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Serrano-León IM, Prieto P, Aguilar M. Telomere and subtelomere high polymorphism might contribute to the specificity of homologous recognition and pairing during meiosis in barley in the context of breeding. BMC Genomics 2023; 24:642. [PMID: 37884878 PMCID: PMC10601145 DOI: 10.1186/s12864-023-09738-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Barley (Hordeum vulgare) is one of the most popular cereal crops globally. Although it is a diploid species, (2n = 2x = 14) the study of its genome organization is necessary in the framework of plant breeding since barley is often used in crosses with other cereals like wheat to provide them with advantageous characters. We already have an extensive knowledge on different stages of the meiosis, the cell division to generate the gametes in species with sexual reproduction, such as the formation of the synaptonemal complex, recombination, and chromosome segregation. But meiosis really starts with the identification of homologous chromosomes and pairing initiation, and it is still unclear how chromosomes exactly choose a partner to appropriately pair for additional recombination and segregation. In this work we present an exhaustive molecular analysis of both telomeres and subtelomeres of barley chromosome arms 2H-L, 3H-L and 5H-L. As expected, the analysis of multiple features, including transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots, G4 quadruplexes, genes and targeted sequence motifs for key DNA-binding proteins, revealed a high degree of variability both in telomeres and subtelomeres. The molecular basis for the specificity of homologous recognition and pairing occurring in the early chromosomal interactions at the start of meiosis in barley may be provided by these polymorphisms. A more relevant role of telomeres and most distal part of subtelomeres is suggested.
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Affiliation(s)
- I M Serrano-León
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal S/N., Campus Alameda del Obispo, 14004, Córdoba, Spain
| | - P Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal S/N., Campus Alameda del Obispo, 14004, Córdoba, Spain.
| | - M Aguilar
- Área de Fisiología Vegetal, Universidad de Córdoba, Campus de Rabanales, Edif. C4, 3ª Planta, Córdoba, Spain
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2
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Li LF, Zhang ZB, Wang ZH, Li N, Sha Y, Wang XF, Ding N, Li Y, Zhao J, Wu Y, Gong L, Mafessoni F, Levy AA, Liu B. Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome. MOLECULAR PLANT 2022; 15:488-503. [PMID: 34979290 DOI: 10.1016/j.molp.2021.12.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/11/2021] [Accepted: 12/28/2021] [Indexed: 05/23/2023]
Abstract
Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related to species of Aegilops, section Sitopsis. Here, we report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides, as well as the partial assembly of the Amblyopyrum muticum (synonym Aegilops mutica) genome for phylogenetic analysis. Our results reveal that the donor of the common wheat B subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae. speltoides and Am. muticum belong. In addition, we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex. The five Sitopsis species have various assembled genome sizes (4.11-5.89 Gb) with high proportions of repetitive sequences (85.99%-89.81%); nonetheless, they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex. Differences in genome size were primarily due to independent post-speciation amplification of transposons. We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding. These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex, as well as for wheat improvement.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Zhi-Bin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; Department of Plant and Environmental Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ning Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yang Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Fabrizio Mafessoni
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Avraham A Levy
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China.
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3
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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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Aguilar M, Prieto P. Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes. THE PLANT GENOME 2020; 13:e20065. [PMID: 33029942 DOI: 10.1002/tpg2.20065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/20/2020] [Accepted: 09/08/2020] [Indexed: 05/23/2023]
Abstract
Bread wheat, Triticum aestivum L., is one of the most important crops in the world. Understanding its genome organization (allohexaploid; AABBDD; 2n = 6x = 42) is essential for geneticists and plant breeders. Particularly, the knowledge of how homologous chromosomes (equivalent chromosomes from the same genome) specifically recognize each other to pair at the beginning of meiosis, the cellular process to generate gametes in sexually reproducing organisms, is fundamental for plant breeding and has a big influence on the fertility of wheat plants. Initial homologous chromosome interactions contribute to specific recognition and pairing between homologues at the onset of meiosis. Understanding the molecular basis of these critical processes can help to develop genetic tools in a breeding context to promote interspecific chromosome associations in hybrids or interspecific genetic crosses to facilitate the transfer of desirable agronomic traits from related species into a crop like wheat. The terminal regions of chromosomes, which include telomeres and subtelomeres, participate in chromosome recognition and pairing. We present a detailed molecular analysis of subtelomeres of wheat chromosome arms 1AS, 4AS, 7AS, 7BS and 7DS. Results showed a high polymorphism in the subtelomeric region among homoeologues (equivalent chromosomes from related genomes) for all the features analyzed, including genes, transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots and targeted sequence motifs for relevant DNA-binding proteins. These polymorphisms might be the molecular basis for the specificity of homologous recognition and pairing in initial chromosome interactions at the beginning of meiosis in wheat.
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Affiliation(s)
- Miguel Aguilar
- Área de Fisiología Vegetal. Universidad de Córdoba. Campus de Rabanales, edif. C4, 3a planta, Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4084, Córdoba, 14080, Spain
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5
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Singh AK, Lo K, Dong C, Zhang P, Trethowan RM, Sharp PJ. Development of RNA-seq-based molecular markers for characterizing Thinopyrum bessarabicum and Secale introgressions in wheat. Genome 2020; 63:525-534. [PMID: 32762630 DOI: 10.1139/gen-2020-0057] [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: 11/22/2022]
Abstract
Sequence-based markers have added a new dimension in the efficiency of identifying alien introgressions in wheat. Expressed sequence tag-sequence tagged sites (EST-STS) markers have proved useful in tracing alien chromatin. In this study, we report the development of Thinopyrum bessarabicum- and Secale anatolicum-specific EST-STS markers and their application in tracing respective alien chromatin introgressions in wheat. The parental lines, Chinese Spring (CS), ISR991.1 (CS/Th. bessarabicum amphidiploid), and ISR1049.2 (CS/Secale anatolicum amphidiploid), were used as core experimental materials. Using comparative analysis of RNA-Seq data, 10 903 and 10 660 candidate sequences specific to Th. bessarabicum and S. anatolicum, respectively, were assembled and identified. To validate the genome specificity of these candidate sequences, 68 and 64 EST-STS markers were developed from randomly selected candidate sequences of Th. bessarabicum and S. anatolicum, respectively, and tested on sets of alien addition lines. Fifty-five and 53 markers for Th. bessarabicum and S. anatolicum chromatin, respectively, were assigned to chromosomal location(s), covering all seven chromosomes. Approximately 83% of S. anatolicum-specific markers were transferable to S. cereale. The genome-specific candidate sequences identified and the EST-STS markers developed will be valuable resources for exploitation of Th. bessarabicum and Secale species diversity in wheat and triticale breeding.
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Affiliation(s)
- Amit K Singh
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Kitty Lo
- School of Mathematics and Statistics, The University of Sydney, NSW 2006, Australia
| | - Chongmei Dong
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Richard M Trethowan
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Peter J Sharp
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
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6
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Singh N, Raupp J, Koo DH, Friebe B, Gill B, Poland J. In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing. PLANT METHODS 2020; 16:45. [PMID: 32280361 PMCID: PMC7137276 DOI: 10.1186/s13007-020-00588-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/23/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Short read sequencing technologies, such as genotyping-by-sequencing (GBS), have been utilized in genetic mapping, marker development, and population genomic studies. High-throughput and multiplexing capability coupled with low cost make GBS an appropriate tool for molecular research. Here, we present the application of GBS to characterize wheat aneuploid stocks and detect chromosomal aberrations including aneuploidy and chromosomal deletions. These aneuploids are an important resource that have been used in wheat genetics and genomics studies to localize genes, determine physical positions, and develop chromosome bin maps. RESULTS Using GBS, we mapped sequence reads and quantified read coverage across chromosome bins. Using this approach, we confirmed known deletions and aneuploid stocks. In addition, we were also able to fully characterize these stocks and to identify several novel deletions and aneuploids. With this knowledge and a quick detection tool at our disposal, we can easily isolate these deletions and aneuploids into distinct lines. CONCLUSION We envision this tool to replace the intensive cytogenetics techniques, such as C-banding, and fluorescent- and genomic-in situ hybridization to accurately detect chromosome dosage and segmental deletions in wheat genetic stocks as well as other crop species.
