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Kroupin PY, Ulyanov DS, Karlov GI, Divashuk MG. The launch of satellite: DNA repeats as a cytogenetic tool in discovering the chromosomal universe of wild Triticeae. Chromosoma 2023:10.1007/s00412-023-00789-4. [PMID: 36905415 DOI: 10.1007/s00412-023-00789-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/16/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023]
Abstract
Fluorescence in situ hybridization is a powerful tool that enables plant researchers to perform systematic, evolutionary, and population studies of wheat wild relatives as well as to characterize alien introgression into the wheat genome. This retrospective review reflects on progress made in the development of methods for creating new chromosomal markers since the launch of this cytogenetic satellite instrument to the present day. DNA probes based on satellite repeats have been widely used for chromosome analysis, especially for "classical" wheat probes (pSc119.2 and Afa family) and "universal" repeats (45S rDNA, 5S rDNA, and microsatellites). The rapid development of new-generation sequencing and bioinformatical tools, and the application of oligo- and multioligonucleotides has resulted in an explosion in the discovery of new genome- and chromosome-specific chromosome markers. Owing to modern technologies, new chromosomal markers are appearing at an unprecedented velocity. The present review describes the specifics of localization when employing commonly used vs. newly developed probes for chromosomes in J, E, V, St, Y, and P genomes and their diploid and polyploid carriers Agropyron, Dasypyrum, Thinopyrum, Pseudoroegneria, Elymus, Roegneria, and Kengyilia. Particular attention is paid to the specificity of probes, which determines their applicability for the detection of alien introgression to enhance the genetic diversity of wheat through wide hybridization. The information from the reviewed articles is summarized into the TRepeT database, which may be useful for studying the cytogenetics of Triticeae. The review describes the trends in the development of technology used in establishing chromosomal markers that can be used for prediction and foresight in the field of molecular biology and in methods of cytogenetic analysis.
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Affiliation(s)
- Pavel Yu Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia.
| | - Daniil S Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Gennady I Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Mikhail G Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
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2
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Fluorescence In Situ Hybridization (FISH) for the Genotyping of Triticeae Tribe Species and Hybrids. Methods Mol Biol 2023; 2638:437-449. [PMID: 36781661 DOI: 10.1007/978-1-0716-3024-2_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
This chapter is dedicated to using fluorescence in situ hybridization (FISH) for the genotyping of Triticeae tribe species and hybrids. The basic method of FISH on metaphase chromosomes is presented with a discussion on its modifications, and deoxyribonucleic acid (DNA) probes that can be useful for genotyping are proposed.
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Zeibig F, Kilian B, Frei M. The grain quality of wheat wild relatives in the evolutionary context. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4029-4048. [PMID: 34919152 PMCID: PMC9729140 DOI: 10.1007/s00122-021-04013-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/06/2021] [Indexed: 05/17/2023]
Abstract
We evaluated the potential of wheat wild relatives for the improvement in grain quality characteristics including micronutrients (Fe, Zn) and gluten and identified diploid wheats and the timopheevii lineage as the most promising resources. Domestication enabled the advancement of civilization through modification of plants according to human requirements. Continuous selection and cultivation of domesticated plants induced genetic bottlenecks. However, ancient diversity has been conserved in crop wild relatives. Wheat (Triticum aestivum L.; Triticum durum Desf.) is one of the most important staple foods and was among the first domesticated crop species. Its evolutionary diversity includes diploid, tetraploid and hexaploid species from the Triticum and Aegilops taxa and different genomes, generating an AA, BBAA/GGAA and BBAADD/GGAAAmAm genepool, respectively. Breeding and improvement in wheat altered its grain quality. In this review, we identified evolutionary patterns and the potential of wheat wild relatives for quality improvement regarding the micronutrients Iron (Fe) and Zinc (Zn), the gluten storage proteins α-gliadins and high molecular weight glutenin subunits (HMW-GS), and the secondary metabolite phenolics. Generally, the timopheevii lineage has been neglected to date regarding grain quality studies. Thus, the timopheevii lineage should be subject to grain quality research to explore the full diversity of the wheat gene pool.
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Affiliation(s)
- Frederike Zeibig
- Department of Agronomy and Crop Physiology, Institute of Agronomy and Plant Breeding I, Justus-Liebig-University, 35392, Giessen, Germany
| | | | - Michael Frei
- Department of Agronomy and Crop Physiology, Institute of Agronomy and Plant Breeding I, Justus-Liebig-University, 35392, Giessen, Germany.
