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Lv R, Gou X, Li N, Zhang Z, Wang C, Wang R, Wang B, Yang C, Gong L, Zhang H, Liu B. Chromosome translocation affects multiple phenotypes, causes genome-wide dysregulation of gene expression, and remodels metabolome in hexaploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1564-1582. [PMID: 37265000 DOI: 10.1111/tpj.16338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Chromosomal rearrangements (CRs) may occur in newly formed polyploids due to compromised meiotic fidelity. Moreover, CRs can be more readily tolerated in polyploids allowing their longer-term retention and hence potential spreading/fixation within a lineage. The direct functional consequences of CRs in plant polyploids remain unexplored. Here, we identified a heterozygous individual from a synthetic allohexaploid wheat in which the terminal parts of the long-arms of chromosomes 2D (approximately 193 Mb) and 4A (approximately 167 Mb) were reciprocally translocated. Five homogeneous translocation lines including both unbalanced and balanced types were developed by selfing fertilization of the founder mutant (RT [2DL; 4AL]-ter/1, reciprocal translocation). We investigated impacts of these translocations on phenotype, genome-wide gene expression and metabolome. We find that, compared with sibling wild-type, CRs in the form of both unbalanced and balanced translocations induced substantial changes of gene expression primarily via trans-regulation in the nascent allopolyploid wheat. The CRs also manifested clear phenotypic and metabolic consequences. In particular, the genetically balanced, stable reciprocal translocations lines showed immediate enhanced reproductive fitness relative to wild type. Our results underscore the profound impact of CRs on gene expression in nascent allopolyploids with wide-ranging phenotypic and metabolic consequences, suggesting CRs are an important source of genetic variation that can be exploited for crop breeding.
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Affiliation(s)
- Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Changyi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruisi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunwu Yang
- 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
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Mayrose I, Lysak MA. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Genome Biol Evol 2020; 13:5923296. [PMID: 33566095 PMCID: PMC7875004 DOI: 10.1093/gbe/evaa220] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.
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Affiliation(s)
- Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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3
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Mandáková T, Pouch M, Brock JR, Al-Shehbaz IA, Lysak MA. Origin and Evolution of Diploid and Allopolyploid Camelina Genomes Were Accompanied by Chromosome Shattering. THE PLANT CELL 2019; 31:2596-2612. [PMID: 31451448 PMCID: PMC6881126 DOI: 10.1105/tpc.19.00366] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/06/2019] [Accepted: 08/26/2019] [Indexed: 05/20/2023]
Abstract
Complexes of diploid and polyploid species have formed frequently during the evolution of land plants. In false flax (Camelina sativa), an important hexaploid oilseed crop closely related to Arabidopsis (Arabidopsis thaliana), the putative parental species as well as the origin of other Camelina species remained unknown. By using bacterial artificial chromosome-based chromosome painting, genomic in situ hybridization, and multi-gene phylogenetics, we aimed to elucidate the origin and evolution of the polyploid complex. Genomes of diploid camelinas (Camelina hispida, n = 7; Camelina laxa, n = 6; and Camelina neglecta, n = 6) originated from an ancestral n = 7 genome. The allotetraploid genome of Camelina rumelica (n = 13, N6H) arose from hybridization between diploids related to C. neglecta (n = 6, N6) and C. hispida (n = 7, H), and the N subgenome has undergone a substantial post-polyploid fractionation. The allohexaploid genomes of C. sativa and Camelina microcarpa (n = 20, N6N7H) originated through hybridization between an auto-allotetraploid C. neglecta-like genome (n = 13, N6N7) and C. hispida (n = 7, H), and the three subgenomes have remained stable overall since the genome merger. Remarkably, the ancestral and diploid Camelina genomes were shaped by complex chromosomal rearrangements, resembling those associated with human disorders and resulting in the origin of genome-specific shattered chromosomes.plantcell;31/11/2596/FX1F1fx1.