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Affiliation(s)
- Narinder Singh
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
- Present Address: Bayer U.S.–Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO 63017 USA
| | - John Raupp
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Bernd Friebe
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Bikram Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
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Wang H, Yu Z, Li G, Yang Z. Diversified Chromosome Rearrangements Detected in a Wheat‒ Dasypyrum breviaristatum Substitution Line Induced by Gamma-Ray Irradiation. PLANTS 2019; 8:plants8060175. [PMID: 31207944 PMCID: PMC6630480 DOI: 10.3390/plants8060175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/09/2019] [Accepted: 06/13/2019] [Indexed: 01/18/2023]
Abstract
To determine the composition of chromosome aberrations in a wheat‒Dasypyrum breviaristatum substitution line with seeds treated by a dose of gamma-rays (200 Gy), sequential non-denaturing fluorescence in situ hybridization (ND-FISH) with multiple oligonucleotide probes was used to screen individual plants of the mutagenized progenies. We identified 122 types of chromosome rearrangements, including centromeric, telomeric, and intercalary chromosome translocations from a total of 772 M1 and 872 M2 plants. The frequency of reciprocal translocations between B- and D-chromosomes was higher than that between A- and D-chromosomes. Eight translocations between D. breviaristatum and wheat chromosomes were also detected. The 13 stable plants with multiple chromosome translocations displayed novel agronomic traits. The newly developed materials will enhance wheat breeding programs through wheat‒Dasypyrum introgression and also facilitate future studies on the genetic and epigenetic effects of translocations in wheat genomics.
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Affiliation(s)
- Hongjin Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Zhihui Yu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
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8
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Miki Y, Yoshida K, Mizuno N, Nasuda S, Sato K, Takumi S. Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops. DNA Res 2019; 26:171-182. [PMID: 30715317 PMCID: PMC6476730 DOI: 10.1093/dnares/dsy047] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/22/2018] [Indexed: 12/16/2022] Open
Abstract
Dramatic changes occasionally occur in intergenic regions leading to genomic alterations during speciation and will consequently obscure the ancestral species that have contributed to the formation of allopolyploid organisms. The S genome of five species of section Sitopsis of genus Aegilops is considered to be an origin of B-genome in cultivated tetraploid and hexaploid wheat species, although its actual donor is still unclear. Here, we attempted to elucidate phylogenetic relationship among Sitopsis species by performing RNA sequencing of the coding regions of each chromosome. Thus, genome-wide polymorphisms were extensively analyzed in 19 accessions of the Sitopsis species in reference to the tetraploid and hexaploid wheat B genome sequences and consequently were efficiently anchored to the B-genome chromosomes. The results of our genome-wide exon sequencing and resultant phylogenetic analysis indicate that Ae. speltoides is likely to be the direct donor of all chromosomes of the wheat B genome. Our results also indicate that the genome differentiation during wheat allopolyploidization from S to B proceeds at different speeds over the chromosomes rather than at constant rate and recombination could be a factor determining the speed. This observation is potentially generalized to genome differentiation during plant allopolyploid evolution.
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Affiliation(s)
- Yuka Miki
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Nobuyuki Mizuno
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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9
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Liu C, Gong W, Han R, Guo J, Li G, Li H, Song J, Liu A, Cao X, Zhai S, Cheng D, Li G, Zhao Z, Yang Z, Liu J, Reader SM. Characterization, identification and evaluation of a set of wheat-Aegilops comosa chromosome lines. Sci Rep 2019; 9:4773. [PMID: 30886203 PMCID: PMC6423130 DOI: 10.1038/s41598-019-41219-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/26/2019] [Indexed: 11/21/2022] Open
Abstract
This study characterized and evaluated a set of wheat-Aegilops comosa introgression lines, including six additions and one substitution. A total of 47 PLUG markers and a set of cytogenetic markers specific for Ae. comosa chromosomes were established after screening 526 PLUG primer pairs and performing FISH using oligonucleotides as probes. Marker analysis confirmed that these lines were wheat-Ae. comosa 2M–7M addition lines and a 6M(6A) substitution line. The molecular and cytogenetic markers developed herein could be used to trace Ae. comosa chromatin in wheat background. In order to evaluate the breeding value of the material, disease resistance tests and agronomical trait investigations were carried out on these alien chromosome introgression lines. Disease resistance tests showed that chromosomes 2M and 7M of Ae. comosa might harbor new stripe rust and powdery mildew resistance genes, respectively, therefore, they could be used as resistance sources for wheat breeding. Investigations into agronomical traits showed that all chromosomes 2M to 7M had detrimental effects on the agronomic performance of wheat, therefore, the selection of plants with relatively negative effects should be avoided when inducing wheat-A. comosa chromosome translocations using chromosome engineering procedures.
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Affiliation(s)
- Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.,Colloge of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Wenping Gong
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Jun Guo
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Haosheng Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Jianmin Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.,Colloge of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Aifeng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Xinyou Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.,Colloge of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Shengnan Zhai
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Dungong Cheng
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.,Colloge of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Zhendong Zhao
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Jianjun Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
| | - Stephen M Reader
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.
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10
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Kwiatek MT, Kurasiak-Popowska D, Mikołajczyk S, Niemann J, Tomkowiak A, Weigt D, Nawracała J. Cytological markers used for identification and transfer of Aegilops spp. chromatin carrying valuable genes into cultivated forms of Triticum. COMPARATIVE CYTOGENETICS 2019; 13:41-59. [PMID: 30854169 PMCID: PMC6403195 DOI: 10.3897/compcytogen.v13i1.30673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/30/2019] [Indexed: 05/26/2023]
Abstract
There are many reports describing chromosome structure, organization and evolution within goatgrasses (Aegilops spp.). Chromosome banding and fluorescence in situ hybridization techniques are main methods used to identify Aegilops Linnaeus, 1753 chromosomes. These data have essential value considering the close genetic and genomic relationship of goatgrasses with wheat (Triticumaestivum Linnaeus, 1753) and triticale (× Triticosecale Wittmack, 1899). A key question is whether those protocols are useful and effective for tracking Aegilops chromosomes or chromosome segments in genetic background of cultivated cereals. This article is a review of scientific reports describing chromosome identification methods, which were applied for development of prebreeding plant material and for transfer of desirable traits into Triticum Linnaeus, 1753 cultivated species. Moreover, this paper is a resume of the most efficient cytomolecular markers, which can be used to follow the introgression of Aegilops chromatin during the breeding process.
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Affiliation(s)
- Michał T. Kwiatek
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Danuta Kurasiak-Popowska
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Sylwia Mikołajczyk
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Jerzy Nawracała
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, PolandPoznań University of Life SciencesPoznańPoland
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Abstract
Background The members of the Triticeae tribe are characterised by the presence of orthologous and homoeologous gene copies regulating flavonoid biosynthesis. Among transcription factors constituting a regulatory MBW complex, the greatest contribution to the regulation of flavonoid biosynthetic pathway is invested by R2R3-Myb-type TFs. Differently expressed R2R3-Myb copies activate the synthesis of various classes of flavonoid compounds in different plant tissues. The aim of this research was the identification, comparison and analysis of full-length sequences of the duplicated R2R3-Myb Mpc1 (Myb protein c1) gene copies in barley and wheat genomes. Results The Mpc1 genes were identified in homoeologous group 4 and 7 chromosomes: a total of 3 copies in barley (Hordeum vulgare L.) and 8 copies in bread wheat (Triticum aestivum L.) genomes. All Mpc1 genes have a similar two-exon structure, and almost all of them are transcriptionally active. The calculation of the divergence time revealed that first duplication between 4 and 7 chromosomes of the common ancestor of the Triticeae tribe occurred about 35–46 million years ago (MYA); the last duplication arised about 16–19 MYA before the divergence Triticum and Hordeum genera The connection between gene expression and the appearance of anthocyanin pigmentation was found for three genes from homoeologous group 4 chromosomes: TaMpc1-A2 (5AL) in wheat coleoptile, HvMpc1-H2 (4HL) in barley lemma and aleurone layer, and HvMpc1-H3 (4HL) in barley aleurone layer. TaMpc1-D4 (4DL) from the wheat genome showed a strong level of expression regardless of the colour of coleoptile or pericarp. It is assumed, that this gene regulates the biosynthesis of uncoloured flavonoids in analysed tissues. Conclusions The regulatory R2R3-Myb genes involved in anthocyanin synthesis were identified and characterised in Triticeae tribe species. Genes designated HvMpc1-H2 and HvMpc1-H3 appeared to be the main factors underlying intraspecific variation of H. vulgare by lemma and aleurone colour. TaMpc1-A2 is the co-regulator of the Mpc1–1 genes in bread wheat genome controlling anthocyanin synthesis in coleoptile. Electronic supplementary material The online version of this article (10.1186/s12862-019-1378-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ksenia V Strygina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva ave. 10, Novosibirsk, 630090, Russia.
