis of sequences obtained from microdissected chromosomes were assayed as potential tools for (1) determining homology and homoeology among chromosome regions of Avena species, and (2) establishing associations between linkage groups and specific chromosomes. Low copy number probes, derived from resistance gene analogues (RGAs) and 2.8-4.5 kb long, successfully produced hybridization signals on specific chromosomes. Four sets of homoeologous chromosome regions were identified in the hexaploids using 3 probes that produced 4 single locus markers in A. strigosa and 2 in A. eriantha. Laser capture microdissection of metaphase I cells of A. sativa monosomic lines allowed the isolation of critical univalents. Sequences derived from 2 RGAs were successfully amplified in DNA extracted from univalents. In one instance, it was possible to map a nucleotide polymorphism specific for 1 chromosome. An association was established between this chromosome and its linkage groups in 2 hexaploid genetic maps. The results indicate that Tyr-FISH is useful in the characterization of homoeologous chromosome segments in hexaploids, whereas chromosome microdissection, as employed in this work, needs to be improved before it can routinely be used with meiotic chromosomes.
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Affiliation(s)
- M J Sanz
- Department of Cell Biology and Genetics, University of Alcalá, Alcalá de Henares, Spain
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10
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Sanz MJ, Jellen EN, Loarce Y, Irigoyen ML, Ferrer E, Fominaya A. A new chromosome nomenclature system for oat (Avena sativa L. and A. byzantina C. Koch) based on FISH analysis of monosomic lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1541-52. [PMID: 20658121 DOI: 10.1007/s00122-010-1409-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 07/08/2010] [Indexed: 05/21/2023]
Abstract
Fluorescent in situ hybridization (FISH) with multiple probes was used to analyze mitotic and meiotic chromosome spreads of Avena sativa cv 'Sun II' monosomic lines, and of A. byzantina cv 'Kanota' monosomic lines from spontaneous haploids. The probes used were A. strigosa pAs120a (a repetitive sequence abundant in A-genome chromatin), A. murphyi pAm1 (a repetitive sequence abundant in C-genome chromatin), A. strigosa pITS (internal transcribed spacer of rDNA) and the wheat rDNA probes pTa71 (nucleolus organizer region or NOR) and pTa794 (5S). Simultaneous and sequential FISH employing pairs of these probes allowed the identification and genome assignation of all chromosomes. FISH mapping using mitotic and meiotic metaphases facilitated the genomic and chromosomal identification of the monosome in each line. Of the 17 'Sun II' lines analyzed, 13 distinct monosomic lines were found, corresponding to four monosomes of the A-genome, five of the C-genome and four of the D-genome. In addition, 12 distinct monosomic lines were detected among the 20 'Kanota' lines examined, corresponding to six monosomes of the A-genome, three of the C-genome and three of the D-genome. The results show that 19 chromosomes out of 21 of the complement are represented by monosomes between the two genetic backgrounds. The identity of the remaining chromosomes can be deduced either from one intergenomic translocation detected on both 'Sun II' and 'Kanota' lines, or from the single reciprocal, intergenomic translocation detected among the 'Sun II' lines. These results permit a new system to be proposed for numbering the 21 chromosome pairs of the hexaploid oat complement. Accordingly, the A-genome contains chromosomes 8A, 11A, 13A, 15A, 16A, 17A and 19A; the C-genome contains chromosomes 1C, 2C, 3C, 4C, 5C, 6C and 7C; and the D-genome consists of chromosomes 9D, 10D, 12D, 14D, 18D, 20D and 21D. Moreover, the FISH patterns of 16 chromosomes in 'Sun II' and 15 in 'Kanota' suggest that these chromosomes could be involved in intergenomic translocations. By comparing the identities of individually translocated chromosomes in the two hexaploid species with those of other hexaploids, we detected different types of intergenomic translocations.
