1
|
Naish M, Henderson IR. The structure, function, and evolution of plant centromeres. Genome Res 2024; 34:161-178. [PMID: 38485193 PMCID: PMC10984392 DOI: 10.1101/gr.278409.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Centromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem repeats (satellites), and/or specific families of transposons. The functional region of the centromere is defined by loading of a specific histone 3 variant (CENH3), which nucleates the kinetochore and shows dynamic regulation. In many plants, the centromeres are composed of satellite repeat arrays that are densely DNA methylated and invaded by centrophilic retrotransposons. In some cases, the retrotransposons become the sites of CENH3 loading. We review the structure of plant centromeres, including monocentric, holocentric, and metapolycentric architectures, which vary in the number and distribution of kinetochore attachment sites along chromosomes. We discuss how variation in CENH3 loading can drive genome elimination during early cell divisions of plant embryogenesis. We review how epigenetic state may influence centromere identity and discuss evolutionary models that seek to explain the paradoxically rapid change of centromere sequences observed across species, including the potential roles of recombination. We outline putative modes of selection that could act within the centromeres, as well as the role of repeats in driving cycles of centromere evolution. Although our primary focus is on plant genomes, we draw comparisons with animal and fungal centromeres to derive a eukaryote-wide perspective of centromere structure and function.
Collapse
Affiliation(s)
- Matthew Naish
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| |
Collapse
|
2
|
Puchta H, Houben A. Plant chromosome engineering - past, present and future. THE NEW PHYTOLOGIST 2024; 241:541-552. [PMID: 37984056 DOI: 10.1111/nph.19414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
Spontaneous chromosomal rearrangements (CRs) play an essential role in speciation, genome evolution and crop domestication. To be able to use the potential of CRs for breeding, plant chromosome engineering was initiated by fragmenting chromosomes by X-ray irradiation. With the rise of the CRISPR/Cas system, it became possible to induce double-strand breaks (DSBs) in a highly efficient manner at will at any chromosomal position. This has enabled a completely new level of predesigned chromosome engineering. The genetic linkage between specific genes can be broken by inducing chromosomal translocations. Natural inversions, which suppress genetic exchange, can be reverted for breeding. In addition, various approaches for constructing minichromosomes by downsizing regular standard A or supernumerary B chromosomes, which could serve as future vectors in plant biotechnology, have been developed. Recently, a functional synthetic centromere could be constructed. Also, different ways of genome haploidization have been set up, some based on centromere manipulations. In the future, we expect to see even more complex rearrangements, which can be combined with previously developed engineering technologies such as recombinases. Chromosome engineering might help to redefine genetic linkage groups, change the number of chromosomes, stack beneficial genes on mini cargo chromosomes, or set up genetic isolation to avoid outcrossing.
Collapse
Affiliation(s)
- Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP) - Molecular Biology, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| |
Collapse
|
3
|
Zhang J, Fan C, Liu Y, Shi Q, Sun Y, Huang Y, Yuan J, Han F. Cytological analysis of the diploid-like inheritance of newly synthesized allotetraploid wheat. Chromosome Res 2023; 32:1. [PMID: 38108925 DOI: 10.1007/s10577-023-09745-5] [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: 06/07/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
Polyploidization is a process which is related to species hybridization and whole genome duplication. It is widespread among angiosperm evolution and is essential for speciation and diversification. Allopolyploidization is mainly derived from interspecific hybridization and is believed to pose chromosome imbalances and genome instability caused by meiotic irregularity. However, the self-compatible allopolyploid in wild nature is cytogenetically and genetically stable. Whether this stabilization form was achieved in initial generation or a consequence of long term of evolution was largely unknown. Here, we synthesized a series of nascent allotetraploid wheat derived from three diploid genomes of A, S*, and D. The chromosome numbers of the majority of the progeny derived from these newly formed allotetraploid wheat plants were found to be relatively consistent, with each genome containing 14 chromosomes. In meiosis, bivalent was the majority of the chromosome configuration in metaphase I which supports the stable chromosome number inheritance in the nascent allotetraploid. These findings suggest that diploidization occurred in the newly formed synthetic allotetraploid wheat. However, we still detected aneuploids in a proportion of newly formed allotetraploid wheat, and meiosis of these materials present more irregular chromosome behavior than the euploid. We found that centromere pairing and centromere clustering in meiosis was affected in the aneuploids, which suggest that aneuploidy may trigger the irregular interactions of centromere in early meiosis which may take participate in promoting meiosis stabilization in newly formed allotetraploid wheat.
Collapse
Affiliation(s)
- Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaolan Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qinghua Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yishuang Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
4
|
Zhang T, Zhao SH, Wang Y, He Y. FIGL1 coordinates with dosage-sensitive BRCA2 in modulating meiotic recombination in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2107-2121. [PMID: 37293848 DOI: 10.1111/jipb.13541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Meiotic crossover (CO) formation between homologous chromosomes ensures their subsequent proper segregation and generates genetic diversity among offspring. In maize, however, the mechanisms that modulate CO formation remain poorly characterized. Here, we found that both maize BREAST CANCER SUSCEPTIBILITY PROTEIN 2 (BRCA2) and AAA-ATPase FIDGETIN-LIKE-1 (FIGL1) act as positive factors of CO formation by controlling the assembly or/and stability of two conserved DNA recombinases RAD51 and DMC1 filaments. Our results revealed that ZmBRCA2 is not only involved in the repair of DNA double-stranded breaks (DSBs), but also regulates CO formation in a dosage-dependent manner. In addition, ZmFIGL1 interacts with RAD51 and DMC1, and Zmfigl1 mutants had a significantly reduced number of RAD51/DMC1 foci and COs. Further, simultaneous loss of ZmFIGL1 and ZmBRCA2 abolished RAD51/DMC1 foci and exacerbated meiotic defects compared with the single mutant Zmbrca2 or Zmfigl1. Together, our data demonstrate that ZmBRCA2 and ZmFIGL1 act coordinately to regulate the dynamics of RAD51/DMC1-dependent DSB repair to promote CO formation in maize. This conclusion is surprisingly different from the antagonistic roles of BRCA2 and FIGL1 in Arabidopsis, implying that, although key factors that control CO formation are evolutionarily conserved, specific characteristics have been adopted in diverse plant species.