| | - Elena K Khlestkina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva ave. 10, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova str., 1, Novosibirsk, 630090, Russia.,N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya Str., 42-44, St. Petersburg, 190000, Russia
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Strygina KV, Khlestkina EK. Myc-like transcriptional factors in wheat: structural and functional organization of the subfamily I members. BMC PLANT BIOLOGY 2019; 19:50. [PMID: 30813892 PMCID: PMC6393960 DOI: 10.1186/s12870-019-1639-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND Myc-like regulatory factors carrying the basic helix-loop-helix (bHLH) domain belong to a large superfamily of transcriptional factors (TFs) present in all eukaryotic kingdoms. In plants, the representatives of this superfamily regulate diverse biological processes including growth and development as well as response to various stresses. As members of the regulatory MBW complexes, they participate in biosynthesis of flavonoids. In wheat, only one member (TaMyc1) of the Myc-like TFs family has been studied, while structural and functional organization of further members remained uncharacterized. From two Myc-subfamilies described recently in the genomes of Triticeae tribe species, we investigated thoroughly the members of the subfamily I which includes the TaMyc1 gene. RESULTS Comparison of the promoter regions of the Myc subfamily I members in wheat suggested their division into two groups (likely homoeologous sets): TaMyc-1 (TaMyc-A1/TaMyc1, TaMyc-B1, TaMyc-D1) and TaMyc-2 (TaMyc-A2 and TaMyc-D2). It was demonstrated that the TaMyc-D1 copy has lost its functionality due to the frame shift mutation. The study of functional features of the other four copies suggested some of them to be involved in the biosynthesis of anthocyanins. In particular, TaMyc-B1 is assumed to be a co-regulator of the gene TaC1-A1 (encoding R2R3-Myb factor) in the MBW regulatory complex activating anthocyanin synthesis in wheat coleoptile. The mRNA levels of the TaMyc-A1, TaMyc-B1, TaMyc-A2 and TaMyc-D2 genes increased significantly in wheat seedlings exposed to osmotic stress. Salinity stress induced expression of TaMyc-B1 and TaMyc-A2, while TaMyc-A1 was repressed. CONCLUSIONS The features of the structural and functional organization of the members of subfamily I of Myc-like TFs in wheat were determined. Myc-like co-regulator (TaMyc-B1) of anthocyanin synthesis in wheat coleoptile was described for the first time. The Myc-encoding genes presumably involved in response to drought and salinity were determined in wheat. The results obtained are important for further manipulations with Myc genes, aimed on increasing wheat adaptability.
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Affiliation(s)
- Ksenia V. Strygina
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Lavrentjeva Ave. 10, Novosibirsk, 630090 Russia
| | - Elena K. Khlestkina
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Lavrentjeva Ave. 10, Novosibirsk, 630090 Russia
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya Str., 42-44, St. Petersburg, 190000 Russia
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Zhang W, Zhang M, Zhu X, Cao Y, Sun Q, Ma G, Chao S, Yan C, Xu SS, Cai X. Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:365-375. [PMID: 29094182 DOI: 10.1007/s00122-017-3007-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/26/2017] [Indexed: 05/18/2023]
Abstract
This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.
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Affiliation(s)
- Wei Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Mingyi Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Yaping Cao
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Qing Sun
- Department of Computer Science, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Shiaoman Chao
- The Red River Valley Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Changhui Yan
- Department of Computer Science, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Steven S Xu
- The Red River Valley Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
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Jugulam M, Gill BS. Molecular cytogenetics to characterize mechanisms of gene duplication in pesticide resistance. PEST MANAGEMENT SCIENCE 2018; 74:22-29. [PMID: 28714247 DOI: 10.1002/ps.4665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 06/07/2023]
Abstract
Recent advances in molecular cytogenetics empower construction of physical maps to illustrate the precise position of genetic loci on the chromosomes. Such maps provide visible information about the position of DNA sequences, including the distribution of repetitive sequences on the chromosomes. This is an important step toward unraveling the genetic mechanisms implicated in chromosomal aberrations (e.g., gene duplication). In response to stress, such as pesticide selection, duplicated genes provide an immediate adaptive advantage to organisms that overcome unfavorable conditions. Although the significance of gene duplication as one of the important events driving genetic diversity has been reported, the precise mechanisms of gene duplication that contribute to pesticide resistance, especially to herbicides, are elusive. With particular reference to pesticide resistance, we discuss the prospects of application of molecular cytogenetic tools to uncover mechanism(s) of gene duplication, and illustrate hypothetical models that predict the evolutionary basis of gene duplication. The cytogenetic basis of duplicated genes, their stability, as well as the magnitude of selection pressure, can determine the dynamics of the genetic locus (loci) conferring pesticide resistance not only at the population level, but also at the individual level. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Mithila Jugulam
- Department of Agronomy Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Majka M, Kwiatek MT, Majka J, Wiśniewska H. Aegilops tauschii Accessions with Geographically Diverse Origin Show Differences in Chromosome Organization and Polymorphism of Molecular Markers Linked to Leaf Rust and Powdery Mildew Resistance Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:1149. [PMID: 28702048 PMCID: PMC5487464 DOI: 10.3389/fpls.2017.01149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/15/2017] [Indexed: 06/02/2023]
Abstract
Aegilops tauschii (2n = 2x = 14) is a diploid wild species which is reported as a donor of the D-genome of cultivated bread wheat. The main goal of this study was to examine the differences and similarities in chromosomes organization among accessions of Ae. tauschii with geographically diversed origin, which is believed as a potential source of genes, especially determining resistance to fungal diseases (i.e., leaf rust and powdery mildew) for breeding of cereals. We established and compared the fluorescence in situ hybridization patterns of 21 accessions of Ae. tauschii using various repetitive sequences mainly from the BAC library of wheat cultivar Chinese Spring. Results obtained for Ae. tauschii chromosomes revealed many similarities between analyzed accessions, however, some hybridization patterns were specific for accessions, which become from cognate regions of the World. The most noticeable differences were observed for accessions from China which were characterized by presence of distinct signals of pTa-535 in the interstitial region of chromosome 3D, less intensity of pTa-86 signals in chromosome 2D, as well as lack of additional signals of pTa-86 in chromosomes 1D, 5D, or 6D. Ae. tauschii of Chinese origin appeared homogeneous and separate from landraces that originated in western Asia. Ae. tauschii chromosomes showed similar hybridization patterns to wheat D-genome chromosomes, but some differences were also observed among both species. What is more, we identified reciprocal translocation between short arm of chromosome 1D and long arm of chromosome 7D in accession with Iranian origin. High polymorphism between analyzed accessions and extensive allelic variation were revealed using molecular markers associated with resistance genes. Majority of the markers localized in chromosomes 1D and 2D showed the diversity of banding patterns between accessions. Obtained results imply, that there is a moderate or high level of polymorphism in the genome of Ae. tauschii determined by a geographical origin, which we proved by cytogenetic and molecular markers analysis. Therefore, selected accessions might constitute an accessible source of variation for improvement of Triticeae species like wheat and triticale.