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Affiliation(s)
- Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Milan Pouch
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jordan R Brock
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Ihsan A Al-Shehbaz
- Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, Missouri 63110
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Dhar MK, Kour J, Kaul S. Origin, Behaviour, and Transmission of B Chromosome with Special Reference to Plantago lagopus. Genes (Basel) 2019; 10:E152. [PMID: 30781667 PMCID: PMC6410184 DOI: 10.3390/genes10020152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 11/30/2022] Open
Abstract
B chromosomes have been reported in many eukaryotic organisms. These chromosomes occur in addition to the standard complement of a species. Bs do not pair with any of the A chromosomes and they have generally been considered to be non-essential and genetically inert. However, due to tremendous advancements in the technologies, the molecular composition of B chromosomes has been determined. The sequencing data has revealed that B chromosomes have originated from A chromosomes and they are rich in repetitive elements. In our laboratory, a novel B chromosome was discovered in Plantago lagopus. Using molecular cytogenetic techniques, the B chromosome was found to be composed of ribosomal DNA sequences. However, further characterization of the chromosome using next generation sequencing (NGS) etc. revealed that the B chromosome is a mosaic of sequences derived from A chromosomes, 5S ribosomal DNA (rDNA), 45S rDNA, and various types of repetitive elements. The transmission of B chromosome through the female sex track did not follow the Mendelian principles. The chromosome was found to have drive due to which it was perpetuating in populations. The present paper attempts to summarize the information on nature, transmission, and origin of B chromosomes, particularly the current status of our knowledge in P. lagopus.
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Affiliation(s)
- Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu-180006, India.
| | - Jasmeet Kour
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu-180006, India.
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu-180006, India.
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Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA, Masonbrink RE, Peterson DG, Wendel JF. The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1541. [PMID: 31827481 PMCID: PMC6890844 DOI: 10.3389/fpls.2019.01541] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/05/2019] [Indexed: 05/20/2023]
Abstract
One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n = 12 (the Hawaiian Kokia and the East African and Madagascan Gossypioides). We generated a high-quality genome sequence of Gossypioides kirkii (n = 12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n = 12) and Gossypium diploids (n = 13). Previous analysis demonstrated that the directionality of their reduced chromosome number was through large structural rearrangements. A series of structural rearrangements were identified comparing the de novo G. kirkii genome sequence to genome sequences of Gossypium, including chromosome fusions and inversions. Genome comparison between G. kirkii and Gossypium suggests that multiple steps are required to generate the extant structural differences.
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Affiliation(s)
- Joshua A. Udall
- Crop Germplasm Research, USDA, College Station, TX, United States
- *Correspondence: Joshua A. Udall, ; Jonathan F. Wendel,
| | - Evan Long
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Thiruvarangan Ramaraj
- National Center of Genome Resources, Santa Fe, NM, United States
- School of Computing, DePaul University, Chicago, IL, United States
| | | | - Daojun Yuan
- EEOB Department, Iowa State University, Ames, IA, United States
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | | | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Mark A. Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Rick E. Masonbrink
- Genome Informatics Facility, Iowa State University, Ames, IA, United States
| | - Daniel G. Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Jonathan F. Wendel
- EEOB Department, Iowa State University, Ames, IA, United States
- *Correspondence: Joshua A. Udall, ; Jonathan F. Wendel,
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Yu F, Wang P, Li X, Huang Y, Wang Q, Luo L, Jing Y, Liu X, Deng Z, Wu J, Yang Y, Chen R, Zhang M, Xu L. Characterization of chromosome composition of sugarcane in nobilization by using genomic in situ hybridization. Mol Cytogenet 2018; 11:35. [PMID: 29977338 PMCID: PMC5992832 DOI: 10.1186/s13039-018-0387-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/24/2018] [Indexed: 11/29/2022] Open
Abstract