Collapse
Affiliation(s)
- Ting Zhang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shuang-Hui Zhao
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yan Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| |
Collapse
|
5
|
Tan EH, Ordoñez B, Thondehaalmath T, Seymour DK, Maloof JN, Maruthachalam R, Comai L. Establishment and inheritance of minichromosomes from Arabidopsis haploid induction. Chromosoma 2023:10.1007/s00412-023-00788-5. [PMID: 36964786 DOI: 10.1007/s00412-023-00788-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/26/2023]
Abstract
Minichromosomes are small, sometimes circular, rearranged chromosomes consisting of one centromere and short chromosomal arms formed by treatments that break DNA, including plant transformation. Minichromosomes have the potential to serve as vectors to quickly move valuable genes across a wide range of germplasm, including into adapted crop varieties. To realize this potential, minichromosomes must be reliably generated, easily manipulated, and stably inherited. Here we show a reliable method for minichromosome formation in haploids resulting from CENH3-mediated genome elimination, a process that generates genome instability and karyotypic novelty specifically on one parental genome. First, we identified 2 out of 260 haploids, each containing a single-copy minichromosome originating from centromeric regions of chromosomes 1 and 3, respectively. The chromosome 1 minichromosome we characterized did not pair at meiosis but displayed consistent transmission over nine selfing generations. Next, we demonstrated that CENH3-based haploid induction can produce minichromosomes in a targeted manner. Haploid inducers carrying a selectable pericentromeric marker were used to isolate additional chromosome-specific minichromosomes, which occurred in 3 out of 163 haploids. Our findings document the formation of heritable, rearranged chromosomes, and we provide a method for convenient minichromosome production.
Collapse
Affiliation(s)
- Ek Han Tan
- Plant Biology and Genome Center, University of California, 1 Shields Avenue, DavisDavis, CA, 95616, USA
- School of Biology and Ecology, University of Maine, Presque Isle, Orono, ME, 04469, USA
| | - Benny Ordoñez
- Plant Biology and Genome Center, University of California, 1 Shields Avenue, DavisDavis, CA, 95616, USA
| | - Tejas Thondehaalmath
- School of Biology, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Danelle K Seymour
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Julin N Maloof
- Plant Biology and Genome Center, University of California, 1 Shields Avenue, DavisDavis, CA, 95616, USA
| | - Ravi Maruthachalam
- School of Biology, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Luca Comai
- Plant Biology and Genome Center, University of California, 1 Shields Avenue, DavisDavis, CA, 95616, USA.
| |
Collapse
|
6
|
Yao M, Wang X, Long J, Bai S, Cui Y, Wang Z, Liu C, Liu F, Wang Z, Li Q. Identification of Key Modules and Candidate Genes for Powdery Mildew Resistance of Wheat-Agropyron cristatum Translocation Line WAT-2020-17-6 by WGCNA. PLANTS (BASEL, SWITZERLAND) 2023; 12:335. [PMID: 36679048 PMCID: PMC9864619 DOI: 10.3390/plants12020335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
As one of the serious diseases of wheat, powdery mildew (Blumeria graminis f. sp. tritici) is a long-term threat to wheat production. Therefore, it is of great significance to explore new powdery mildew-resistant genes for breeding. The wild relative species of wheat provide gene resources for resistance to powdery mildew breeding. Agropyron cristatum (2n = 4x = 28, genomes PPPP) is an important wild relative of wheat, carrying excellent genes for high yield, disease resistance, and stress resistance, which can be used for wheat improvement. To understand the molecular mechanism of powdery mildew resistance in the wheat-A. cristatum translocation line WAT2020-17-6, transcriptome sequencing was performed, and the resistance genes were analyzed by weighted gene co-expression network analysis (WGCNA). In the results, 42,845 differentially expressed genes were identified and divided into 18 modules, of which six modules were highly correlated with powdery mildew resistance. Gene ontology (GO) enrichment analysis showed that the six interested modules related to powdery mildew resistance were significantly enriched in N-methyltransferase activity, autophagy, mRNA splicing via spliceosome, chloroplast envelope, and AMP binding. The candidate hub genes of the interested modules were further identified, and their regulatory relationships were analyzed based on co-expression data. The temporal expression pattern of the 12 hub genes was verified within 96 h after powdery mildew inoculation by RT-PCR assay. In this study, we preliminarily explained the resistance mechanism of the wheat-A. cristatum translocation lines and obtained the hub candidate genes, which laid a foundation in the exploration of resistance genes in A. cristatum for powdery mildew-resistant breeding in wheat.
Collapse
Affiliation(s)
- Mingming Yao
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Xinhua Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaohui Long
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Shuangyu Bai
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Yuanyuan Cui
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Zhaoyi Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Caixia Liu
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Fenglou Liu
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Zhangjun Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Qingfeng Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| |
Collapse
|
7
|
Guo W, Comai L, Henry IM. Chromoanagenesis in plants: triggers, mechanisms, and potential impact. Trends Genet 2023; 39:34-45. [PMID: 36055901 DOI: 10.1016/j.tig.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022]
Abstract
Chromoanagenesis is a single catastrophic event that involves, in most cases, localized chromosomal shattering and reorganization, resulting in a dramatically restructured chromosome. First discovered in cancer cells, it has since been observed in various other systems, including plants. In this review, we discuss the origin, characteristics, and potential mechanisms underlying chromoanagenesis in plants. We report that multiple processes, including mutagenesis and genetic engineering, can trigger chromoanagenesis via a variety of mechanisms such as micronucleation, breakage-fusion-bridge (BFB) cycles, or chain-like translocations. The resulting rearranged chromosomes can be preserved during subsequent plant growth, and sometimes inherited to the next generation. Because of their high tolerance to genome restructuring, plants offer a unique system for investigating the evolutionary consequences and potential practical applications of chromoanagenesis.
Collapse
Affiliation(s)
- Weier Guo
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Luca Comai
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Genome Center and Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
| |
Collapse
|
8
|
Gomide MDS, Leitão MDC, Coelho CM. Biocircuits in plants and eukaryotic algae. FRONTIERS IN PLANT SCIENCE 2022; 13:982959. [PMID: 36212277 PMCID: PMC9545776 DOI: 10.3389/fpls.2022.982959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As one of synthetic biology's foundations, biocircuits are a strategy of genetic parts assembling to recognize a signal and to produce a desirable output to interfere with a biological function. In this review, we revisited the progress in the biocircuits technology basis and its mandatory elements, such as the characterization and assembly of functional parts. Furthermore, for a successful implementation, the transcriptional control systems are a relevant point, and the computational tools help to predict the best combinations among the biological parts planned to be used to achieve the desirable phenotype. However, many challenges are involved in delivering and stabilizing the synthetic structures. Some research experiences, such as the golden crops, biosensors, and artificial photosynthetic structures, can indicate the positive and limiting aspects of the practice. Finally, we envision that the modulatory structural feature and the possibility of finer gene regulation through biocircuits can contribute to the complex design of synthetic chromosomes aiming to develop plants and algae with new or improved functions.