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Affiliation(s)
- Maciej Majka
- Cereal Genomics Team, Department of Genomics, Institute of Plant Genetics, Polish Academy of SciencesPoznań, Poland
| | - Michał T. Kwiatek
- Cereal Genomics Team, Department of Genomics, Institute of Plant Genetics, Polish Academy of SciencesPoznań, Poland
| | - Joanna Majka
- Plant Molecular Physiology and Cytogenetics Team, Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of SciencesPoznań, Poland
| | - Halina Wiśniewska
- Cereal Genomics Team, Department of Genomics, Institute of Plant Genetics, Polish Academy of SciencesPoznań, Poland
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Tang Y, Kang HY, Tang L, Diao CD, Li DY, Zhu W, Fan X, Wang Y, Zeng J, Xu LL, Sha LN, Yu XF, Zhang HQ, Zhou YH. Phylogenetic analysis of tetraploid wheat based on nuclear DMC1 gene. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Kwiatek M, Majka M, Majka J, Belter J, Suchowilska E, Wachowska U, Wiwart M, Wiśniewska H. Intraspecific Polymorphisms of Cytogenetic Markers Mapped on Chromosomes of Triticum polonicum L. PLoS One 2016; 11:e0158883. [PMID: 27391447 PMCID: PMC4938433 DOI: 10.1371/journal.pone.0158883] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/23/2016] [Indexed: 01/23/2023] Open
Abstract
Triticum genus encloses several tetraploid species that are used as genetic stocks for expanding the genetic variability of wheat (Triticum aestivum L.). Although the T. aestivum (2n = 6x = 42, AABBDD) and T. durum (2n = 4x = 28, AABB) karyotypes were well examined by chromosome staining, Giemsa C-banding and FISH markers, other tetraploids are still poorly characterized. Here, we established and compared the fluorescence in situ hybridization (FISH) patterns on chromosomes of 20 accessions of T. polonicum species using different repetitive sequences from BAC library of wheat ‘Chinese Spring’. The chromosome patterns of Polish wheat were compared to tetraploid (2n = 4x = 28, AABB) Triticum species: T. durum, T. diccocon and T. turanicum, as well. A combination of pTa-86, pTa-535 and pTa-713 probes was the most informative among 6 DNA probes tested. Probe pTa-k374, which is similar to 28S rDNA sequence enabled to distinguish signal size and location differences, as well as rDNA loci elimination. Furthermore, pTa-465 and pTa-k566 probes are helpful for the detection of similar organized chromosomes. The polymorphisms of signals distribution were observed in 2A, 2B, 3B, 5B, 6A and 7B chromosomes. Telomeric region of the short arm of 6B chromosome was the most polymorphic. Our work is novel and contributes to the understanding of T. polonicum genome organization which is essential to develop successful advanced breeding strategies for wheat. Collection and characterization of this germplasm can contribute to the wheat biodiversity safeguard.
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Affiliation(s)
- Michał Kwiatek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
- * E-mail:
| | - Maciej Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Joanna Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Jolanta Belter
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Elżbieta Suchowilska
- Department of Plant Breeding and Seed Production, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 3, 10–727 Olsztyn, Poland
| | - Urszula Wachowska
- Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 3, 10–727 Olsztyn, Poland
| | - Marian Wiwart
- Department of Plant Breeding and Seed Production, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 3, 10–727 Olsztyn, Poland
| | - Halina Wiśniewska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
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Evtushenko EV, Levitsky VG, Elisafenko EA, Gunbin KV, Belousov AI, Šafář J, Doležel J, Vershinin AV. The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements. BMC Genomics 2016; 17:337. [PMID: 27146967 PMCID: PMC4857426 DOI: 10.1186/s12864-016-2667-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained. RESULTS Using a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences. The arrays show significant heterogeneity in monomer organization. 454 reads were used to gain a representation of the expansion of these tandem repeats across the whole rye genome. The presence of multiple, relatively short monomer arrays, coupled with the mainly star-like topology of the monomer phylogenetic trees, was taken as indicative of a rapid expansion of the pSc200 and pSc250 arrays. The evolution of subtelomeric heterochromatin appears to have included a significant contribution of illegitimate recombination. The composition of transposable elements (TEs) within the regions flanking the pSc200 and pSc250 arrays differed markedly from that in the genome a whole. Solo-LTRs were strongly enriched, suggestive of a history of active ectopic exchange. Several DNA motifs were over-represented within the LTR sequences. CONCLUSION The large blocks of subtelomeric heterochromatin have arisen from the combined activity of TEs and the expansion of the tandem repeats. The expansion was likely based on a highly complex network of recombination mechanisms.
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Affiliation(s)
- E V Evtushenko
- Institute of Molecular and Cellular Biology, Siberian Branch of the RAS, Novosibirsk, Russia
| | - V G Levitsky
- Institute of Cytology and Genetics, Siberian Branch of the RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - E A Elisafenko
- Institute of Cytology and Genetics, Siberian Branch of the RAS, Novosibirsk, Russia
| | - K V Gunbin
- Institute of Cytology and Genetics, Siberian Branch of the RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - A I Belousov
- Institute of Molecular and Cellular Biology, Siberian Branch of the RAS, Novosibirsk, Russia
| | - J Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - J Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - A V Vershinin
- Institute of Molecular and Cellular Biology, Siberian Branch of the RAS, Novosibirsk, Russia.
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Zhang J, Jiang Y, Guo Y, Li G, Yang Z, Xu D, Xuan P. Identification of Novel Chromosomal Aberrations Induced by (60)Co-γ-Irradiation in Wheat-Dasypyrum villosum Lines. Int J Mol Sci 2015; 16:29787-96. [PMID: 26694350 PMCID: PMC4691081 DOI: 10.3390/ijms161226134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/20/2015] [Accepted: 11/25/2015] [Indexed: 12/02/2022] Open
Abstract
Mutations induced by radiation are widely used for developing new varieties of plants. To better understand the frequency and pattern of irradiation-induced chromosomal rearrangements, we irradiated the dry seeds of Chinese Spring (CS)-Dasypyrum villosum nullisomic-tetrasomic (6A/6D) addition (6V) line (2n = 44), WD14, with (60)Co-γ-rays at dosages of 100, 200, and 300 Gy. The M₀ and M₁ generations were analyzed using Feulgen staining and non-denaturing fluorescence in situ hybridization (ND-FISH) by using oligonucleotide probes. Abnormal mitotic behavior and chromosomes with structural changes were observed in the M₀ plants. In all, 39 M₁ plants had structurally changed chromosomes, with the B genome showing the highest frequency of aberrations and tendency to recombine with chromosomes of the D genome. In addition, 19 M₁ plants showed a variation in chromosome number. The frequency of chromosome loss was considerably higher for 6D than for the alien chromosome 6V, indicating that 6D is less stable after irradiation. Our findings suggested that the newly obtained γ-induced genetic materials might be beneficial for future wheat breeding programs and functional gene analyses.
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Affiliation(s)
- Jie Zhang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, China.
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, China.
| | - Yuanlin Guo
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, China.
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Delin Xu
- Department of Cell Biology and Genetics, Zunyi Medical University, Zunyi 563000, Guizhou, China.
| | - Pu Xuan
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, China.
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China.