Background Interspecific hybridization is an effective strategy for germplasm innovation in sugarcane. Nobilization refers to the breeding theory of development and utilization of wild germplasm. Saccharum spontaneum is the main donor of resistance and adaptive genes in the nobilization breeding process. Chromosome transfer in sugarcane is complicated; thus, research of different inheritance patterns can provide guidance for optimal sugarcane breeding. Results Through chromosome counting and genomic in situ hybridization, we found that six clones with 80 chromosomes were typical S. officinarum and four other clones with more than 80 chromosomes were interspecific hybrids between S. officinarum and S. spontaneum. These data support the classical view that S. officinarum is characterized by 2n = 80. In addition, genomic in situ hybridization showed that five F1 clones were products of a 2n + n transmission and one F1 clone was the product of an n + n transmission in clear pedigree noble hybrids between S. officinarum and S. spontaneum. Interestingly, Yacheng 75–408 and Yacheng 75–409 were the sibling lines of the F1 progeny from the same parents but with different genetic transmissions. Conclusions This is the first clear evidence of Loethers, Crystallina, Luohanzhe, Vietnam Niuzhe, and Nanjian Guozhe were typical S. officinarum by GISH. Furthermore, for the first time, we identified the chromosome transmission of six F1 hybrids between S. officinarum and S. spontaneum. These findings may provide a theoretical basis for germplasm innovation in sugarcane breeding and guidance for further sugarcane nobilization. Electronic supplementary material The online version of this article (10.1186/s13039-018-0387-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan Yu
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ping Wang
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueting Li
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongji Huang
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinnan Wang
- 2Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Ling Luo
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanfen Jing
- Sugarcane Research Institute of Yunnan Agriculture Science Academy, Kaiyuan, China
| | - Xinlong Liu
- Sugarcane Research Institute of Yunnan Agriculture Science Academy, Kaiyuan, China
| | - Zuhu Deng
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China.,4Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi University, Nanning, China
| | - Jiayun Wu
- 2Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Yongqing Yang
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rukai Chen
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muqing Zhang
- 4Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi University, Nanning, China
| | - Liangnian Xu
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
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Edet OU, Kim JS, Okamoto M, Hanada K, Takeda T, Kishii M, Gorafi YSA, Tsujimoto H. Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers. BMC Genet 2018; 19:18. [PMID: 29587653 PMCID: PMC5872505 DOI: 10.1186/s12863-018-0603-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/13/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. RESULTS We generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes. CONCLUSION The efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines.
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Affiliation(s)
- Offiong Ukpong Edet
- Arid Land Research Center, Tottori University, Tottori, Japan
- United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - June-Sik Kim
- RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074 Japan
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Tomoyuki Takeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Masahiro Kishii
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University, Tottori, Japan
- Agricultural Research Corporation (ARC), Wad Madani, Sudan
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Danilova TV, Akhunova AR, Akhunov ED, Friebe B, Gill BS. Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:317-330. [PMID: 28776783 DOI: 10.1111/tpj.13657] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/21/2017] [Accepted: 07/31/2017] [Indexed: 05/19/2023]
Abstract
During evolutionary history many grasses from the tribe Triticeae have undergone interspecific hybridization, resulting in allopolyploidy; whereas homoploid hybrid speciation was found only in rye. Homoeologous chromosomes within the Triticeae preserved cross-species macrocolinearity, except for a few species with rearranged genomes. Aegilops markgrafii, a diploid wild relative of wheat (2n = 2x = 14), has a highly asymmetrical karyotype that is indicative of chromosome rearrangements. Molecular cytogenetics and next-generation sequencing were used to explore the genome organization. Fluorescence in situ hybridization with a set of wheat cDNAs allowed the macrostructure and cross-genome homoeology of the Ae. markgrafii chromosomes to be established. Two chromosomes maintained colinearity, whereas the remaining were highly rearranged as a result of inversions and inter- and intrachromosomal translocations. We used sets of barley and wheat orthologous gene sequences to compare discrete parts of the Ae. markgrafii genome involved in the rearrangements. Analysis of sequence identity profiles and phylogenic relationships grouped chromosome blocks into two distinct clusters. Chromosome painting revealed the distribution of transposable elements and differentiated chromosome blocks into two groups consistent with the sequence analyses. These data suggest that introgressive hybridization accompanied by gross chromosome rearrangements might have had an impact on karyotype evolution and homoploid speciation in Ae. markgrafii.