Collapse
Affiliation(s)
- Mayna da Silveira Gomide
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
- School of Medicine, Federal University of Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | - Matheus de Castro Leitão
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
| |
Collapse
|
9
|
Kan M, Huang T, Zhao P. Artificial chromosome technology and its potential application in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:970943. [PMID: 36186059 PMCID: PMC9519882 DOI: 10.3389/fpls.2022.970943] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Plant genetic engineering and transgenic technology are powerful ways to study the function of genes and improve crop yield and quality in the past few years. However, only a few genes could be transformed by most available genetic engineering and transgenic technologies, so changes still need to be made to meet the demands for high throughput studies, such as investigating the whole genetic pathway of crop traits and avoiding undesirable genes simultaneously in the next generation. Plant artificial chromosome (PAC) technology provides a carrier which allows us to assemble multiple and specific genes to produce a variety of products by minichromosome. However, PAC technology also have limitations that may hinder its further development and application. In this review, we will introduce the current state of PACs technology from PACs formation, factors on PACs formation, problems and potential solutions of PACs and exogenous gene(s) integration.
Collapse
Affiliation(s)
- Manman Kan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Panpan Zhao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| |
Collapse
|
10
|
Venter JC, Glass JI, Hutchison CA, Vashee S. Synthetic chromosomes, genomes, viruses, and cells. Cell 2022; 185:2708-2724. [DOI: 10.1016/j.cell.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 10/17/2022]
|
11
|
Abstract
The supernumerary B chromosome of maize is dispensable, containing no vital genes, and thus is variable in number and presence in lines of maize. In order to be maintained in populations, it has a drive mechanism consisting of nondisjunction at the pollen mitosis that produces the two sperm cells, and then the sperm with the two B chromosomes has a preference for fertilizing the egg as opposed to the central cell in the process of double fertilization. The sequence of the B chromosome coupled with B chromosomal aberrations has localized features involved with nondisjunction and preferential fertilization, which are present at the centromeric region. The predicted genes from the sequence have paralogues dispersed across all A chromosomes and have widely different divergence times suggesting that they have transposed to the B chromosome over evolutionary time followed by degradation or have been co-opted for the selfish functions of the supernumerary chromosome.
Collapse
Affiliation(s)
- James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
12
|
The r-X1 deletion induces terminal deficiencies in the maize B chromosome. Chromosome Res 2021; 29:351-360. [PMID: 34480269 DOI: 10.1007/s10577-021-09671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 10/20/2022]
Abstract
In addition to causing the nondisjunction of maize B and normal A chromosomes at the second megaspore division during embryo sac development, the r-X1 deletion results in terminal deficiencies (TDs) in various A chromosomal arms, but whether the r-X1 deletion also induces TDs of the maize B chromosome remains unknown. To answer this question, the chromosomal composition in the r-X1-containing progeny of r-X1/R-r female parents carrying two standard B chromosomes was determined. Nine of 104 (8.7%) examined kernels contained a smaller telocentric B chromosome, and one of these (designated Bdef-1) was further identified as a TD with a breakpoint in the third distal heterochromatic region of the B chromosome. Thus, the results indicated that the r-X1 deletion could also induce TDs of the maize B chromosome during megaspore divisions. The Bdef-1 chromosome lacked nondisjunctional behavior, and this behavior was restored by the presence of the B chromosome in the cell. A transmission analysis of the Bdef-1 chromosome revealed that loss of the distal portion of the B chromosome reduced female but not male transmission of the B chromosome. Furthermore, the Bdef-1 chromosome was used to more finely map B-derived miRNA genes on the B chromosome. Our results indicate that the r-X1 deletion results in TDs of the B chromosome in maize, and the r-X1 deletion system can thus be used to generate a series of terminally truncated B chromosomes that may be used to map features of the B chromosome, including genes and properties related to B chromosome functions.
Collapse
|
13
|
Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution. Proc Natl Acad Sci U S A 2021; 118:2104254118. [PMID: 34088847 PMCID: PMC8201846 DOI: 10.1073/pnas.2104254118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
B chromosomes are enigmatic elements in thousands of plant and animal genomes that persist in populations despite being nonessential. They circumvent the laws of Mendelian inheritance but the molecular mechanisms underlying this behavior remain unknown. Here we present the sequence, annotation, and analysis of the maize B chromosome providing insight into its drive mechanism. The sequence assembly reveals detailed locations of the elements involved with the cis and trans functions of its drive mechanism, consisting of nondisjunction at the second pollen mitosis and preferential fertilization of the egg by the B-containing sperm. We identified 758 protein-coding genes in 125.9 Mb of B chromosome sequence, of which at least 88 are expressed. Our results demonstrate that transposable elements in the B chromosome are shared with the standard A chromosome set but multiple lines of evidence fail to detect a syntenic genic region in the A chromosomes, suggesting a distant origin. The current gene content is a result of continuous transfer from the A chromosomal complement over an extended evolutionary time with subsequent degradation but with selection for maintenance of this nonvital chromosome.
Collapse
|
14
|
Zhang T, Jing JL, Liu L, He Y. ZmRAD17 Is Required for Accurate Double-Strand Break Repair During Maize Male Meiosis. FRONTIERS IN PLANT SCIENCE 2021; 12:626528. [PMID: 33719299 PMCID: PMC7952653 DOI: 10.3389/fpls.2021.626528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
RAD17, a replication factor C (RFC)-like DNA damage sensor protein, is involved in DNA checkpoint control and required for both meiosis and mitosis in yeast and mammals. In plant, the meiotic function of RAD17 was only reported in rice so far. Here, we identified and characterized the RAD17 homolog in maize. The Zmrad17 mutants exhibited normal vegetative growth but male was partially sterile. In Zmrad17 pollen mother cells, non-homologous chromosome entanglement and chromosome fragmentation were frequently observed. Immunofluorescence analysis manifested that DSB formation occurred as normal and the loading pattern of RAD51 signals was similar to wild-type at the early stage of prophase I in the mutants. The localization of the axial element ASY1 was normal, while the assembly of the central element ZYP1 was severely disrupted in Zmrad17 meiocytes. Surprisingly, no obvious defect in female sterility was observed in Zmrad17 mutants. Taken together, our results suggest that ZmRAD17 is involved in DSB repair likely by promoting synaptonemal complex assembly in maize male meiosis. These phenomena highlight a high extent of divergence from its counterpart in rice, indicating that the RAD17 dysfunction can result in a drastic dissimilarity in meiotic outcome in different plant species.