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Affiliation(s)
- R. A. McIntosh
- University of Sydney; Plant Breeding Institute; Castle Hill, N.S.W. Australia
| | - Jane E. Cusick
- University of Sydney; Plant Breeding Institute; Castle Hill, N.S.W. Australia
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Gornicki P, Zhu H, Wang J, Challa GS, Zhang Z, Gill BS, Li W. The chloroplast view of the evolution of polyploid wheat. THE NEW PHYTOLOGIST 2014; 204:704-714. [PMID: 25059383 DOI: 10.1111/nph.12931] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 06/07/2014] [Indexed: 05/20/2023]
Abstract
Polyploid wheats comprise four species: Triticum turgidum (AABB genomes) and T. aestivum (AABBDD) in the Emmer lineage, and T. timopheevii (AAGG) and T. zhukovskyi (AAGGA(m) A(m) ) in the Timopheevi lineage. Genetic relationships between chloroplast genomes were studied to trace the evolutionary history of the species. Twenty-five chloroplast genomes were sequenced, and 1127 plant accessions were genotyped, representing 13 Triticum and Aegilops species. The A. speltoides (SS genome) diverged before the divergence of T. urartu (AA), A. tauschii (DD) and the Aegilops species of the Sitopsis section. Aegilops speltoides forms a monophyletic clade with the polyploid Emmer and Timopheevi wheats, which originated within the last 0.7 and 0.4 Myr, respectively. The geographic distribution of chloroplast haplotypes of the wild tetraploid wheats and A. speltoides illustrates the possible geographic origin of the Emmer lineage in the southern Levant and the Timopheevi lineage in northern Iraq. Aegilops speltoides is the closest relative of the diploid donor of the chloroplast (cytoplasm), as well as the B and G genomes to Timopheevi and Emmer lineages. Chloroplast haplotypes were often shared by species or subspecies within major lineages and between the lineages, indicating the contribution of introgression to the evolution and domestication of polyploid wheats.
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Affiliation(s)
- Piotr Gornicki
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 E 58th St, Chicago, IL, 60637, USA
| | - Huilan Zhu
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
| | - Junwei Wang
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
| | - Ghana S Challa
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
| | - Zhengzhi Zhang
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, Manhattan, KS, 66506, USA
- Biotechnology Section, Faculty of Sciences, King Abdulaziz University, Jeddeh, Saudi Arabia
| | - Wanlong Li
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
- Department of Plant Science, South Dakota State University, 247 North Plain Biostress, Brookings, SD, 57007, USA
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Wang J, Zhang W, Zhao H, Li FR, Wang ZG, Ji J, Zhang XQ, Wang DW, Li JM. Molecular cytogenetic characterization of the Aegilops biuncialis karyotype. GENETICS AND MOLECULAR RESEARCH 2013; 12:683-92. [PMID: 23546950 DOI: 10.4238/2013.march.11.16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Aegilops biuncialis can be hybridized with wheat (Triticum spp) and has been used for wheat breeding and genetic studies. The A. biuncialis karyotype (U(b) U(b) M(b) M(b)) was investigated based on three A. biuncialis accessions grown in China. Two pairs of SAT chromosomes were identified as 1U(b) and 5U(b), with a karyotype formula of 2n = 4x = 28 = 14m + 10sm + 4st. Fluorescence in situ hybridization (FISH) and C-banding approaches were used to analyze the A. biuncialis accession chromosomes at the mitotic stage. Based on the C-banding and FISH patterns, all U(b) and M(b) chromosomes could be discriminated simultaneously; the three A. biuncialis accessions exhibited similar patterns, suggesting a common origin. The U(b) genome from A. biuncialis resembled the U genome in the diploid species A. umbellulata, and it may be related to the tetraploid species containing the U genome. The M(b) genome had some differences compared to the M genome in the diploid species A. comosa, and it may be related to the tetraploid species possessing the M genome. A generalized ideogram was proposed for the A. biuncialis genome, which could be useful for standardized and accurate identification of the A. biuncialis karyotype and chromosomes.
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Affiliation(s)
- J Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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Komuro S, Endo R, Shikata K, Kato A. Genomic and chromosomal distribution patterns of various repeated DNA sequences in wheat revealed by a fluorescence in situ hybridization procedure. Genome 2013; 56:131-7. [DOI: 10.1139/gen-2013-0003] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Wheat (Triticum aestivum L.) is an allohexaploid, in which each of the three genomes has a high 1C content. This indicates the presence of multiple tandemly repeated sequences, which should be detectable using in situ hybridization. Some repeats have already been described, but others remain to be recognized. To discover others, 2000 plasmid wheat clones were examined for signal presence after fluorescence in situ hybridization and microscopic signal observation. Among them, 47 clones produced strong discrete signals on wheat chromosomes. Two of the newly identified clones (pTa-535 and pTa-713) were determined to have especially valuable sequences for chromosome identification. In combination with pTa-86 (the pSc119 homologous sequence), these probes enable unambiguous discrimination of all wheat chromosomes including orientation. Four newly identified sequences (pTa-465, pTa-k566, pTa-s120, and pTa-s126) were useful in that they produced discrete signals on various wheat chromosome arms. Two other clones (pTa-k288 and pTa-k229) produced GISH-like (genomic in situ hybridization) signals because they allowed the A, B, and D genomes to be distinguished simultaneously. In addition, centromere, centromere-related, and ribosomal DNA clones were identified. Also described are improvements on slide preparation and reprobing procedures. To enhance discrete signal detection, a new direct fluorescent-labeling procedure, namely the VentR (exo-) terminal extension method, was employed.
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Affiliation(s)
- Shirabe Komuro
- Laboratory of Plant Breeding, Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto-shi, Kyoto-fu 606-0823, Japan
| | - Ryota Endo
- Laboratory of Plant Breeding, Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto-shi, Kyoto-fu 606-0823, Japan
| | - Kaori Shikata
- Laboratory of Plant Breeding, Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto-shi, Kyoto-fu 606-0823, Japan
| | - Akio Kato
- Laboratory of Plant Breeding, Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto-shi, Kyoto-fu 606-0823, Japan
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Salina EA, Sergeeva EM, Adonina IG, Shcherban AB, Belcram H, Huneau C, Chalhoub B. The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats. BMC PLANT BIOLOGY 2011; 11:99. [PMID: 21635794 PMCID: PMC3129301 DOI: 10.1186/1471-2229-11-99] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 06/03/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Transposable elements (TEs) are a rapidly evolving fraction of the eukaryotic genomes and the main contributors to genome plasticity and divergence. Recently, occupation of the A- and D-genomes of allopolyploid wheat by specific TE families was demonstrated. Here, we investigated the impact of the well-represented family of gypsy LTR-retrotransposons, Fatima, on B-genome divergence of allopolyploid wheat using the fluorescent in situ hybridisation (FISH) method and phylogenetic analysis. RESULTS FISH analysis of a BAC clone (BAC_2383A24) initially screened with Spelt1 repeats demonstrated its predominant localisation to chromosomes of the B-genome and its putative diploid progenitor Aegilops speltoides in hexaploid (genomic formula, BBAADD) and tetraploid (genomic formula, BBAA) wheats as well as their diploid progenitors. Analysis of the complete BAC_2383A24 nucleotide sequence (113,605 bp) demonstrated that it contains 55.6% TEs, 0.9% subtelomeric tandem repeats (Spelt1), and five genes. LTR retrotransposons are predominant, representing 50.7% of the total nucleotide sequence. Three elements of the gypsy LTR retrotransposon family Fatima make up 47.2% of all the LTR retrotransposons in this BAC. In situ hybridisation of the Fatima_2383A24-3 subclone suggests that individual representatives of the Fatima family contribute to the majority of the B-genome specific FISH pattern for BAC_2383A24. Phylogenetic analysis of various Fatima elements available from databases in combination with the data on their insertion dates demonstrated that the Fatima elements fall into several groups. One of these groups, containing Fatima_2383A24-3, is more specific to the B-genome and proliferated around 0.5-2.5 MYA, prior to allopolyploid wheat formation. CONCLUSION The B-genome specificity of the gypsy-like Fatima, as determined by FISH, is explained to a great degree by the appearance of a genome-specific element within this family for Ae. speltoides. Moreover, its proliferation mainly occurred in this diploid species before it entered into allopolyploidy.Most likely, this scenario of emergence and proliferation of the genome-specific variants of retroelements, mainly in the diploid species, is characteristic of the evolution of all three genomes of hexaploid wheat.