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Affiliation(s)
- Tatiana V Danilova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Alina R Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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9
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Wicker T, Wing RA, Schubert I. Recurrent sequence exchange between homeologous grass chromosomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:747-59. [PMID: 26408412 DOI: 10.1111/tpj.13040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/03/2015] [Accepted: 09/14/2015] [Indexed: 05/10/2023]
Abstract
All grass species evolved from an ancestor that underwent a whole-genome duplication (WGD) approximately 70 million years ago. Interestingly, the short arms of rice chromosomes 11 and 12 (and independently their homologs in sorghum) were found to be much more similar to each other than other homeologous regions within the duplicated genome. Based on detailed analysis of rice chromosomes 11 and 12 and their homologs in seven grass species, we propose a mechanism that explains the apparently 'younger' age of the duplication in this region of the genome, assuming a small number of reciprocal translocations at the chromosome termini. In each case the translocations were followed by unbalanced transmission and subsequent lineage sorting of the involved chromosomes to offspring. Molecular dating of these translocation events also allowed us to date major chromosome 'fusions' in the evolutionary lineages that led to Brachypodium and Triticeae. Furthermore, we provide evidence that rice is exceptional regarding the evolution of chromosomes 11 and 12, inasmuch as in other species the process of sequence exchange between homeologous chromosomes ceased much earlier than in rice. We presume that random events rather than selective forces are responsible for the observed high similarity between the short arm ends of rice chromosomes 11 and 12.
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Affiliation(s)
- Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, D-06466, Germany
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
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10
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Huang Y, Wu J, Wang P, Lin Y, Fu C, Deng Z, Wang Q, Li Q, Chen R, Zhang M. Characterization of Chromosome Inheritance of the Intergeneric BC2 and BC3 Progeny between Saccharum spp. and Erianthus arundinaceus. PLoS One 2015. [PMID: 26196281 PMCID: PMC4510360 DOI: 10.1371/journal.pone.0133722] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Erianthus arundinaceus (E. arundinaceus) has many desirable agronomic traits for sugarcane improvement, such as high biomass, vigor, rationing ability, tolerance to drought, and water logging, as well as resistance to pests and disease. To investigate the introgression of the E. arundinaceus genome into sugarcane in the higher generations, intergeneric BC2 and BC3 progeny generated between Saccharum spp. and E. arundinaceus were studied using the genomic in situ hybridization (GISH) technique. The results showed that the BC2 and BC3 generations resulted from n + n chromosome transmission. Furthermore, chromosome translocation occurred at terminal fragments from the E. arundinaceus chromosome in some progeny of Saccharum spp. and E. arundinaceus. Notably, the translocated chromosomes could be stably transmitted to their progeny. This study illustrates the characterization of chromosome inheritance of the intergeneric BC2 and BC3 progeny between Saccharum spp. and E. arundinaceus. This work could provide more useful molecular cytogenetic information for the germplasm resources of E. arundinaceus, and may promote further understanding of the germplasm resources of E. arundinaceus for sugarcane breeders to accelerate its progress in sugarcane commercial breeding.