Collapse
Affiliation(s)
- Ting Zhang
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Ju-Li Jing
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Lei Liu
- Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, Beijing, China
| | - Yan He
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| |
Collapse
|
15
|
Dawe RK. Charting the path to fully synthetic plant chromosomes. Exp Cell Res 2020; 390:111951. [PMID: 32151492 DOI: 10.1016/j.yexcr.2020.111951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
The concepts of synthetic biology have the potential to transform plant genetics, both in how we analyze genetic pathways and how we transfer that knowledge into useful applications. While synthetic biology can be applied at the level of the single gene or small groups of genes, this commentary focuses on the ultimate challenge of designing fully synthetic plant chromosomes. Engineering at this scale will allow us to manipulate whole genome architecture and to modify multiple pathways and traits simultaneously. Advances in genome synthesis make it likely that the initial phases of plant chromosome construction will occur in bacteria and yeast. Here I discuss the next steps, including specific ways of overcoming technical barriers associated with plant transformation, functional centromere design, and ensuring accurate meiotic transmission.
Collapse
Affiliation(s)
- R Kelly Dawe
- Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
16
|
The Behavior of the Maize B Chromosome and Centromere. Genes (Basel) 2018; 9:genes9100476. [PMID: 30275397 PMCID: PMC6210970 DOI: 10.3390/genes9100476] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/16/2018] [Accepted: 09/25/2018] [Indexed: 12/15/2022] Open
Abstract
The maize B chromosome is a non-essential chromosome with an accumulation mechanism. The dispensable nature of the B chromosome facilitates many types of genetic studies in maize. Maize lines with B chromosomes have been widely used in studies of centromere functions. Here, we discuss the maize B chromosome alongside the latest progress of B centromere activities, including centromere misdivision, inactivation, reactivation, and de novo centromere formation. The meiotic features of the B centromere, related to mini-chromosomes and the control of the size of the maize centromere, are also discussed.
Collapse
|
17
|
Liu Y, Su H, Liu Y, Zhang J, Dong Q, Birchler JA, Han F. Cohesion and centromere activity are required for phosphorylation of histone H3 in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1121-1131. [PMID: 29032586 DOI: 10.1111/tpj.13748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/03/2017] [Accepted: 10/10/2017] [Indexed: 05/03/2023]
Abstract
Haspin-mediated phosphorylation of histone H3 at threonine 3 (H3T3ph) promotes proper deposition of Aurora B at the inner centromere to ensure faithful chromosome segregation in metazoans. However, the function of H3T3ph remains relatively unexplored in plants. Here, we show that in maize (Zea mays L.) mitotic cells, H3T3ph is concentrated at pericentromeric and centromeric regions. Additional weak H3T3ph signals occur between cohered sister chromatids at prometaphase. Immunostaining on dicentric chromosomes reveals that an inactive centromere cannot maintain H3T3ph at metaphase, indicating that a functional centromere is required for H3T3 phosphorylation. H3T3ph locates at a newly formed centromeric region that lacks detectable CentC sequences and strongly reduced CRM and ZmBs repeat sequences at metaphase II. These results suggest that centromeric localization of H3T3ph is not dependent on centromeric sequences. In maize meiocytes, H3T3 phosphorylation occurs at the late diakinesis and extends to the entire chromosome at metaphase I, but is exclusively limited to the centromere at metaphase II. The H3T3ph signals are absent in the afd1 (absence of first division) and sgo1 (shugoshin) mutants during meiosis II when the sister chromatids exhibit random distribution. Further, we show that H3T3ph is mainly located at the pericentromere during meiotic prophase II but is restricted to the inner centromere at metaphase II. We propose that this relocation of H3T3ph depends on tension at the centromere and is required to promote bi-orientation of sister chromatids.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qianhua Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
18
|
Tseng SH, Peng SF, Cheng YM. Analysis of B chromosome nondisjunction induced by the r-X1 deficiency in maize. Chromosome Res 2017; 26:153-162. [PMID: 29159670 DOI: 10.1007/s10577-017-9567-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 02/02/2023]
Abstract
The maize B chromosome typically undergoes nondisjunction during the second microspore division. For normal A chromosomes, the r-X1 deficiency in maize can induce nondisjunction during the second megaspore and first microspore divisions. However, it is not known whether the r-X1 deficiency also induces nondisjunction of the maize B chromosome during these cell divisions. To answer this question, chromosome numbers were determined in the progeny of r-X1/R-r female parents carrying two B chromosomes. Some of the r-X1-lacking progeny (21.2%) contained zero or two B chromosomes. However, a much higher percentage of the r-X1-containing progeny (43.4%) exhibited zero or two B chromosomes, but none displayed more than two B chromosomes. Thus, the results indicated that the r-X1 deficiency could also induce nondisjunction of the B chromosome during the second megaspore division; moreover, the B chromosome in itself could undergo nondisjunction during the same division. In addition, pollen grains from plants with two B chromosomes lacking or exhibiting the r-X1 deficiency were compared via pollen fluorescence in situ hybridization (FISH) using a B chromosome-specific probe. The results revealed that the r-X1 deficiency could induce the occurrence of B chromosome nondisjunction during the first microspore division and that the B chromosome in itself could undergo nondisjunction during the same division at a lower frequency. Our data shed more light on the behavior of the maize B chromosome during cell division.
Collapse
Affiliation(s)
- Shih-Hsuan Tseng
- Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan
| | - Shu-Fen Peng
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Ya-Ming Cheng
- Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan.
| |
Collapse
|
19
|
Zhang F, Tang D, Shen Y, Xue Z, Shi W, Ren L, Du G, Li Y, Cheng Z. The F-Box Protein ZYGO1 Mediates Bouquet Formation to Promote Homologous Pairing, Synapsis, and Recombination in Rice Meiosis. THE PLANT CELL 2017; 29:2597-2609. [PMID: 28939596 PMCID: PMC5774573 DOI: 10.1105/tpc.17.00287] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/18/2017] [Accepted: 09/20/2017] [Indexed: 05/18/2023]
Abstract
Telomere bouquet formation, a highly conserved meiotic event, plays an important role in homologous pairing and therefore progression of meiosis; however, the underlying molecular mechanism remains largely unknown. Here, we identified ZYGOTENE1 (ZYGO1), a novel F-box protein in rice (Oryza sativa), and verified its essential role in bouquet formation during early meiosis. In zygo1 mutants, zygotene chromosome aggregation and telomere clustering failed to occur. The suppressed telomere clustering in homologous pairing aberration in rice meiosis1 (pair1) zygo1 and rice completion of meiotic recombination (Oscom1) zygo1 double mutants, together with the altered localization of OsSAD1 (a SUN protein associated with the nuclear envelope) in zygo1, showed that ZYGO1 has a significant function in bouquet formation. In addition, the interaction between ZYGO1 and rice SKP1-like protein 1 suggested that ZYGO1 might modulate bouquet formation as a component of the SKP1-Cullin1-F-box complex. Although double-strand break formation and early recombination element installation occurred normally, zygo1 mutants showed defects in full-length pairing and synaptonemal complex assembly. Furthermore, crossover (CO) formation was disturbed, and foci of Human enhancer of invasion 10 were restricted to the partially synapsed chromosome regions, indicating that CO reduction might be caused by the failure of full-length chromosome alignment in zygo1 Therefore, we propose that ZYGO1 mediates bouquet formation to efficiently promote homolog pairing, synapsis, and CO formation in rice meiosis.