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Affiliation(s)
- Elena A Salina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Lavrentieva ave. 10, Novosibirsk, 630090, Russia
| | - Ekaterina M Sergeeva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Lavrentieva ave. 10, Novosibirsk, 630090, Russia
| | - Irina G Adonina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Lavrentieva ave. 10, Novosibirsk, 630090, Russia
| | - Andrey B Shcherban
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Lavrentieva ave. 10, Novosibirsk, 630090, Russia
| | - Harry Belcram
- UMR INRA 1165 - CNRS 8114 UEVE - Unite de Recherche en Genomique Vegetale (URGV), 2, rue Gaston Cremieux, CP5708, 91057 Evry cedex, France
| | - Cecile Huneau
- UMR INRA 1165 - CNRS 8114 UEVE - Unite de Recherche en Genomique Vegetale (URGV), 2, rue Gaston Cremieux, CP5708, 91057 Evry cedex, France
| | - Boulos Chalhoub
- UMR INRA 1165 - CNRS 8114 UEVE - Unite de Recherche en Genomique Vegetale (URGV), 2, rue Gaston Cremieux, CP5708, 91057 Evry cedex, France
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Ehtemam MH, Rahiminejad MR, Saeidi H, Tabatabaei BES, Krattinger SG, Keller B. Relationships among the A Genomes of Triticum L. species as evidenced by SSR markers, in Iran. Int J Mol Sci 2010; 11:4309-25. [PMID: 21151440 PMCID: PMC3000084 DOI: 10.3390/ijms11114309] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 10/06/2010] [Accepted: 10/22/2010] [Indexed: 11/16/2022] Open
Abstract
The relationships among 55 wheat accessions (47 accessions collected from Iran and eight accessions provided by the Institute of Plant Biology of the University of Zurich, Switzerland) belonging to eight species carrying A genome (Triticum monococcum L., T. boeoticum Boiss., T. urartu Tumanian ex Gandilyan, T. durum Desf., T. turgidum L., T. dicoccum Schrank ex Schübler, T. dicoccoides (Körn. ex Asch. & Graebner) Schweinf. and T. aestivum L.) were evaluated using 31 A genome specific microsatellite markers. A high level of polymorphism was observed among the accessions studied (PIC = 0.77). The highest gene diversity was revealed among T. durum genotypes, while the lowest genetic variation was found in T. dicoccoides accessions. The analysis of molecular variance (AMOVA) showed a significant genetic variance (75.56%) among these accessions, representing a high intra-specific genetic diversity within Triticum taxa in Iran. However, such a variance was not observed among their ploidy levels. Based on the genetic similarity analysis, the accessions collected from Iran were divided into two main groups: diploids and polyploids. The genetic similarity among the diploid and polyploid species was 0.85 and 0.89 respectively. There were no significant differences in A genome diversity from different geographic regions. Based on the genetic diversity analyses, we consider there is value in a greater sampling of each species in Iran to discover useful genes for breeding purposes.
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Affiliation(s)
- Mohammad Hosein Ehtemam
- Department of Biology, University of Isfahan, Isfahan, 81746-73441, Iran; E-Mails: (M.H.E.); (H.S.)
| | | | - Hojjatollah Saeidi
- Department of Biology, University of Isfahan, Isfahan, 81746-73441, Iran; E-Mails: (M.H.E.); (H.S.)
| | | | - Simon G. Krattinger
- Institute of Plant Biology, University of Zurich, Switzerland; E-Mails: (S.G.K.); (B.K.)
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, Switzerland; E-Mails: (S.G.K.); (B.K.)
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Kushnir U, Halloran GM. Evidence for AEGILOPS SHARONENSIS Eig as the Donor of the B Genome of Wheat. Genetics 2010; 99:495-512. [PMID: 17249127 PMCID: PMC1214517 DOI: 10.1093/genetics/99.3-4.495] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A number of lines of evidence are advanced for the candidacy of Aegilops sharonensis Eig as the donor of the B genome of wheat. The cytoplasm of Ae. sharonensis is compatible with tetraploid wheat Triticum turgidum dicoccoides, as evidenced by the high level of chromosome pairing and fertility of the amphiploid Ae. sharonensisxT. turgidum dicoccoides. Ae. sharonensis chromosomes exhibit high levels of pairing with those of the B genome of wheat in hybrids with Ph-deficient hexaploid wheat and low levels of homoeologous pairing with T. monococcum chromosomes.--The amphidiploid between Ae. sharonensis and T. monococcum is very similar to T. turgidum dicoccoides in spike, spikelet and grain morphology. The karyotype of Ae. sharonensis resembles more closely that of extrapolated B genome karyotypes of wheat than do the karyotypes of other proposed B-genome donor species of Aegilops. Because of distinctiveness in cytological affinity and karyotype morphology between Ae. sharonensis and Ae. longissima, a separate genome symbol S(sh) is proposed for the former species.
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Affiliation(s)
- U Kushnir
- School of Agriculture, University of Melbourne, Parkville, Victoria, Australia, 3052
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29
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Jan CC, Dvorák J, Qualset CO, Soliman KM. Selection and identification of a spontaneous alien chromosome translocation in wheat. Genetics 2010; 98:389-98. [PMID: 17249090 PMCID: PMC1214447 DOI: 10.1093/genetics/98.2.389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A wheat (Triticum aestivum L. emend Thell) disomic addition line (2n = 6x = 44), SH1-152-2, with a pair of Elytrigia pontica (Podp.) Holub 2n = 10x = 70 [syn. Agropyron elongatum (Host) P.B.] chromosomes controlling blue aleurone color was crossed with a short-statured spring wheat ;Sonora 64' (T. aestivum). Isoline pairs of blue-disomic addition lines and nonblue euploid lines were produced by selecting plants segregating for blue aleurone for 12 generations. Nineteen of 20 blue aleurone lines were 2n = 44 addition lines, and one had 2n = 42 chromosomes. Several lines of evidence showed that this line had a spontaneous translocation in which the beta arm of wheat chromosome 4A was replaced by an Elytrigia chromosome arm carrying the blue aleurone gene. The Elytrigia chromosome in SH1-152-2 appeared to be homologous with E. pontica chromosome 4el(1), which also carries the blue aleurone gene. It was concluded that the spontaneous translocation originated from simultaneous misdivision of univalents and subsequent reunion at the centromere of chromosome arm 4Aalpha with the Elytrigia chromosome arm.
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Affiliation(s)
- C C Jan
- Department of Agronomy and Range Science, University of California, Davis, California 95616
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30
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Muravenko OV, Zelenin AV. Chromosomal organization of the genomes of small-chromosome plants. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409110088] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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HENEEN WAHEEBK. Chromosomal polymorphism in isolated populations of Elymus (Agropyron) in the Aegean:. Hereditas 2009. [DOI: 10.1111/j.1601-5223.1977.tb01233.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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33
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LINDE-LAURSEN IB, BOTHMER ROLAND, JACOBSEN NIELS. Giemsa C-banding in Asiatic taxa of Hordeum section Stenostachys with notes on chromosome morphology. Hereditas 2009. [DOI: 10.1111/j.1601-5223.1980.tb01364.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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NIEMEYER HERMANNM, COPAJA SYLVIAV, BARRIA BERNARDITAN. The Triticeae as sources of hydroxamic acids, secondary metabolites in wheat conferring resistance against aphids. Hereditas 2008. [DOI: 10.1111/j.1601-5223.1992.tb00158.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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37
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LINDE-LAURSEN IB, FREDERIKSEN SIGNE. Comparison of the Giemsa C-banded karyotypes of Dasy-pyrum villosum (2x) and D. breviaristatum (4x) from Greece. Hereditas 2008. [DOI: 10.1111/j.1601-5223.1991.tb00330.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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38
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NIEMEYER HERMANNM, COPAJA SYLVIAV, BARRIA BERNARDITAN. The Triticeae as sources of hydroxamic acids, secondary metabolites in wheat conferring resistance against aphids. Hereditas 2008. [DOI: 10.1111/j.1601-5223.1992.tb00840.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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39
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Zoshchuk SA, Badaeva ED, Zoshchuk NV, Adonina IG, Shcherban’ AB, Salina EA. Intraspecific divergence in wheats of the Timopheevi group as revealed by in situ hybridization with tandem repeats of the Spelt1 and Spelt52 families. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407060063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Zhang P, Friebe B, Gill B, Park RF. Cytogenetics in the age of molecular genetics. ACTA ACUST UNITED AC 2007. [DOI: 10.1071/ar07054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
From the beginning of the 20th Century, we have seen tremendous advances in knowledge and understanding in almost all biological disciplines, including genetics, molecular biology, structural and functional genomics, and biochemistry. Among these advances, cytogenetics has played an important role. This paper details some of the important milestones of modern cytogenetics. Included are the historical role of cytogenetics in genetic studies in general and the genetics stocks produced using cytogenetic techniques. The basic biological questions cytogenetics can address and the important role and practical applications of cytogenetics in applied sciences, such as in agriculture and in breeding for disease resistance in cereals, are also discussed. The goal of this paper is to show that cytogenetics remains important in the age of molecular genetics, because it is inseparable from overall genome analysis. Cytogenetics complements studies in other disciplines within the field of biology and provides the basis for linking genetics, molecular biology and genomics research.