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Affiliation(s)
- M J Sanz
- Department of Cell Biology and Genetics, University of Alcalá, 28871, Alcalá de Henares (Madrid), Spain
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11
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Fat element—a new marker for chromosome and genome analysis in the Triticeae. Chromosome Res 2010; 18:697-709. [DOI: 10.1007/s10577-010-9151-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 07/05/2010] [Accepted: 07/29/2010] [Indexed: 10/19/2022]
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12
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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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13
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Plant highly repeated satellite DNA: Molecular evolution, distribution and use for identification of hybrids. SYST BIODIVERS 2007. [DOI: 10.1017/s147720000700240x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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Irigoyen ML, Ferrer E, Loarce Y. Cloning and characterization of resistance gene analogs from Avena species. Genome 2006; 49:54-63. [PMID: 16462901 DOI: 10.1139/g05-087] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sequences analogous to plant resistance genes of the NBS–LRR class were cloned from the genomic DNA of 11 Avena species with different genomes and levels of ploidy. Three pairs of degenerate primers were used, based on conserved DNA sequence motifs belonging to the NBS domain, and 33 sequences were identified. These were subdivided into 7 classes depending on nucleotide sequence identity. Despite the high level of degeneracy, the primers behaved in a highly selective way; the majority of sequences from the different species obtained with every primer combin ation showed strong identity and were considered homologous. For most species, only one sequence of each class was identified in each genome, suggesting that duplicated sequences are fairly divergent. The strong identity among specific NBS sequences precludes any conclusions being made on the evolution of these species. The genomic organization of the RGA sequences was explored using those of A. strigosa as probes in Southern blots involving digested DNA from 15 Avena species. The hybridization patterns showed wide diversity both among sequences within a species and among species for each sequence. However, the dendrogram generated using the RFLPs showed relationships among species to be in good agreement with those previously established using other molecular markers.Key words: resistance gene analog (RGA), disease resistance genes, diversity, Avena, oats.
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Affiliation(s)
- M L Irigoyen
- Department of Cell Biology and Genetics, University of Alcalá, Alcalá de Henares, Madrid, Spain
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15
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Drossou A, Katsiotis A, Leggett JM, Loukas M, Tsakas S. Genome and species relationships in genus Avena based on RAPD and AFLP molecular markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:48-54. [PMID: 15014877 DOI: 10.1007/s00122-004-1615-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2003] [Accepted: 01/20/2004] [Indexed: 05/23/2023]
Abstract
Species and genome relationships among 11 diploid (A and C genomes), five tetraploid (AB and AC genomes) and two hexaploid (ACD genome) Avena taxa were investigated using amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNA (RAPD) markers. The two primer pairs used for the AFLP reactions produced a total of 354 polymorphic bands, while 187 reproducible bands were generated using ten RAPD primers. Genetic similarities amongst the entries were estimated using the Jaccard and Dice algorithms, and cluster analyses were performed using UPGMA and neighbor joining methods. Principle coordinate analysis was also applied. The highest cophenetic correlation coefficient was obtained for the Jaccard algorithm and UPGMA clustering method ( r=0.99 for AFLP and r=0.94 for RAPD). No major clustering differences were present between phenograms produced with AFLPs and RAPDs. Furthermore, data produced with AFLPs and RAPDs were highly correlated ( r=0.92), indicating the reliability of our results. All A genome diploid taxa are clustered together according to their karyotype. The AB genome tetraploids were found to form a subcluster within the A(s )genome diploids (AFLPs), indicating their near-autoploid origin. The AC genome tetraploids are clustered to the ACD genome hexaploids. Finally, the C genome diploids form an outer branch, indicating the major genomic divergence between the A and C genomes in Avena.
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Affiliation(s)
- A Drossou
- Department of Genetics, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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16
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Irigoyen ML, Linares C, Ferrer E, Fominaya A. Fluorescence in situ hybridization mapping of Avena sativa L. cv. SunII and its monosomic lines using cloned repetitive DNA sequences. Genome 2002; 45:1230-7. [PMID: 12502269 DOI: 10.1139/g02-076] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fluorescent in situ hybridization (FISH) employing multiple probes was used with mitotic or meiotic chromosome spreads of Avena sativa L. cv. SunII and its monosomic lines to produce physical chromosome maps. The probes used were Avena strigosa pAs120a (which hybridizes exclusively to A-genome chromosomes), Avena murphyi pAm1 (which hybridizes exclusively to C-genome chromosomes), A. strigosa pAs121 (which hybridizes exclusively to A- and D-genome chromosomes), and the wheat rDNA probes pTa71 and pTa794. Simultaneous and sequential FISH employing two-by-two combinations of these probes allowed the unequivocal identification and genome assignation of all chromosomes. Ten pairs were found carrying intergenomic translocations: (i) between the A and C genomes (chromosome pair 5A); (ii) between the C and D genomes (pairs 1C, 2C, 4C, 10C, and 16C); and (iii) between the D and C genomes (pairs 9D, 11D, 13D, and 14D). The existence of a reciprocal intergenomic translocation (10C-14D) is also proposed. Comparing these results with those of other hexaploids, three intergenomic translocations (10C, 9D, and 14D) were found to be unique to A. sativa cv. SunII, supporting the view that 'SunII' is genetically distinct from other hexaploid Avena species and from cultivars of the A. sativa species. FISH mapping using meiotic and mitotic metaphases facilitated the genomic and chromosomal identification of the aneuploid chromosome in each monosomic line. Of the 18 analyzed, only 11 distinct monosomic lines were actually found, corresponding to 5 lines of the A genome, 2 lines of the C genome, and 4 lines of the D genome. The presence or absence of the 10C-14D interchange was also monitored in these lines.