Collapse
Affiliation(s)
- Fanfan Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihui Xue
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenqing Shi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lijun Ren
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guijie Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
20
|
Yan X, Li C, Yang J, Wang L, Jiang C, Wei W. Induction of telomere-mediated chromosomal truncation and behavior of truncated chromosomes in Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:700-713. [PMID: 28500683 DOI: 10.1111/tpj.13598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
Engineered minichromosomes could be stably inherited and serve as a platform for simultaneously transferring and stably expressing multiple genes. Chromosomal truncation mediated by repeats of telomeric sequences is a promising approach for the generation of minichromosomes. In the present work, direct repetitive sequences of Arabidopsis telomere were used to study telomere-mediated truncation of chromosomes in Brassica napus. Transgenes containing alien Arabidopsis telomere were successfully obtained, and Southern blotting and fluorescence in situ hybridization (FISH) results show that the transgenes resulted in successful chromosomal truncation in B. napus. In addition, truncated chromosomes were inherited at rates lower than that predicted by Mendelian rules. To determine the potential manipulations and applications of the engineered chromosomes, such as the stacking of multiple transgenes and the Cre/lox and FRT/FLP recombination systems, both amenable to genetic manipulations through site-specific recombination in somatic cells, were tested for their ability to undergo recombination in B. napus. These results demonstrate that alien Arabidopsis telomere is able to mediate chromosomal truncation in B. napus. This technology would be feasible for chromosomal engineering and for studies on chromosome structure and function in B. napus.
Collapse
Affiliation(s)
- Xiaohong Yan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Chen Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
- College of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Xinxiang, 453003, China
- College of Food Science and Technology, Agricultural University of Hebei, Baoding, 071001, China
| | - Jie Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Lijun Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Chenghong Jiang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Wenhui Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
- College of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Xinxiang, 453003, China
| |
Collapse
|
21
|
Su H, Liu Y, Dong Q, Feng C, Zhang J, Liu Y, Birchler JA, Han F. Dynamic location changes of Bub1-phosphorylated-H2AThr133 with CENH3 nucleosome in maize centromeric regions. THE NEW PHYTOLOGIST 2017; 214:682-694. [PMID: 28079247 DOI: 10.1111/nph.14415] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 11/27/2016] [Indexed: 05/03/2023]
Abstract
The genomic stability of all organisms requires precise cell division with proper chromosome orientation. The Bub1-H2Aph-Sgo1 pathway and spindle assembly checkpoint (SAC) components have been identified in yeast and mammals that are important for sister centromere orientation and chromosome segregation. However, their roles in plants are not clear. Maize meiotic mutants and minichromosomes were used to study the role of H2AThr133 phosphorylation and SAC components in sister centromere orientation and chromosome segregation. Unlike previously reported, SAC protein Bub1-Sgo1 recruitment was independent of Rec8 in maize and did not play a role in centromere protection in meiosis I. Chromatin immunoprecipitation sequencing analysis with immnolocalization results indicate most CENH3 nucleosomes contain phosphorylated H2AThr133 in centromeric regions. H2AThr133ph spreads to encompass centromeric regions including the inner centromeric and pericentromeric regions during (pro)metaphase. The presence and localization of SAC components and H2AThr133ph on maize lines containing sister chromatids separate precociously in anaphase I revealed no direct role of these proteins on centromere orientation in meiosis I . This work sheds light on the relationship between H2AThr133ph and CENH3 nucleosome in plants, and the phosphorylation with dynamic location changes in centomeric regions suggests temporal and spatial regulation roles for H2A phosphorylation in chromosome segregation.
Collapse
Affiliation(s)
- Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qianhua Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao Feng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
22
|
Yang R, Li Y, Su Y, Shen Y, Tang D, Luo Q, Cheng Z. A functional centromere lacking CentO sequences in a newly formed ring chromosome in rice. J Genet Genomics 2016; 43:694-701. [PMID: 27965027 DOI: 10.1016/j.jgg.2016.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/10/2016] [Accepted: 09/22/2016] [Indexed: 11/29/2022]
Abstract
An awned rice (Oryza sativa) plant carrying a tiny extra chromosome was discovered among the progeny of a telotrisomic line 2n+4L. Fluorescence in situ hybridization (FISH) using chromosome specific BAC clones revealed that this extra chromosome was a ring chromosome derived from part of the long arm of chromosome 4. So the aneuploidy plant was accordingly named as 2n+4L ring. We did not detect any CentO FISH signals on the ring chromosome, and found only the centromeric probe Centromeric Retrotransposon of Rice (CRR) was co-localized with the centromere-specific histone CENH3 as revealed by sequential FISH after immunodetection. The extra ring chromosome exhibited a unique segregation pattern during meiosis, including no pairing between the ring chromosome and normal chromosome 4 during prophase I and pre-separation of sister chromatids at anaphase I.
Collapse
Affiliation(s)
- Rui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming 650201, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics, Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Su
- State Key Laboratory of Plant Genomics, Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics, Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics, Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiong Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming 650201, China.
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
23
|
Plant minichromosomes. Curr Opin Biotechnol 2016; 37:135-142. [DOI: 10.1016/j.copbio.2015.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/06/2015] [Accepted: 11/23/2015] [Indexed: 11/23/2022]
|
24
|
Cheng YM, Feng YR, Lin YP, Peng SF. Cytomolecular characterization and origin of de novo formed maize B chromosome variants. Chromosome Res 2016; 24:183-95. [PMID: 26748511 DOI: 10.1007/s10577-015-9516-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/20/2015] [Accepted: 12/29/2015] [Indexed: 10/22/2022]
Abstract
B chromosomes are dispensable elements that occur in many species, including maize. The maize B chromosome is acrocentric and highly heterochromatic and undergoes nondisjunction during the second pollen mitosis. In this study, we determined the genetic behavior and organization of two naturally occurring B chromosome variants (designated B(ta) and B(tb)). The morphology and genetic behavior of the B(ta) chromosome were similar to those of the typical B chromosome, but the B(ta) chromosome contained a deletion in the first heterochromatin region and had higher transmission frequencies through both male and female parents. The B(tb) chromosome was reduced in size, consisted primarily of heterochromatin, and had a lower transmission frequency. The B(tb) chromosome lacked nondisjunctional behavior, which was restored by the presence of normal B chromosomes in the cell. Furthermore, the B(tb) chromosome contained two centromeric regions, only one of which was active. The organization of these two naturally occurring B chromosome variants was also determined using fluorescence in situ hybridization with B-associated sequences and by amplification of B-specific molecular markers to create possible evolutionary models.