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Friebe B, Kynast RG, Zhang P, Qi L, Dhar M, Gill BS. Chromosome healing by addition of telomeric repeats in wheat occurs during the first mitotic divisions of the sporophyte and is a gradual process. Chromosome Res 2001; 9:137-46. [PMID: 11321369 DOI: 10.1023/a:1009283003903] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Alien gametocidal chromosomes cause extensive chromosome breakage prior to S-phase in the first mitotic division of gametophytes lacking the alien chromosome. The broken chromosomes may be healed either by addition of telomeric repeats in the gametophyte or undergo fusions to form dicentric or translocation chromosomes. We show that dicentric chromosomes undergo breakage fusion-bridge (BFB) cycles in the first few mitotic divisions of the sporophyte, are partially healed before the germ line differentiation regimen, and are healed completely in the ensuing gametophytic stage. The gametocidal factor on chromosome 4Mg of Aegilops geniculata was used to induce dicentrics involving the satellite chromosomes1B and 6B of wheat, Triticum aestivum. The dicentrics 1BS x 1BL-2AL x 2AS and 6BS x 6BL-4BL x 4BS initiated BFB cycles that ceased 2 to 4 weeks after seed germination. At the end of the BFB cycles, we observed deficient 1B and 6B chromosomes with breakpoints in proximal regions of the 1BL and 6BL arms. The process of chromosome healing was analyzed in root tip meristems, at meiotic metaphase I, and in the derived progenies by fluorescence in-situ hybridization analysis using a telomeric probe pAtT4. The results show that chromosome healing in wheat occurs during very early mitotic divisions in the sporophyte by de-novo addition of telomeric repeats and is a gradual process. Broken chromosome ends have to pass through several cell divisions in the sporophyte to acquire the full telomeric repeat length.
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Affiliation(s)
- B Friebe
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan 66506-5502, USA.
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Tsujimoto H, Yamada T, Hasegawa K, Usami N, Kojima T, Endo TR, Ogihara Y, Sasakuma T. Large-scale selection of lines with deletions in chromosome 1B in wheat and applications for fine deletion mapping. Genome 2001. [DOI: 10.1139/g01-039] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Terminal deletions of chromosome 1B in common wheat were selected on a large scale. The gametocidal gene of Aegilops cylindrica was used as the inducer of chromosome breakage. First, genes for endosperm storage proteins located on both arms of chromosome 1B were used as the selection markers. However, it was found that the chromosome breakage occurred during female gametogenesis, causing genotypic inconsistency between the embryo and endosperm. Thus, we isolated plants with terminal deletions in chromosome 1B by C-banding. Of 1327 plants examined, 128 showed aberrations in chromosome 1B: 47 in the short arm, 76 in the long arm, and 5 in both arms. The present deletions tended to have the breakpoint at more proximal regions than those produced previously by T.R. Endo and B.S. Gill. Using 33 deletion lines produced in this study and 34 lines previously produced, we mapped 39 RFLP loci and a nucleolar organizer region (NOR) on a specific region of chromosome 1B. The NOR was found to consist of two subregions with different repetitive units, which were termed NOR-B1d and NOR-B1p. Based on this fine deletion map and genotypic inconsistency between embryo and endosperm, the features of the gametocidal gene are discussed.Key words: deletion line, gametocidal gene, Triticum aestivum, deletion map, nucleolar organizer region.
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Friebe B, Kynast RG, Gill BS. Gametocidal factor-induced structural rearrangements in rye chromosomes added to common wheat. Chromosome Res 2001; 8:501-11. [PMID: 11032320 DOI: 10.1023/a:1009219722418] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The gametocidal factor on the Aegilops cylindrica chromosome 2Cc was used to induce and analyze the nature of chromosomal rearrangements in rye chromosomes added to wheat. For this purpose we isolated plants disomic for a given rye chromosome and monosomic for 2Cc and analyzed their progenies cytologically. Rearranged rye chromosomes were identified in 7% of the progenies and consisted of rye deficiencies (4.6%), wheat rye dicentric and rye ring chromosomes (1.8%), and terminal translocations (0.6%). The dicentric and ring chromosomes initiated breakage-fusion-bridge cycles (BFB) that ceased within a few weeks after germination as the result of chromosome healing. Of 56 rye deficiencies identified, after backcrossing and selfing, only 33 were recovered in either homozygous or heterozygous condition covering all rye chromosomes except 7R. The low recovery rate is probably caused by the presence of multiple rearrangements induced in the wheat genome that resulted in poor plant vigor and seed set, low transmission, and an underestimation of the frequency of wheat rye dicentric chromosomes. Genomic in-situ hybridization (GISH) analysis of the 33 recovered rye deficiencies revealed that 30 resulted from a single break in one chromosome arm followed by the loss of the segment distal to the breakpoint. Only three had a wheat segment attached distal to the breakpoint. Although some of the Gc-induced rye rearrangements were derived from BFB cycles, all of the recovered rye rearrangements were simple in structure. The healing of the broken chromosome ends was achieved either by the de-novo addition of telomeric repeats leading to deficiencies and telocentric chromosomes or by the fusion with other broken ends in the form of stable monocentric terminal translocation chromosomes.
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Affiliation(s)
- B Friebe
- Wheat Genetics Resources Center, Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan 66506-5502, USA.
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45
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Bálint AF, Kovács G, Sutka J. ORIGIN AND TAXONOMY OF WHEAT IN THE LIGHT OF RECENT RESEARCH. ACTA ACUST UNITED AC 2000. [DOI: 10.1556/aagr.48.2000.3.11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
There is still disagreement among scientists on the exact origin of common wheat (Triticum aestivum ssp. aestivum), one of the most important crops in the world. The first step in the development of the hexaploid aestivum group (ABD) may have been hybridisation between T. urartu (A), as pollinator, and a species related to the Sitopsis section of the Aegilops genus (S) as cytoplasm donor, leading to the creation of the tetraploid species T. turgidum ssp. dicoccoides (AB). The following step may have involved hybridisation between T. turgidum ssp. dicoccon (AB genome, cytoplasm donor), a descendant of T. turgidum ssp. dicoccoides, and Ae. tauschii (D genome, pollinator), resulting in the hexaploid species T. aestivum ssp. spelta (ABD) or some other hulled type. This form may have given rise to naked types, including T. aestivum ssp. aestivum (ABD). The ancestors of the tetraploid T. timopheevii (AG) may have been the diploid T. urartu (A genome, pollinator) and Ae. speltoides (S genome, cytoplasm donor). Species in the timopheevii group developed later than those in the turgidum group, as confirmed by the fact that the G genome is practically identical to the S genome of Ae. speltoides, while the more ancient B genome has undergone divergent evolution. Hybridisation between T. timopheevii (AG, cytoplasm donor) and T. monococcum (A m, pollinator) may have resulted in the species T. zhukovskyi (AGA m). Research into the relationships between the various species is of assistance in compiling the taxonomy of wheat and in avoiding misunderstandings arising from the fact that some species are known by two or more synonymous names.