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von Well E, Booyse M, Fossey A. Effect of gamma irradiation on nucleolar activity in root tip cells of tetraploid Triticum turgidum ssp. durum L. PROTOPLASMA 2022; 259:453-468. [PMID: 34191122 DOI: 10.1007/s00709-021-01684-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Ionizing irradiation induces positive or negative changes in plant growth (M1) depending on the amount of irradiation applied to seeds or plant parts. The effect of 50-350 Gy gamma irradiation of kernels on nucleolar activity, as an indicator of metabolic activity, in root tip cells of tetraploid wheat Triticum turgidum ssp. durum L. cv. Orania (AABB) was investigated. The number of nucleoli present in nuclei and micronuclei as well as the mitotic index in the different irradiation dosages was used as an indicator of the cells entering mitosis, the chromosomes with nucleolar organizer regions that are active as well as chromosome doubling in the event of unsuccessful mitotic division. Nucleolar activity was investigated from 17.5 to 47.5 h after the onset of imbibition to study the first mitotic division and its consequences on the cells that were in G2 and G1 phases at the time of gamma irradiation. Untreated material produced a maximum of four nucleoli formed by the nucleolar organizing regions (NORs) on chromosomes 1B and 6B. In irradiated material, additional nucleoli were noted that are due to the activation of the NORs on chromosome 1A in micronuclei. The onset of mitosis was highly significantly retarded in comparison to the control due to checkpoints in the G2 phase for the repairing of damaged DNA. This study is the first to report on the appearance of nucleoli in micronuclei as well as activation of NORs in the micronuclei that are inactive in the nucleus and the effect of chromosome doubling on nucleolar activity in the event of unsuccessful mitotic division.
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Affiliation(s)
- Eben von Well
- ARC-Small Grain, Field Crops, Division, Private Bag X29, Bethlehem, 9700, South Africa.
| | - Mardé Booyse
- ARC-Biometry, Private Bag X5013, Stellenbosch, 7599, South Africa
| | - Annabel Fossey
- Central University of Technology, 1 Park Street, Bloemfontein, 9301, South Africa
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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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Zhang Y, Fan C, Chen Y, Wang RRC, Zhang X, Han F, Hu Z. Genome evolution during bread wheat formation unveiled by the distribution dynamics of SSR sequences on chromosomes using FISH. BMC Genomics 2021; 22:55. [PMID: 33446108 PMCID: PMC7809806 DOI: 10.1186/s12864-020-07364-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During the bread wheat speciation by polyploidization, a series of genome rearrangement and sequence recombination occurred. Simple sequence repeat (SSR) sequences, predominately located in heterochromatic regions of chromosomes, are the effective marker for tracing the genomic DNA sequence variations. However, to date the distribution dynamics of SSRs on chromosomes of bread wheat and its donors, including diploid and tetraploid Triticum urartu, Aegilops speltoides, Aegilops tauschii, Triticum turgidum ssp. dicocoides, reflecting the genome evolution events during bread wheat formation had not been comprehensively investigated. RESULTS The genome evolution was studied by comprehensively comparing the distribution patterns of (AAC)n, (AAG)n, (AGC)n and (AG)n in bread wheat Triticum aestivum var. Chinese Spring and its progenitors T. urartu, A. speltoides, Ae. tauschii, wild tetroploid emmer wheat T. dicocoides, and cultivated emmer wheat T. dicoccum. Results indicated that there are specific distribution patterns in different chromosomes from different species for each SSRs. They provided efficient visible markers for identification of some individual chromosomes and SSR sequence evolution tracing from the diploid progenitors to hexaploid wheat. During wheat speciation, the SSR sequence expansion occurred predominately in the centromeric and pericentromeric regions of B genome chromosomes accompanied by little expansion and elimination on other chromosomes. This result indicated that the B genome might be more sensitive to the "genome shock" and more changeable during wheat polyplodization. CONCLUSIONS During the bread wheat evolution, SSRs including (AAC)n, (AAG)n, (AGC)n and (AG)n in B genome displayed the greatest changes (sequence expansion) especially in centromeric and pericentromeric regions during the polyploidization from Ae. speltoides S genome, the most likely donor of B genome. This work would enable a better understanding of the wheat genome formation and evolution and reinforce the viewpoint that B genome was originated from S genome.