Collapse
Affiliation(s)
- Ya-Ming Cheng
- Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan.
| | - Ying-Ru Feng
- Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan
| | - Yao-Pin Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Fen Peng
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
| |
Collapse
|
25
|
Teotia S, Singh D, Tang X, Tang G. Essential RNA-Based Technologies and Their Applications in Plant Functional Genomics. Trends Biotechnol 2016; 34:106-123. [PMID: 26774589 DOI: 10.1016/j.tibtech.2015.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/19/2015] [Accepted: 12/07/2015] [Indexed: 12/20/2022]
Abstract
Genome sequencing has not only extended our understanding of the blueprints of many plant species but has also revealed the secrets of coding and non-coding genes. We present here a brief introduction to and personal account of key RNA-based technologies, as well as their development and applications for functional genomics of plant coding and non-coding genes, with a focus on short tandem target mimics (STTMs), artificial microRNAs (amiRNAs), and CRISPR/Cas9. In addition, their use in multiplex technologies for the functional dissection of gene networks is discussed.
Collapse
Affiliation(s)
- Sachin Teotia
- Provincial State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; School of Biotechnology, Gautam Buddha University, Greater Noida, UP 201312, India; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Deepali Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, UP 201312, India; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Xiaoqing Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Guiliang Tang
- Provincial State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA.
| |
Collapse
|
26
|
Generation of a Maize B Centromere Minimal Map Containing the Central Core Domain. G3-GENES GENOMES GENETICS 2015; 5:2857-64. [PMID: 26511496 PMCID: PMC4683656 DOI: 10.1534/g3.115.022889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The maize B centromere has been used as a model for centromere epigenetics and as the basis for building artificial chromosomes. However, there are no sequence resources for this important centromere. Here we used transposon display for the centromere-specific retroelement CRM2 to identify a collection of 40 sequence tags that flank CRM2 insertion points on the B chromosome. These were confirmed to lie within the centromere by assaying deletion breakpoints from centromere misdivision derivatives (intracentromere breakages caused by centromere fission). Markers were grouped together on the basis of their association with other markers in the misdivision series and assembled into a pseudocontig containing 10.1 kb of sequence. To identify sequences that interact directly with centromere proteins, we carried out chromatin immunoprecipitation using antibodies to centromeric histone H3 (CENH3), a defining feature of functional centromeric sequences. The CENH3 chromatin immunoprecipitation map was interpreted relative to the known transmission rates of centromere misdivision derivatives to identify a centromere core domain spanning 33 markers. A subset of seven markers was mapped in additional B centromere misdivision derivatives with the use of unique primer pairs. A derivative previously shown to have no canonical centromere sequences (Telo3-3) lacks these core markers. Our results provide a molecular map of the B chromosome centromere and identify key sequences within the map that interact directly with centromeric histone H3.
Collapse
|
27
|
|
28
|
Abstract
Engineered minimal chromosomes with sufficient mitotic and meiotic stability have an enormous potential as vectors for stacking multiple genes required for complex traits in plant biotechnology. Proof of principle for essential steps in chromosome engineering such as truncation of chromosomes by T-DNA-mediated telomere seeding and de novo formation of centromeres by cenH3 fusion protein tethering has been recently obtained. In order to generate robust protocols for application in plant biotechnology, these steps need to be combined and supplemented with additional methods such as site-specific recombination for the directed transfer of multiple genes of interest on the minichromosomes. At the same time, the development of these methods allows new insight into basic aspects of plant chromosome functions such as how centromeres assure proper distribution of chromosomes to daughter cells or how telomeres serve to cap the chromosome ends to prevent shortening of ends over DNA replication cycles and chromosome end fusion.
Collapse
Affiliation(s)
- Michael Florian Mette
- Research Group Chromosome Structure and Function, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany,
| | | |
Collapse
|
29
|
Liu Y, Su H, Zhang J, Liu Y, Han F, Birchler JA. Dynamic epigenetic states of maize centromeres. FRONTIERS IN PLANT SCIENCE 2015; 6:904. [PMID: 26579154 PMCID: PMC4620398 DOI: 10.3389/fpls.2015.00904] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/10/2015] [Indexed: 05/03/2023]
Abstract
The centromere is a specialized chromosomal region identified as the major constriction, upon which the kinetochore complex is formed, ensuring accurate chromosome orientation and segregation during cell division. The rapid evolution of centromere DNA sequence and the conserved centromere function are two contradictory aspects of centromere biology. Indeed, the sole presence of genetic sequence is not sufficient for centromere formation. Various dicentric chromosomes with one inactive centromere have been recognized. It has also been found that de novo centromere formation is common on fragments in which centromeric DNA sequences are lost. Epigenetic factors play important roles in centromeric chromatin assembly and maintenance. Non-disjunction of the supernumerary B chromosome centromere is independent of centromere function, but centromere pairing during early prophase of meiosis I requires an active centromere. This review discusses recent studies in maize about genetic and epigenetic elements regulating formation and maintenance of centromere chromatin, as well as centromere behavior in meiosis.
Collapse
Affiliation(s)
- Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri at Columbia, ColumbiaMO, USA
- *Correspondence: James A. Birchler,
| |
Collapse
|
30
|
Birchler JA. Engineered minichromosomes in plants. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:76-80. [PMID: 24906050 DOI: 10.1016/j.pbi.2014.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/23/2014] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
Platforms for the development of synthetic chromosomes in plants have been produced in several species using telomere mediated chromosomal truncation with the simultaneous inclusion of sites that facilitate further additions to the newly generated minichromosome. By utilizing truncated supernumerary or B chromosomes, the output of the genes on the minichromosome can be amplified. Proof of concept experiments have been successful illustrating that minichromosome platforms can be modified in vivo. Engineered minichromosomes can likely be combined with haploid breeding if they are incorporated into inducer lines given that the observations that basically inert chromosomes from haploid inducer lines can be recovered at workable frequencies in otherwise haploid plants. Future needs of synthetic chromosome development are discussed.