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Affiliation(s)
- Yongji Huang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayun Wu
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Ping Wang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanquan Lin
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cheng Fu
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Zuhu Deng
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Guangxi Collaborative Center for Sugarcane & Cane Sugar Industries, Guangxi, China
- * E-mail:
| | - Qinnan Wang
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Qiwei Li
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Rukai Chen
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muqing Zhang
- Guangxi Collaborative Center for Sugarcane & Cane Sugar Industries, Guangxi, China
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11
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Castillo A, Atienza SG, Martín AC. Fertility of CMS wheat is restored by two Rf loci located on a recombined acrocentric chromosome. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6667-77. [PMID: 25271260 PMCID: PMC4246193 DOI: 10.1093/jxb/eru388] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cytoplasmic male sterility (CMS) results from incompatibility between nuclear and cytoplasmic genomes, and is characterized by the inability to produce viable pollen. The restoration of male fertility generally involves the introgression of nuclear genes, termed restorers of fertility (Rf). CMS has been widely used for hybrid seed production in many crops but not in wheat, partly owing to the complex genetics of fertility restoration. In this study, an acrocentric chromosome that restores pollen fertility of CMS wheat in Hordeum chilense cytoplasm (msH1 system) is studied. The results show that this chromosome, of H. chilense origin and named H(ch)ac, originated from a complex reorganization of the short arm of chromosomes 1H(ch) (1H(ch)S) and 6H(ch) (6H(ch)S). Diversity arrays technology (DArT) markers and cytological analysis indicate that H(ch)ac is a kind of `zebra-like' chromosome composed of chromosome 1H(ch)S and alternate fragments of interstitial and distal regions of chromosome 6H(ch)S. PCR-based markers together with FISH, GISH, and meiotic pairing analysis support this result. A restorer of fertility gene, named Rf6H(ch)S, has been identified on the short arm of chromosome 6H(ch)S. Moreover, restoration by the addition of chromosome 1H(ch)S has been observed at a very low frequency and under certain environmental conditions. Therefore, the results indicate the presence of two Rf genes on the acrocentric chromosome: Rf6H(ch)S and Rf1H(ch)S, the restoration potential of Rf6H(ch)S being greater. The stable and high restoration of pollen fertility in the msH1 system is therefore the result of the interaction between these two restorer genes.
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Affiliation(s)
- Almudena Castillo
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, Córdoba E-14080, Spain
| | - Sergio G Atienza
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, Córdoba E-14080, Spain
| | - Azahara C Martín
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, Córdoba E-14080, Spain * Present address: John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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Song L, Jiang L, Han H, Gao A, Yang X, Li L, Liu W. Efficient induction of Wheat-agropyron cristatum 6P translocation lines and GISH detection. PLoS One 2013; 8:e69501. [PMID: 23874966 PMCID: PMC3707604 DOI: 10.1371/journal.pone.0069501] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 06/09/2013] [Indexed: 01/02/2023] Open
Abstract
The narrow genetic background restricts wheat yield and quality improvement. The
wild relatives of wheat are the huge gene pools for wheat improvement and can
broaden its genetic basis. Production of wheat-alien translocation lines can
transfer alien genes to wheat. So it is important to develop an efficient method
to induce wheat-alien chromosome translocation. Agropyroncristatum (P genome)
carries many potential genes beneficial to disease resistance, stress tolerance
and high yield. Chromosome 6P possesses the desirable genes
exhibiting good agronomic traits, such as high grain number per spike, powdery
mildew resistance and stress tolerance. In this study, the wheat-A. cristatum disomic addition was
used as bridge material to produce wheat-A. cristatum translocation lines
induced by 60Co-γirradiation. The results of genomic in
situ hybridization showed that 216 plants contained alien
chromosome translocation among 571 self-pollinated progenies. The frequency of
translocation was 37.83%, much higher than previous reports. Moreover, various
alien translocation types were identified. The analysis of M2 showed
that 62.5% of intergeneric translocation lines grew normally without losing the
translocated chromosomes. The paper reported a high efficient technical method
for inducing alien translocation between wheat and Agropyroncristatum. Additionally, these
translocation lines will be valuable for not only basic research on genetic
balance, interaction and expression of different chromosome segments of wheat
and alien species, but also wheat breeding programs to utilize superior
agronomic traits and good compensation effect from alien chromosomes.