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Affiliation(s)
- Yingxin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China
| | - Chengming Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yuhong Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Richard R-C Wang
- United States Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT, 84322-6300, USA
| | - Xiangqi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zanmin Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Agriculture, University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Feng Z, Zhang M, Liu X, Liang D, Liu X, Hao M, Liu D, Ning S, Yuan Z, Jiang B, Chen X, Chen X, Zhang L. FISH karyotype comparison between A b- and A-genome chromosomes using oligonucleotide probes. J Appl Genet 2020; 61:313-322. [PMID: 32248406 DOI: 10.1007/s13353-020-00555-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/26/2020] [Accepted: 03/16/2020] [Indexed: 02/03/2023]
Abstract
Triticum boeoticum (2n = 2x = 14, AbAb) contains beneficial traits for common wheat improvement. The discrimination of Ab-genome chromosomes from A-genome chromosomes is an important step in gene transfer from T. boeoticum to common wheat. In this study, fluorescence in situ hybridization (FISH) analysis using nine oligonucleotide probes revealed high divergence between chromosomes of the common wheat germplasm Crocus and T. boeoticum accession G52. The combination of Oligo-pTa535-HM and Oligo-pSc119.2-HM can differentiate Ab and A chromosomes within homologous groups 2, 4, 5, and 6; chromosomes 2Ab and 6Ab can be identified by using (ACT)7, (CTT)7, and (GAA)7. The probes Oligo-pTa713 and (ACT)7 can be utilized for the identification of chromosomes 1Ab and 3Ab, respectively. Probes (CAG)7 and (CAC)7 can be applied in the identification of 7Ab. Moreover, probe combinations consisting of Oligo-pTa535-HM and (AAC)7 with (ACT)7 or (CTT)7 and of Oligo-pTa535-HM and Oligo-pTa713 with (CAC)7 or (CTT)7 will help discriminate the Ab-genome chromosomes of T. boeoticum. These probes are being used as potential markers to select common wheat Crocus-T. boeoticum G52 alien chromosome lines. Moreover, FISH patterns are highly divergent between Ab- and A-genome chromosomes, indicating that obvious chromosome structural variations arose during wheat evolution.
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Affiliation(s)
- Zhen Feng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Minghu Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xin Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Dongyu Liang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xiaojuan Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. .,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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8
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Ernetti JR, Gazolla CB, Recco-Pimentel SM, Luca EM, Bruschi DP. Non-random distribution of microsatellite motifs and (TTAGGG)n repeats in the monkey frog Pithecopus rusticus (Anura, Phyllomedusidae) karyotype. Genet Mol Biol 2020; 42:e20190151. [PMID: 31968045 PMCID: PMC7198017 DOI: 10.1590/1678-4685-gmb-2019-0151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023] Open
Abstract
The monkey frog, Pithecopus rusticus (Anura, Phyllomedusidae) is endemic to the grasslands of the Araucarias Plateau, southern Brazil. This species is known only from a small population found at the type locality. Here, we analyzed for the first time the chromosomal organization of the repetitive sequences, including seven microsatellite repeats and telomeric sequences (TTAGGG)n in the karyotype of the species by Fluorescence in situ Hybridization. The dinucleotide motifs had a pattern of distribution clearly distinct from those of the tri- and tetranucleotides. The dinucleotide motifs are abundant and widely distributed in the chromosomes, located primarily in the subterminal regions. The tri- and tetranucleotides, by contrast, tend to be clustered, with signals being observed together in the secondary constriction of the homologs of pair 9, which are associated with the nucleolus organizer region. As expected, the (TTAGGG)n probe was hybridized in all the telomeres, with hybridization signals being detected in the interstitial regions of some chromosome pairs. We demonstrated the variation in the abundance and distribution of the different microsatellite motifs and revealed their non-random distribution in the karyotype of P. rusticus. These data contribute to understand the role of repetitive sequences in the karyotype diversification and evolution of this taxon.