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Affiliation(s)
- M L Irigoyen
- Department of Cell Biology and Genetics, University of Alcalá, Campus Universitario, ES-28871 Alcalá de Henares, Madrid, Spain
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17
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Ananiev EV, Vales MI, Phillips RL, Rines HW. Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa. Genome 2002; 45:431-41. [PMID: 11962640 DOI: 10.1139/g01-148] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.
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Affiliation(s)
- Evgueni V Ananiev
- Department of Agronomy and Plant Genetics and Plant Molecular Genetics Institute, University of Minnesota, St. Paul 55108-6026, USA
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18
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Linares C, Serna A, Fominaya A. Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species. Genome 1999; 42:706-13. [PMID: 10464792 DOI: 10.1139/g99-007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A repetitive sequence, pAs17, was isolated from Avena strigosa (As genome) and characterized. The insert was 646 bp in length and showed 54% AT content. Databank searches revealed its high homology to the long terminal repeat (LTR) sequences of the specific family of Ty1-copia retrotransposons represented by WIS2-1A and Bare. It was also found to be 70% identical to the LTR domain of the WIS2-1A retroelement of wheat and 67% identical to the Bare-1 retroelement of barley. Southern hybridizations of pAs17 to diploid (A or C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) oat species revealed that it was absent in the C diploid species. Slot-blot analysis suggested that both diploid and tetraploid oat species contained 1.3 x 10(4) copies, indicating that they are a component of the A-genome chromosomes. The hexaploid species contained 2.4 x 10(4) copies, indicating that they are a component of both A- and D-genome chromosomes. This was confirmed by fluorescent in situ hybridization analyses using pAs17, two ribosomal sequences, and a C-genome specific sequence as probes. Further, the chromosomes involved in three C-A and three C-D intergenomic translocations in Avena murphyi (AC genomes) and Avena sativa cv. Extra Klock (ACD genomes), respectively, were identified. Based on its physical distribution and Southern hybridization patterns, a parental retrotransposon represented by pAs17 appears to have been active at least once during the evolution of the A genome in species of the Avena genus.
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Affiliation(s)
- C Linares
- Department of Cell Biology and Genetics, University of Alcalá, Madrid, Spain
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19
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Linares C, Ferrer E, Fominaya A. Discrimination of the closely related A and D genomes of the hexaploid oat Avena sativa L. Proc Natl Acad Sci U S A 1998; 95:12450-5. [PMID: 9770506 PMCID: PMC22851 DOI: 10.1073/pnas.95.21.12450] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A satellite DNA sequence, As120a, specific to the A-genome chromosomes in the hexaploid oat, Avena sativa L., was isolated by subcloning a fragment with internal tandem repeats from a plasmid, pAs120, that had been obtained from an Avena strigosa (As genome) genomic library. Southern and in situ hybridization showed that sequences with homology to sequences within pAs120 were dispersed throughout the genome of diploid (A and C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) Avena species. In contrast, sequences homologous to As120a were found in two A-genome species (A. strigosa and Avena longiglumis) and in the hexaploid A. sativa whereas this sequence was little amplified in the tetraploid Avena murphyi and was absent in the remaining A- and C-genome diploid species. In situ hybridization of pAs120a to hexaploid oat species revealed the distribution of elements of the As120a repeated family over both arms of 14 of 42 chromosomes of this species. By using double in situ hybridization with pAs120a and a C genome-specific probe, three sets of 14 chromosomes were revealed corresponding to the A, C, and D genomes of the hexaploid species. Simultaneous in situ hybridizations with pAs120a and ribosomal probes were used to assign the SAT chromosomes of hexaploid species to their correct genomes. This work reports a sequence able to distinguish between the closely related A and D genomes of hexaploid oats. This sequence offers new opportunities to analyze the relationships of Avena species and to explore the possible evolution of various polyploid oat species.