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Affiliation(s)
- Liqiang Song
- National Key Facility for Crop Gene Resources and Genetic
Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing, China
| | - Lili Jiang
- National Key Facility for Crop Gene Resources and Genetic
Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing, China
| | - Haiming Han
- National Key Facility for Crop Gene Resources and Genetic
Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing, China
| | - Ainong Gao
- National Key Facility for Crop Gene Resources and Genetic
Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing, China
| | - Xinming Yang
- National Key Facility for Crop Gene Resources and Genetic
Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing, China
| | - Lihui Li
- National Key Facility for Crop Gene Resources and Genetic
Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing, China
- * E-mail: (WL)
| | - Weihua Liu
- National Key Facility for Crop Gene Resources and Genetic
Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing, China
- (LL)
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13
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In vitro culture and induced differentiation of sheep skeletal muscle satellite cells. Cell Biol Int 2012; 36:579-87. [PMID: 22233500 DOI: 10.1042/cbi20110487] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Skeletal muscle satellite cells are adult muscle-derived stem cells receiving increasing attention. Sheep satellite cells have a greater similarity to human satellite cells with regard to metabolism, life span, proliferation and differentiation, than satellite cells of the rat and mouse. We have used 2-step enzymatic digestion and differential adhesion methods to isolate and purify sheep skeletal muscle satellite cells, identified the cells and induced differentiation to examine their pluripotency. The most efficient method for the isolation of sheep skeletal muscle satellite cells was the type I collagenase and trypsin 2-step digestion method, with the best conditions for in vitro culture being in medium containing 20% FBS+10% horse serum. Immunofluorescence staining showed that satellite cells expressed Desmin, α-Sarcomeric Actinin, MyoD1, Myf5 and PAX7. After myogenic induction, multinucleated myotubes formed, as indicated by the expression of MyoG and fast muscle myosin. After osteogenic induction, cells expressed Osteocalcin, with Alizarin Red and ALP (alkaline phosphatase) staining results both being positive. After adipogenic induction, cells expressed PPARγ2 (peroxisome-proliferator-activated receptor γ2) and clear lipid droplets were present around the cells, with Oil Red-O staining giving a positive result. In summary, a successful system has been established for the isolation, purification and identification of sheep skeletal muscle satellite cells.
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Liu C, Qi L, Liu W, Zhao W, Wilson J, Friebe B, Gill BS. Development of a set of compensating Triticum aestivum-Dasypyrum villosum Robertsonian translocation lines. Genome 2011; 54:836-44. [PMID: 21961939 DOI: 10.1139/g11-051] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dasypyrum villosum (L.) Candargy, a wild relative of bread wheat ( Triticum aestivum L.), is the source of many agronomically important genes for wheat improvement. Production of compensating Robertsonian translocations (cRobTs), consisting of D. villosum chromosome arms translocated to homoeologous wheat chromosome arms, is one of the initial steps in exploiting this variation. The cRobTs for D. villosum chromosomes 1V, 4V, and 6V have been reported previously. Here we report attempted cRobTs for wheat - D. villosum chromosome combinations 2D/2V, 3D/3V, 5D/5V, and 7D/7V. The cRobTs for all D. villosum chromosomes were recovered except for the 2VS and 5VL arms. As was the case with the 6D/6V combination, no cRobTs involving 2D/2V chromosomes were recovered; instead, cRobT T2BS·2VL involving a nontargeted chromosome was recovered. All cRobTs are fertile, although the level of spike fertility and hundred kernel weight (HKW) varied among the lines. The set of cRobTs involving 12 of the 14 D. villosum chromosomes will be useful in wheat improvement programs. In fact, among the already reported cRobTs, T6AL·6VS carrying the Pm21 gene is deployed in agriculture and many useful genes have been reported on other cRobTs including resistance to stem rust race UG99 on T6AS·6VL.