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Affiliation(s)
- Julia R Ernetti
- Programa de Pós-graduação em Ciências Ambientais, Área de Ciências Exatas e Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, SC, Brazil
| | - Camilla B Gazolla
- Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Shirlei M Recco-Pimentel
- Departamento de Biologia Estrutural e Funcional, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Elaine M Luca
- Programa de Pós-graduação em Ciências Ambientais, Área de Ciências Exatas e Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, SC, Brazil
- Departamento de Zootecnia e Ciências Biológicas, Universidade Federal de Santa Maria, Campus de Palmeira das Missões, Palmeira das Missões, RS, Brazil
| | - Daniel P Bruschi
- Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
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Badaeva ED, Fisenko AV, Surzhikov SA, Yankovskaya AA, Chikida NN, Zoshchuk SA, Belousova MK, Dragovich AY. Genetic Heterogeneity of a Diploid Grass Aegilops tauschii Revealed by Chromosome Banding Methods and Electrophoretic Analysis of the Seed Storage Proteins (Gliadins). RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419110024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Grewal S, Hubbart-Edwards S, Yang C, Scholefield D, Ashling S, Burridge A, Wilkinson PA, King IP, King J. Detection of T. urartu Introgressions in Wheat and Development of a Panel of Interspecific Introgression Lines. FRONTIERS IN PLANT SCIENCE 2018; 9:1565. [PMID: 30420865 PMCID: PMC6216105 DOI: 10.3389/fpls.2018.01565] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/08/2018] [Indexed: 05/23/2023]
Abstract
Tritcum urartu (2n = 2x = 14, AuAu), the A genome donor of wheat, is an important source for new genetic variation for wheat improvement due to its high photosynthetic rate and disease resistance. By facilitating the generation of genome-wide introgressions leading to a variety of different wheat-T. urartu translocation lines, T. urartu can be practically utilized in wheat improvement. Previous studies that have generated such introgression lines have been unable to successfully use cytological methods to detect the presence of T. urartu in these lines. Many have, thus, used a variety of molecular markers with limited success due to the low-density coverage of these markers and time-consuming nature of the techniques rendering them unsuitable for large-scale breeding programs. In this study, we report the generation of a resource of single nucleotide polymorphic (SNP) markers, present on a high-throughput SNP genotyping array, that can detect the presence of T. urartu in a hexaploid wheat background making it a potentially valuable tool in wheat pre-breeding programs. A whole genome introgression approach has resulted in the transfer of different chromosome segments from T. urartu into wheat which have then been detected and characterized using these SNP markers. The molecular analysis of these wheat-T. urartu recombinant lines has resulted in the generation of a genetic map of T. urartu containing 368 SNP markers, spread across all seven chromosomes of T. urartu. Comparative analysis of the genetic map of T. urartu and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of the 4/5 translocation in T. urartu also present in the A genome of wheat. A panel of 17 wheat-T. urartu recombinant lines, which consisted of introgressed segments that covered the whole genome of T. urartu, were also selected for self-fertilization to provide a germplasm resource for future trait analysis. This valuable resource of high-density molecular markers specifically designed for detecting wild relative chromosomes and a panel of stable interspecific introgression lines will greatly enhance the efficiency of wheat improvement through wild relative introgressions.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Caiyun Yang
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Amanda Burridge
- Cereal Genomics Lab, Life Sciences Building, School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Paul Anthony Wilkinson
- Cereal Genomics Lab, Life Sciences Building, School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Ian P. King
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
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11
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Ruban AS, Badaeva ED. Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis. FRONTIERS IN PLANT SCIENCE 2018; 9:1756. [PMID: 30564254 PMCID: PMC6288319 DOI: 10.3389/fpls.2018.01756] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/12/2018] [Indexed: 05/20/2023]
Abstract
Five diploid Aegilops species of the Sitopsis section: Ae. speltoides, Ae. longissima, Ae. sharonensis, Ae. searsii, and Ae. bicornis, two tetraploid species Ae. peregrina (= Ae. variabilis) and Ae. kotschyi (Aegilops section) and hexaploid Ae. vavilovii (Vertebrata section) carry the S-genomes. The B- and G-genomes of polyploid wheat are also the derivatives of the S-genome. Evolution of the S-genome species was studied using Giemsa C-banding and fluorescence in situ hybridization (FISH) with DNA probes representing 5S (pTa794) and 18S-5.8S-26S (pTa71) rDNAs as well as nine tandem repeats: pSc119.2, pAesp_SAT86, Spelt-1, Spelt-52, pAs1, pTa-535, and pTa-s53. To correlate the C-banding and FISH patterns we used the microsatellites (CTT)10 and (GTT)9, which are major components of the C-banding positive heterochromatin in wheat. According to the results obtained, diploid species split into two groups corresponding to Emarginata and Truncata sub-sections, which differ in the C-banding patterns, distribution of rDNA and other repeats. The B- and G-genomes of polyploid wheat are most closely related to the S-genome of Ae. speltoides. The genomes of allopolyploid wheat have been evolved as a result of different species-specific chromosome translocations, sequence amplification, elimination and re-patterning of repetitive DNA sequences. These events occurred independently in different wheat species and in Ae. speltoides . The 5S rDNA locus of chromosome 1S was probably lost in ancient Ae. speltoides prior to formation of Timopheevii wheat, but after the emergence of ancient emmer. Evolution of Emarginata species was associated with an increase of C-banding and (CTT)10-positive heterochromatin, amplification of Spelt-52, re-pattering of the pAesp_SAT86, and a gradual decrease in the amount of the D-genome-specific repeats pAs1, pTa-535, and pTa-s53. The emergence of Ae. peregrina and Ae. kotschyi did not lead to significant changes of the S*-genomes. However, partial elimination of 45S rDNA repeats from 5S* and 6S* chromosomes and alterations of C-banding and FISH-patterns have been detected. Similarity of the Sv-genome of Ae. vavilovii with the Ss genome of diploid Ae. searsii confirmed the origin of this hexaploid. A model of the S-genome evolution is suggested.