Collapse
Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
| |
Collapse
|
31
|
|
32
|
Zhang J, Zhang B, Su H, Birchler JA, Han F. Molecular mechanisms of homologous chromosome pairing and segregation in plants. J Genet Genomics 2014; 41:117-23. [PMID: 24656232 DOI: 10.1016/j.jgg.2013.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/09/2013] [Accepted: 12/09/2013] [Indexed: 11/18/2022]
Abstract
In most eukaryotic species, three basic steps of pairing, recombination and synapsis occur during prophase of meiosis I. Homologous chromosomal pairing and recombination are essential for accurate segregation of chromosomes. In contrast to the well-studied processes such as recombination and synapsis, many aspects of chromosome pairing are still obscure. Recent progress in several species indicates that the telomere bouquet formation can facilitate homologous chromosome pairing by bringing chromosome ends into close proximity, but the sole presence of telomere clustering is not sufficient for recognizing homologous pairs. On the other hand, accurate segregation of the genetic material from parent to offspring during meiosis is dependent on the segregation of homologs in the reductional meiotic division (MI) with sister kinetochores exhibiting mono-orientation from the same pole, and the segregation of sister chromatids during the equational meiotic division (MII) with kinetochores showing bi-orientation from the two poles. The underlying mechanism of orientation and segregation is still unclear. Here we focus on recent studies in plants and other species that provide insight into how chromosomes find their partners and mechanisms mediating chromosomal segregation.
Collapse
Affiliation(s)
- Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James A Birchler
- Division of Biological Sciences, 311 Tucker Hall, University of Missouri, Columbia, MO 65211, USA.
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
33
|
Birchler JA, Han F. Meiotic behavior of small chromosomes in maize. FRONTIERS IN PLANT SCIENCE 2013; 4:505. [PMID: 24381575 PMCID: PMC3865424 DOI: 10.3389/fpls.2013.00505] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/25/2013] [Indexed: 05/15/2023]
Abstract
The typical behavior of chromosomes in meiosis is that homologous pairs synapse, recombine, and then separate at anaphase I. At anaphase II, sister chromatids separate. However, studies of small chromosomes in maize derived from a variety of sources typically have failure of sister chromatid cohesion at anaphase I. This failure occurs whether there is pairing of two copies of a minichromosome or not. These characteristics have implications for managing the transmission of the first generation artificial chromosomes in plants. Procedures to address these issues of minichromosomes are discussed.
Collapse
Affiliation(s)
- James A. Birchler
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
- *Correspondence: James A. Birchler, Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO 65211-7400, USA e-mail:
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| |
Collapse
|
34
|
Alteration of terminal heterochromatin and chromosome rearrangements in derivatives of wheat-rye hybrids. J Genet Genomics 2013; 40:413-20. [PMID: 23969250 DOI: 10.1016/j.jgg.2013.05.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/28/2013] [Accepted: 05/03/2013] [Indexed: 11/21/2022]
Abstract
Wheat-rye addition and substitution lines and their self progenies revealed variations in telomeric heterochromatin and centromeres. Furthermore, a mitotically unstable dicentric chromosome and stable multicentric chromosomes were observed in the progeny of a Chinese Spring-Imperial rye 3R addition line. An unstable multicentric chromosome was found in the progeny of a 6R/6D substitution line. Drastic variation of terminal heterochromatin including movement and disappearance of terminal heterochromatin occurred in the progeny of wheat-rye addition line 3R, and the 5RS ditelosomic addition line. Highly stable minichromosomes were observed in the progeny of a monosomic 4R addition line, a ditelosomic 5RS addition line and a 6R/6D substitution line. Minichromosomes, with and without the FISH signals for telomeric DNA (TTTAGGG)n, derived from a monosomic 4R addition line are stable and transmissible to the next generation. The results indicated that centromeres and terminal heterochromatin can be profoundly altered in wheat-rye hybrid derivatives.
Collapse
|
35
|
Masonbrink RE, Fu S, Han F, Birchler JA. Heritable loss of replication control of a minichromosome derived from the B chromosome of maize. Genetics 2013; 193:77-84. [PMID: 23114381 PMCID: PMC3527256 DOI: 10.1534/genetics.112.146126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 10/29/2012] [Indexed: 01/24/2023] Open
Abstract
During an accumulation regime of a small telomere-truncated B chromosome, a derivative with large variations in size and multiple punctate centromere loci exhibiting amplified copy numbers was discovered. Multiple centromere satellite loci or transgene signals were documented in amplified chromosomes, suggesting over-replication. Immunolocalization studies revealed multiple foci of biochemical markers characteristic of active centromeres such as CENP-C and phosphorylation of histones H3S10 and H2AThr133. The amplified chromosomes exhibit an absence of chromosome disjunction in meiosis I and an infrequent chromosome disjunction in meiosis II. Despite their unusual structure and behavior these chromosomes were observed in the lineage for seven generations during the course of this study. While severely truncated relative to a normal B chromosome, the progenitor minichromosome is estimated to be at least several megabases in size. Given that the centromere and transgene signals at opposite ends of the chromosome generally match in copy number, the replication control is apparently lost over several megabases.
Collapse
Affiliation(s)
- Rick E. Masonbrink
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Shulan Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese National Academy of Sciences, Beijing, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese National Academy of Sciences, Beijing, China
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| |
Collapse
|
36
|
Masonbrink RE, Gaeta RT, Birchler JA. Multiple maize minichromosomes in meiosis. Chromosome Res 2012; 20:395-402. [DOI: 10.1007/s10577-012-9283-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/09/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
|
37
|
[Establishment of wheat-rye addition lines and De Novo powdery mildew resistance gene from chromosome 5R]. YI CHUAN = HEREDITAS 2011; 33:1258-62. [PMID: 22120083 DOI: 10.3724/sp.j.1005.2011.01258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The F5 plants derived from octoploid triticale × common wheat were investigated by FISH methods using repetitive DNA sequences pAS1 and pSc119.2 as probes. The disease resistance of these plants was also screened and evaluated in the field. The 1R, 2R, 3R, 4R, 5R, 6R and 7R monosomic addition lines and 1R and 2R disomic addition lines were found. The occurrence frequencies of chromosomes 1R and 4R addition lines were higher than that of chromosomes 2R, 3R, 5R, 6R, and 7R addition lines in the high generation screened. The 5R and 6R monosomic addition lines were immune to powdery mildew. The chromosome 5R in this study might carry new powdery mildew resistance gene(s). In addition, the preferential elimination of chromosome 4B was observed in several plants.