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Affiliation(s)
- Cheng Liu
- Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, 66506-5502, USA
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15
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Qi LL, Pumphrey MO, Friebe B, Zhang P, Qian C, Bowden RL, Rouse MN, Jin Y, Gill BS. A novel Robertsonian translocation event leads to transfer of a stem rust resistance gene (Sr52) effective against race Ug99 from Dasypyrum villosum into bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:159-67. [PMID: 21437597 DOI: 10.1007/s00122-011-1574-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 03/11/2011] [Indexed: 05/21/2023]
Abstract
Stem rust (Puccinia graminis f. sp. tritici Eriks. & E. Henn.) (the causal agent of wheat stem rust) race Ug99 (also designated TTKSK) and its derivatives have defeated several important stem rust resistance genes widely used in wheat (Triticum aestivum L.) production, rendering much of the worldwide wheat acreage susceptible. In order to identify new resistance sources, a large collection of wheat relatives and genetic stocks maintained at the Wheat Genetic and Genomic Resources Center was screened. The results revealed that most accessions of the diploid relative Dasypyrum villosum (L.) Candargy were highly resistant. The screening of a set of wheat-D. villosum chromosome addition lines revealed that the wheat-D. villosum disomic addition line DA6V#3 was moderately resistant to race Ug99. The objective of the present study was to produce and characterize compensating wheat-D. villosum whole arm Robertsonian translocations (RobTs) involving chromosomes 6D of wheat and 6V#3 of D. villosum through the mechanism of centric breakage-fusion. Seven 6V#3-specific EST-STS markers were developed for screening F(2) progeny derived from plants double-monosomic for chromosomes 6D and 6V#3. Surprisingly, although 6D was the target chromosome, all recovered RobTs involved chromosome 6A implying a novel mechanism for the origin of RobTs. Homozygous translocations (T6AS·6V#3L and T6AL·6V#3S) with good plant vigor and full fertility were selected from F(3) families. A stem rust resistance gene was mapped to the long arm 6V#3L in T6AS·6V#3L and was designated as Sr52. Sr52 is temperature-sensitive and is most effective at 16°C, partially effective at 24°C, and ineffective at 28°C. The T6AS·6V#3L stock is a new source of resistance to Ug99, is cytogenetically stable, and may be useful in wheat improvement.
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Affiliation(s)
- L L Qi
- USDA-ARS, Northern Crop Science Lab, Fargo, ND 58102-2765, USA
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Abstract
B chromosomes are dispensable elements of the genome that do not recombine with the A chromosomes of the regular complement and that follow their own evolutionary pathway. Here, we survey current knowledge on the DNA/chromatin composition, origin, and drive mechanisms of B chromosomes and discuss the potential research applications of supernumerary chromosomes.
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Affiliation(s)
- Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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17
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Schubert I, Schubert V, Fuchs J. No evidence for "break-induced replication" in a higher plant - but break-induced conversion may occur. FRONTIERS IN PLANT SCIENCE 2011; 2:8. [PMID: 22639575 PMCID: PMC3355710 DOI: 10.3389/fpls.2011.00008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 03/23/2011] [Indexed: 05/16/2023]
Abstract
"Break-induced replication" (BIR) is considered as one way to repair DNA double-strand breaks (DSBs). BIR is defined as replication of the proximal break-ends up to the end of the broken chromosome using an undamaged (homologous) double-stranded template and mimicking a non-reciprocal translocation. This phenomenon was detected by genetic experiments in yeast. BIR is assumed to occur also in mammals, but experimental evidence is not yet at hand. We have studied chromosomes of the field bean, Vicia faba L., with respect to the occurrence of BIR after DSB induction during S and G2 phase. Simultaneous incorporation of the base analog ethynyldeoxyuridine (EdU) revealed no chromosomal replication pattern indicative of BIR. Thus, if occurring at all, BIR does not play a major role in DSB repair in higher plants with large chromosome arms. However, the frequency of interstitial asymmetric EdU incorporation within heterochromatic regions, visible on metaphase chromosomes, increased after chromosome breakage during S and G2 phase. Such asymmetric labeling could be interpreted as conservative replication up to the next replicon, circumventing a DSB, and yielding an interstitial conversion-like event.