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Affiliation(s)
- Alevtina S. Ruban
- Laboratory of Chromosome Structure and Function, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ekaterina D. Badaeva
- Laboratory of Genetic Basis of Plant Identification, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Molecular Karyology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Ekaterina D. Badaeva
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Samans B, Chalhoub B, Snowdon RJ. Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus. THE PLANT GENOME 2017; 10. [PMID: 29293818 DOI: 10.3835/plantgenome2017.02.0013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. In both synthetic and natural , a subgenome bias was observed toward exchanges replacing larger chromosome segments from the C-subgenome by their smaller, homeologous A-subgenome segments, driving postpolyploidization genome size reduction. Selection in natural favored segmental deletions involving genes associated with immunity, reproduction, and adaptation. Deletions affecting mismatch repair system genes, which are assumed to control homeologous recombination, were also found to be under selection. Structural exchanges between homeologous subgenomes appear to be a major source of novel genetic diversity in de novo allopolyploids. Documenting the consequences of genomic collision by genomic resequencing gives insights into the adaptive processes accompanying allopolyploidization.
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Linc G, Gaál E, Molnár I, Icsó D, Badaeva E, Molnár-Láng M. Molecular cytogenetic (FISH) and genome analysis of diploid wheatgrasses and their phylogenetic relationship. PLoS One 2017; 12:e0173623. [PMID: 28278169 PMCID: PMC5344461 DOI: 10.1371/journal.pone.0173623] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/23/2017] [Indexed: 11/22/2022] Open
Abstract
This paper reports detailed FISH-based karyotypes for three diploid wheatgrass species Agropyron cristatum (L.) Beauv., Thinopyrum bessarabicum (Savul.&Rayss) A. Löve, Pseudoroegneria spicata (Pursh) A. Löve, the supposed ancestors of hexaploid Thinopyrum intermedium (Host) Barkworth & D.R.Dewey, compiled using DNA repeats and comparative genome analysis based on COS markers. Fluorescence in situ hybridization (FISH) with repetitive DNA probes proved suitable for the identification of individual chromosomes in the diploid JJ, StSt and PP genomes. Of the seven microsatellite markers tested only the (GAA)n trinucleotide sequence was appropriate for use as a single chromosome marker for the P. spicata AS chromosome. Based on COS marker analysis, the phylogenetic relationship between diploid wheatgrasses and the hexaploid bread wheat genomes was established. These findings confirmed that the J and E genomes are in neighbouring clusters.