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Affiliation(s)
- C Linares
- Department of Cell Biology and Genetics, University of Alcalá, Campus Universitario, ES-28871 Alcalá de Henares, Madrid, Spain
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20
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Grebenstein B, Grebenstein O, Sauer W, Hemleben V. Distribution and complex organization of satellite DNA sequences in Aveneae species. Genome 1996; 39:1045-50. [PMID: 8983180 DOI: 10.1139/g96-131] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Distribution, organization, and molecular analysis of four unrelated satellite DNA components in Aveneae species are described. Highly repeated DNA elements were cloned from Helictotrichon convolutum (CON1 and CON2) and Helictotrichon compressum (COM1 and COM2). The lengths of the repeat monomers are 365 bp (CON1), 562 bp (CON2), 346 bp (COM1), and 476 bp (COM2). Similar repeats were detected by dot blots, Southern blots, and by DNA sequencing in other species of the genus Helictotrichon, in Aveneae species, and in species of the tribes Andropogoneae and Oryzeae. All four satellite DNAs are differently distributed in the taxonomic groups mentioned above. Remarkably, the longer elements are built up in a complex pattern of either shorter subrepeats arranged in tandem (COM2) or by duplications inserted into an original 369-bp element (CON2). Shorter representatives, 190 bp, similar to CON1 elements occur in Holcus species. In Koeleria species, COM1-related repeats are only 180 bp in length. No similarity was found among the sequences CON2, COM1, and COM2 or with sequences of other repetitive DNA elements of the grasses, but CON1 shows sequence similarity to an A genome specific repetitive DNA of Oryza (rice).
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Affiliation(s)
- B Grebenstein
- Lehrstuhl für Spezielle Botanik, Universität Tübingen, Deutschland
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21
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Katsiotis A, Schmidt T, Heslop-Harrison JS. Chromosomal and genomic organization of Ty1-copia-like retrotransposon sequences in the genus Avena. Genome 1996; 39:410-7. [PMID: 8984007 DOI: 10.1139/g96-052] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A cloned repetitive sequence, pAvKB30, obtained from an Avena vaviloviana (AB genome) genomic library, along with two polymerase chain reaction products derived from the conserved region of the reverse transcriptase (RT) gene of retrotransposons, were characterized molecularly and cytologically. The cloned DNA fragment was a dispersed repeat present in all Avena species used in this study (A. strigosa, A. clauda, A. vaviloviana, A. magna, and A. sativa). The fragment was sequenced (210 bp) and found to be 69.5% homologous to part of WIS-2-1A, and 60.5% homologous to the leader sequence of BARE-1; both of these elements have been characterized as Ty1-copia-like retrotransposons in wheat and barley, respectively. In situ hybridization of pAvKB30 to diploid, tetraploid, and hexaploid oat species revealed that the probe is present on both arms of all chromosomes (A, B, C, and D genomes) but is excluded from their centromeric and nucleolar organizer regions. By using double in situ hybridization in hexaploid A. sativa (ACD genome), pAvKB30 was found to be present in lower copy numbers in C-genome chromosomes compared with A- and D-genome chromosomes. Furthermore, under low stringency conditions, pAvKB30 hybridized on Southern blots containing barley, wheat, rye, and Arrhenatherum DNA. However, under high stringency conditions, it hybridized only on Arrhenatherum DNA, which is considered to be the genus most closely related to Avena. All Avena species included in this study yielded a PCR product when the primers from the RT domain of retrotransposons were used. Two products, rtA, obtained by using A. strigosa (A(s) genome) as template, and rtC, obtained by using A. clauda (Cp genome) as template, gave Southern and in situ hybridization results similar to pAvKB30, but each was more abundant in its genome of origin.