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Affiliation(s)
- Ingo Schubert
- Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
- *Correspondence: Ingo Schubert, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, D-06466 Gatersleben, Germany. e-mail:
| | - Veit Schubert
- Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Jörg Fuchs
- Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
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18
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Xie S, Khan N, Ramanna MS, Niu L, Marasek-Ciolakowska A, Arens P, van Tuyl JM. An assessment of chromosomal rearrangements in neopolyploids of Lilium hybrids. Genome 2010; 53:439-46. [DOI: 10.1139/g10-018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two types of newly induced polyploids (neopolyploids) of Lilium hybrids were monitored for the occurrence of chromosomal rearrangements through genomic in situ hybridization (GISH) technique. One of the populations was obtained through crossing an allotriploid Longiflorum × Oriental hybrid (LLO) with an allotetraploid Longiflorum × Trumpet hybrid (LLTT), both of which were derived from somatic chromosome doubling. The other type of allopolyploid population was derived from meiotic chromosome doubling in which numerically unreduced (2n) gametes from two different interspecific hybrids, namely, Longiflorum × Asiatic (LA) and Oriental × Asiatic (OA), were used to get backcross progeny with the Asiatic parents. GISH clearly discriminated the three constituent genomes (L, T, and O) in the complements of the progeny obtained from mitotic chromosome doubling. A total of 26 individuals were analyzed from this population and there was no evidence of chromosomal rearrangements. However, in the case of meiotically doubled allopolyploid progeny, considerable frequencies of chromosomal rearrangements were observed through GISH. The so-called chromosomal rearrangements in meiotic polyploids are the result of homoeologous recombination rather than translocations. Furthermore, evidence for the occurrence of meiotic recombination in the LA hybrids has been confirmed with GISH on meiotic chromosomes. Thus, there was evidence that neopolyploids of Lilium hybrids did not possess any noticeable chromosome rearrangements.
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Affiliation(s)
- Songlin Xie
- College of Horticulture, Northwest A&F University, Yangling Shaanxi 712100, People’s Republic of China
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
- Research Institute of Pomology and Floriculture, Department of Physiology and Biochemistry, Pomologiczna Str. 18, 96-100 Skierniewice, Poland
| | - Nadeem Khan
- College of Horticulture, Northwest A&F University, Yangling Shaanxi 712100, People’s Republic of China
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
- Research Institute of Pomology and Floriculture, Department of Physiology and Biochemistry, Pomologiczna Str. 18, 96-100 Skierniewice, Poland
| | - M. S. Ramanna
- College of Horticulture, Northwest A&F University, Yangling Shaanxi 712100, People’s Republic of China
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
- Research Institute of Pomology and Floriculture, Department of Physiology and Biochemistry, Pomologiczna Str. 18, 96-100 Skierniewice, Poland
| | - Lixin Niu
- College of Horticulture, Northwest A&F University, Yangling Shaanxi 712100, People’s Republic of China
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
- Research Institute of Pomology and Floriculture, Department of Physiology and Biochemistry, Pomologiczna Str. 18, 96-100 Skierniewice, Poland
| | - Agnieszka Marasek-Ciolakowska
- College of Horticulture, Northwest A&F University, Yangling Shaanxi 712100, People’s Republic of China
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
- Research Institute of Pomology and Floriculture, Department of Physiology and Biochemistry, Pomologiczna Str. 18, 96-100 Skierniewice, Poland
| | - Paul Arens
- College of Horticulture, Northwest A&F University, Yangling Shaanxi 712100, People’s Republic of China
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
- Research Institute of Pomology and Floriculture, Department of Physiology and Biochemistry, Pomologiczna Str. 18, 96-100 Skierniewice, Poland
| | - Jaap M. van Tuyl
- College of Horticulture, Northwest A&F University, Yangling Shaanxi 712100, People’s Republic of China
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
- Research Institute of Pomology and Floriculture, Department of Physiology and Biochemistry, Pomologiczna Str. 18, 96-100 Skierniewice, Poland
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