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Affiliation(s)
- Gabriella Linc
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
- * E-mail:
| | - Eszter Gaál
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - István Molnár
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Diana Icsó
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Ekaterina Badaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Márta Molnár-Láng
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
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Cytomolecular discrimination of the A m chromosomes of Triticum monococcum and the A chromosomes of Triticum aestivum using microsatellite DNA repeats. J Appl Genet 2016. [PMID: 27468932 DOI: 10.1007/s13353‐016‐0361‐6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
The cytomolecular discrimination of the Am- and A-genome chromosomes facilitates the selection of wheat-Triticum monococcum introgression lines. Fluorescence in situ hybridisation (FISH) with the commonly used DNA probes Afa family, 18S rDNA and pSc119.2 showed that the more complex hybridisation pattern obtained in T. monococcum relative to bread wheat made it possible to differentiate the Am and A chromosomes within homoeologous groups 1, 4 and 5. In order to provide additional chromosomal landmarks to discriminate the Am and A chromosomes, the microsatellite repeats (GAA)n, (CAG)n, (CAC)n, (AAC)n, (AGG)n and (ACT)n were tested as FISH probes. These showed that T. monococcum chromosomes have fewer, generally weaker, simple sequence repeat (SSR) signals than the A-genome chromosomes of hexaploid wheat. A differential hybridisation pattern was observed on 6Am and 6A chromosomes with all the SSR probes tested except for the (ACT)n probe. The 2Am and 2A chromosomes were differentiated by the signals given by the (GAA)n, (CAG)n and (AAC)n repeats, while only (GAA)n discriminated the chromosomes 3Am and 3A. Chromosomes 7Am and 7A could be differentiated by the lack of (GAA)n and (AGG)n signals on 7A. As potential landmarks for identifying the Am chromosomes, SSR repeats will facilitate the introgression of T. monococcum chromatin into wheat.
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Cytomolecular discrimination of the A m chromosomes of Triticum monococcum and the A chromosomes of Triticum aestivum using microsatellite DNA repeats. J Appl Genet 2016; 58:67-70. [PMID: 27468932 DOI: 10.1007/s13353-016-0361-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
Abstract
The cytomolecular discrimination of the Am- and A-genome chromosomes facilitates the selection of wheat-Triticum monococcum introgression lines. Fluorescence in situ hybridisation (FISH) with the commonly used DNA probes Afa family, 18S rDNA and pSc119.2 showed that the more complex hybridisation pattern obtained in T. monococcum relative to bread wheat made it possible to differentiate the Am and A chromosomes within homoeologous groups 1, 4 and 5. In order to provide additional chromosomal landmarks to discriminate the Am and A chromosomes, the microsatellite repeats (GAA)n, (CAG)n, (CAC)n, (AAC)n, (AGG)n and (ACT)n were tested as FISH probes. These showed that T. monococcum chromosomes have fewer, generally weaker, simple sequence repeat (SSR) signals than the A-genome chromosomes of hexaploid wheat. A differential hybridisation pattern was observed on 6Am and 6A chromosomes with all the SSR probes tested except for the (ACT)n probe. The 2Am and 2A chromosomes were differentiated by the signals given by the (GAA)n, (CAG)n and (AAC)n repeats, while only (GAA)n discriminated the chromosomes 3Am and 3A. Chromosomes 7Am and 7A could be differentiated by the lack of (GAA)n and (AGG)n signals on 7A. As potential landmarks for identifying the Am chromosomes, SSR repeats will facilitate the introgression of T. monococcum chromatin into wheat.
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Diversification of the Homoeologous Lr34 Sequences in Polyploid Wheat Species and Their Diploid Progenitors. J Mol Evol 2016; 82:291-302. [PMID: 27300207 DOI: 10.1007/s00239-016-9748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
Allopolyploidization induces a multiple processes of genomic reorganization, including the structurally functional diversification of the homoeologous genes. An example of such diversification is the appearance of the Lr34 gene on chromosome 7D of bread wheat T. aestivum (BAD), the gene conferring durable, race non-specific protection against three fungal pathogens. In this study, we focused on the variability of a functionally critical region between exons 10-12 of Lr34 among diploid progenitors of wheat genomes and their respective polyploids. In the diploid A-genome species, two basic forms of the studied region have been revealed: (1) non-functional forms containing stop codons, or/and frameshifts (T. monococcum/T. urartu) and (2) forms with no such a mutations (T. boeoticum). The Lr34 sequence of T. urartu containing a TGA stop codon was inherited by the first tetraploid T. dicoccoides (BA), and then reorganized in some accessions of this species due to the insertion of an LTR retroelement in exon 10. Besides T. boeoticum, the second form of the Lr34 sequence is also characteristic of A. speltoides, which presumably donated this form to all polyploid descendants bearing B-genome. No differences were found between the D-genome-specific Lr34 sequences studied here and downloaded from databases, implying the highest level of conservation of the Lr34 predecessor throughout evolution. The sequence data were later used to construct phylograms, and apparent peculiarities in the evolution of the studied region of Lr34 genes discussed.
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