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Affiliation(s)
- A. F. Bálint
- 1 Agricultural Research Institute of the Hungarian Academy of Sciences Martonvásár, Hungary
| | - G. Kovács
- 2 Agricultural Research Institute of the Hungarian Academy of Sciences Martonvásár, Hungary
| | - J. Sutka
- 3 Agricultural Research Institute of the Hungarian Academy of Sciences Martonvásár, Hungary
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Rodríguez S, Maestra B, Perera E, Díez M, Naranjo T. Pairing affinities of the B- and G-genome chromosomes of polyploid wheats with those of Aegilops speltoides. Genome 2000; 43:814-9. [PMID: 11081971 DOI: 10.1139/g00-055] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chromosome pairing at metaphase I was studied in different interspecific hybrids involving Aegilops speltoides (SS) and polyploid wheats Triticum timopheevii (AtAtGG), T. turgidum (AABB), and T. aestivum (AABBDD) to study the relationships between the S, G, and B genomes. Individual chromosomes and their arms were identified by means of C-banding. Pairing between chromosomes of the G and S genomes in T. timopheevii x Ae. speltoides (AtGS) hybrids reached a frequency much higher than pairing between chromosomes of the B and S genomes in T. turgidum x Ae. speltoides (ABS) hybrids and T. aestivum x Ae. speltoides (ABDS) hybrids, and pairing between B- and G-genome chromosomes in T. turgidum x T. timopheevii (AAtBG) hybrids or T. aestivum x T. timopheevii (AAtBGD) hybrids. These results support a higher degree of closeness of the G and S genomes to each other than to the B genome. Such relationships are consistent with independent origins of tetraploid wheats T. turgidum and T. timopheevii and with a more recent formation of the timopheevi lineage.
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Affiliation(s)
- S Rodríguez
- Departamento de Genética, Facultad de Biología, Universidad Complutense, Madrid, Spain
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Yan L, Bhave M, Fairclough R, Konik C, Rahman S, Appels R. The genes encoding granule-bound starch synthases at the waxy loci of the A, B, and D progenitors of common wheat. Genome 2000; 43:264-72. [PMID: 10791814 DOI: 10.1139/g99-117] [Citation(s) in RCA: 25] [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
Three genes encoding granule-bound starch synthase (wx-TmA, wx-TsB, and wx-TtD) have been isolated from Triticum monococcum (AA), and Triticum speltoides (BB), by the polymerase chain reaction (PCR) approach, and from Triticum tauschii (DD), by screening a genomic DNA library. Multiple sequence alignment indicated that the wx-TmA, wx-TsB, and wx-TtD genes had the same extron and (or) intron structure as the previously reported waxy gene from barley. The lengths of the three wx-TmA, wx-TsB, and wx-TtD genes were 2834 bp, 2826 bp, and 2893 bp, respectively, each covering 31 bp in the untranslated leader and the entire coding region consisting of 11 exons and 10 introns. The three genes had identical lengths of exons, except exonl, and shared over 95% identity with each other within the exon regions. The majority of introns were significantly variable in length and sequence, differing mainly in length (1-57 bp) as a result of insertion and (or) deletion events. The deduced amino acid sequence from these three genes indicated that the mature WX-TMA, -TSB, and -TTD proteins contained the same number of amino acids, but differed in predicted molecular weight and isoelectric point (pI) due to amino acid substitutions (13-18). The predicted physical characteristics of the WX proteins matched the respective proteins in wheat very closely, but the match was not perfect. Furthermore the exon5 sequences of the wx-TmA, wx-TsB, and wx-TtD genes were different from a cDNA encoding a waxy gene of common wheat previously reported. The striking difference was that an insertion of 11 amino acids occurred in the cDNA sequence that could not be observed in the exons of the A, B, and D genes. It was noted, however, that the 3' end of intron4 of these genes could account for the additional 11 amino acids. The sequence information from the available waxy genes identified the intron4-exon5-intron5 region as being diagnostic for sequence variation in waxy. The sequence variation in the waxy genes provides the basis for primer design to distinguish the respective genes in common wheat, and its progenitors, using PCR.
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Affiliation(s)
- L Yan
- School of Life Sciences and Technology, Victoria University of Technology, Melbourne, Australia
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48
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Wetzel JB, Rayburn AL. Use of fluorescence genomic in situ hybridization (GISH) to detect the presence of alien chromatin in wheat lines differing in nuclear DNA content. ACTA ACUST UNITED AC 2000. [DOI: 10.1002/1097-0320(20000901)41:1<36::aid-cyto5>3.0.co;2-o] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Daud HM, Gustafson JP. Molecular evidence forTriticum speltoidesas a B-genome progenitor of wheat (Triticum aestivum). Genome 1996; 39:543-8. [DOI: 10.1139/g96-069] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In polyploid wheat, the origin of the B-genome donor has remained relatively unknown in spite of a number of investigations attempting to identify the parental species. A project was designed to isolate and clone a genome-specific DNA sequence from Triticum speltoides L. to determine if that species could be the B-genome donor. A cloning scheme involving the prescreening of 1-kb fragments followed by colony, dot blot, and Southern blot hybridization screenings was used to isolate a speltoides-specific sequence (pSp89.XI). The methods used allowed for rapid isolation of a genome-specific sequence when screened against total DNA from closely related species. Subsequent analyses showed that the sequence was barely detected in any of the other genomes of the annual Sitopsis section. The results of dot blot and Southern blot analyses established that (i) the sequence pSP89.XI, specific to T. speltoides relative to the other species of the Sitopsis section, was present in the genomes of tetraploid and hexaploid wheat, (ii) the relative abundance of pSp89.XI seemed to decrease from the diploid to the polyploid wheats, and (iii) the existence of a related, but modified B genome in polyploid wheat compared with that in modern T. speltoides was probable. Key words : genome-specific, DNA.
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Nelson JC, Sorrells ME, Van Deynze AE, Lu YH, Atkinson M, Bernard M, Leroy P, Faris JD, Anderson JA. Molecular mapping of wheat: major genes and rearrangements in homoeologous groups 4, 5, and 7. Genetics 1995; 141:721-31. [PMID: 8647405 PMCID: PMC1206768 DOI: 10.1093/genetics/141.2.721] [Citation(s) in RCA: 249] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A molecular-marker linkage map of hexaploid wheat (Triticum aestivum L. em. Thell) provides a framework for integration with teh classical genetic map and a record of the chromosomal rearrangements involved in the evolution of this crop species. We have constructed restriction fragment length polymorphism (RFLP) maps of the A-, B-, and D-genome chromosomes of homoeologous groups 4, 5, and 7 of wheat using 114 F7 lines from a synthetic X cultivated wheat cross and clones from 10 DNA libraries. Chromosomal breakpoints for known ancestral reciprocal translocations involving these chromosomes and for a known pericentric inversion on chromosome 4A were localized by linkage and aneuploid analysis. Known genes mapped include the major vernalization genes Vrn1 and Vrn3 on chromosome arms 5AL and 5DL, the red-coleoptile gene Rc1 on 7AS, and presumptively the leaf-rust (Puccinia recondita f.sp. tritici) resistance gene Lr34 on 7DS and the kernel-hardness gene Ha on 5DS. RFLP markers previously obtained for powdery-mildew (Blumeria graminis f.sp. tritici) resistance genes Pm2 and Pm1 were localized on chromosome arms 5DS and 7AL.
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Affiliation(s)
- J C Nelson
- Department of Plant Breeding and Biometry, Cornell University, Ithaca, New York 14853, USA
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