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Affiliation(s)
- A Katsiotis
- Karyobiology Group, John Innes Centre, Norwich, U.K
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22
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Arnholdt-Schmitt B. Physiological aspects of genome variability in tissue culture. II. Growth phase-dependent quantitative variability of repetitive BstNI fragments of primary cultures of Daucus carota L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:816-23. [PMID: 24169922 DOI: 10.1007/bf00220965] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/1995] [Accepted: 04/21/1995] [Indexed: 05/05/2023]
Abstract
Systematic investigations on the occurrence of differential DNA replication in carrot cultures, expressed at the total genome level, were performed. The genome of Daucus carota L. could be characterized by a pattern of repetitive BstNI fragments that was independent of tissue specificity or cultivar differences. Characterization of the genomic DNA of the secondary phloem of carrot roots, in comparison to the DNA of the induced primary cultures at different growth phases, revealed dramatic differences in the copy number of the repetitive fragments. Highly proliferative tissue showed extensive reduction in the proportion of repetitive sequences in the genome in all of the 37 investigated variants. In contrast, during subsequent transition to stationary growth the repetitive fragments re-amplified. The results suggest that the quantitative genome organisation was involved in the regulation of the growth potential of cells. A hypothesis is discussed suggesting a determining influence of the observed differential DNA replication on cell-cycle rates and the cell program of proliferative tissue by structural and positioning effects on DNA loops. To study the causality of somaclonal variation, research on the relationship between physiological genome variability and the induction of heritable changes is recommended.
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Affiliation(s)
- B Arnholdt-Schmitt
- Institut für Pflanzenernährung, Abteilung Gewebekultur, Justus-Liebig-Universität Giessen, Suedanlage 6, D-35390, Giessen, Germany
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23
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Fominaya A, Hueros G, Loarce Y, Ferrer E. Chromosomal distribution of a repeated DNA sequence from C-genome heterochromatin and the identification of a new ribosomal DNA locus in the Avena genus. Genome 1995; 38:548-57. [PMID: 7557363 DOI: 10.1139/g95-071] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Satellite DNA specific to the oat C genome was sequenced and located on chromosomes of diploid, tetraploid, and hexaploid Avena ssp. using in situ hybridization. The sequence was present on all seven C genome chromosome pairs and hybridized to the entire length of each chromosome, with the exception of the terminal segments of some chromosome pairs. Three chromosome pairs belonging to the A genome showed hybridization signals near the telomeres of their long arms. The existence of intergenomic chromosome rearrangements and the deletions of the repeated units are deduced from these observations. The number of rDNA loci (18S-5.8S-26S rDNA) was determined for the tetraploid and hexaploid oat species. Simultaneous in situ hybridization with the satellite and rDNA probes was used to assign the SAT chromosomes of these species to their correct genomes.
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Affiliation(s)
- A Fominaya
- Department of Cell Biology and Genetics, University of Alcalá de Henares, Madrid, Spain
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24
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Röder MS, Sorrells ME, Tanksley SD. Pulsed-field gel analysis of 5S and satellite DNA in barley. Genome 1995; 38:153-7. [PMID: 7729679 DOI: 10.1139/g95-019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pulsed-field gel electrophoresis was used to study the variability of clustered tandemly repeated sequences in barley. Twelve spring barley cultivars were investigated with a heterologous 5S DNA probe and the 118 base pair barley satellite DNA probe HVT01. On a per fragment basis, the 5S probe was 5 times and the barley satellite probe 6.7 times more variable than single- or low-copy RFLP markers, demonstrating their usefulness for cultivar distinction.
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Affiliation(s)
- M S Röder
- Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany
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25
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Preiszner J, Takács I, Bilgin M, Györgyey J, Dudits D, Fehér A. Organization of a Solatium brevidens repetitive sequence related to the TGRI subtelomeric repeats of Lycopersicon esculentum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 89:1-8. [PMID: 24177761 DOI: 10.1007/bf00226974] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/1993] [Accepted: 02/02/1994] [Indexed: 06/02/2023]
Abstract
A species-specific repetitive DNA fragment has been isolated from a genomic library of Solanum brevidens. Sequence analysis revealed a regular organization of three non-homologous subrepeats forming tandemly-arranged composite repetitive units. Interpretation of Southern hybridization patterns based on the known sequence data suggests that the isolated sequence element represents an abundant organization type, although the presence of simple tandem arrays of the subrepeats is also indicated. Seventy-four percent sequence similarity was found between one of the S. brevidens subrepeats (Sb4AX) and a satellite DNA (TGRI) localized as a subtelomeric repeat on almost all Lycopersicon esculentum chromosomes. Insitu hybridization indicated that, similarly to TGRI, the S. brevidens-specific repeats are located at the ends of the arms of several chromosomes. On the basis of the data obtained, a common ancestral sequence can be proposed for the tomato (TGRI) and the S. brevidens (Sb4AX) repeat however, the molecular organization of this element in these two species evolved in a basically different manner.
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Affiliation(s)
- J Preiszner
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, P.O.Box 521, H-6701, Szeged, Hungary
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