Collapse
|
38
|
Gaeta RT, Masonbrink RE, Krishnaswamy L, Zhao C, Birchler JA. Synthetic chromosome platforms in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 63:307-330. [PMID: 22136564 DOI: 10.1146/annurev-arplant-042110-103924] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Synthetic chromosomes provide the means to stack transgenes independently of the remainder of the genome. Combining them with haploid breeding could provide the means to transfer many transgenes more easily among varieties of the same species. The epigenetic nature of centromere formation complicates the production of synthetic chromosomes. However, telomere-mediated truncation coupled with the introduction of site-specific recombination cassettes has been used to produce minichromosomes consisting of little more than a centromere. Methods that have been developed to modify genes in vivo could be applied to minichromosomes to improve their utility and to continue to increase their length and genic content. Synthetic chromosomes establish the means to add or subtract multiple transgenes, multigene complexes, or whole biochemical pathways to plants to change their properties for agricultural applications or to use plants as factories for the production of foreign proteins or metabolites.
Collapse
Affiliation(s)
- Robert T Gaeta
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | | | | | | |
Collapse
|
39
|
Dhar MK, Kaul S, Kour J. Towards the development of better crops by genetic transformation using engineered plant chromosomes. PLANT CELL REPORTS 2011; 30:799-806. [PMID: 21249368 DOI: 10.1007/s00299-011-1001-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/03/2011] [Accepted: 01/04/2011] [Indexed: 05/30/2023]
Abstract
Plant Biotechnology involves manipulation of genetic material to develop better crops. Keeping in view the challenges being faced by humanity in terms of shortage of food and other resources, we need to continuously upgrade the genomic technologies and fine tune the existing methods. For efficient genetic transformation, Agrobacterium-mediated as well as direct delivery methods have been used successfully. However, these methods suffer from many disadvantages especially in terms of transfer of large genes, gene complexes and gene silencing. To overcome these problems, recently, some efforts have been made to develop genetic transformation systems based on engineered plant chromosomes called minichromosomes or plant artificial chromosomes. Two approaches namely, "top-down" or "bottom-up" have been used for minichromosomes. The former involves engineering of the existing chromosomes within a cell and the latter de novo assembling of chromosomes from the basic constituents. While some success has been achieved using these chromosomes as vectors for genetic transformation in maize, however, more studies are needed to extend this technology to crop plants. The present review attempts to trace the genesis of minichromosomes and discusses their potential of development into plant artificial chromosome vectors. The use of these vectors in genetic transformation will greatly ameliorate the food problem and help to achieve the UN Millennium development goals.
Collapse
Affiliation(s)
- Manoj K Dhar
- Plant Genomics Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India.
| | | | | |
Collapse
|
40
|
Koo DH, Han F, Birchler JA, Jiang J. Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome. Genome Res 2011; 21:908-14. [PMID: 21518739 DOI: 10.1101/gr.116202.110] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Centromeres are determined by poorly understood epigenetic mechanisms. Centromeres can be activated or inactivated without changing the underlying DNA sequences. However, virtually nothing is known about the epigenetic transition of a centromere from an active to an inactive state because of the lack of examples of the same centromere exhibiting alternative forms and being distinguishable from other centromeres. The centromere of the supernumerary B chromosome of maize provides such an opportunity because its functional core can be cytologically tracked, and an inactive version of the centromere is available. We developed a DNA fiber-based technique that can be used to assess the levels of cytosine methylation associated with repetitive DNA sequences. We report that DNA sequences in the normal B centromere exhibit hypomethylation. This methylation pattern is not affected by the genetic background or structural rearrangement of the B chromosome, but is slightly changed when the B chromosome is transferred to oat as an addition chromosome. In contrast, an inactive version of this same centromere exhibits hypermethylation, indicating that the inactive centromere was modified into a different epigenetic state at the DNA level.
Collapse
Affiliation(s)
- Dal-Hoe Koo
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | | | | |
Collapse
|
41
|
Affiliation(s)
- James A. Birchler
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211-7400;
| | - Fangpu Han
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211-7400;
| |
Collapse
|
42
|
Han F, Gao Z, Birchler JA. Reactivation of an inactive centromere reveals epigenetic and structural components for centromere specification in maize. THE PLANT CELL 2009; 21:1929-39. [PMID: 19602622 PMCID: PMC2729603 DOI: 10.1105/tpc.109.066662] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Stable maize (Zea mays) chromosomes were recovered from an unstable dicentric containing large and small versions of the B chromosome centromere. In the stable chromosome, the smaller centromere had become inactivated. This inactive centromere can be inherited from one generation to the next attached to the active version and loses all known cytological and molecular properties of active centromeres. When separated from the active centromere by intrachromosomal recombination, the inactive centromere can be reactivated. The reactivated centromere regains the molecular attributes of activity in anaphase I of meiosis. When two copies of the dicentric chromosome with one active and one inactive centromere are present, homologous chromosome pairing reduces the frequency of intrachromosomal recombination and thus decreases, but does not eliminate, the reactivation of inactive centromeres. These findings indicate an epigenetic component to centromere specification in that centromere inactivation can be directed by joining two centromeres in opposition. These findings also indicate a structural aspect to centromere specification revealed by the gain of activity at the site of the previously inactive sequences.
Collapse
Affiliation(s)
- Fangpu Han
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211-7400, USA
| | | | | |
Collapse
|
43
|
Birchler JA, Gao Z, Han F. A tale of two centromeres--diversity of structure but conservation of function in plants and animals. Funct Integr Genomics 2008; 9:7-13. [PMID: 19083033 DOI: 10.1007/s10142-008-0104-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 11/24/2008] [Accepted: 11/25/2008] [Indexed: 02/04/2023]
Abstract
The structural and functional aspects of two specific centromeres, one drawn from the animal kingdom (Drosophila) and the other from the plant kingdom (maize), are compared. Both cases illustrate an epigenetic component to centromere specification. The observations of neocentromeres in Drosophila and inactive centromeres in maize constitute one line of evidence for this hypothesis. Another common feature is the divisibility of centromere function with reduced stability as the size decreases. The systems differ in that Drosophila has no common sequence repeat at all centromeres, whereas maize has a 150-bp unit present in tandem arrays together with a centromere-specific transposon, centromere retrotransposon maize, present at all primary constrictions. Aspects of centromere structure known only from one or the other system might be common to both, namely, the presence of centromere RNAs in the kinetochore as found in maize and the organization of the centromeric histone 3 in tetrameric nucleosomes.
Collapse
Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
| | | | | |
Collapse
|
44
|
Artificial chromosome formation in maize (Zea mays L.). Chromosoma 2008; 118:157-77. [DOI: 10.1007/s00412-008-0191-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 10/22/2008] [Accepted: 10/23/2008] [Indexed: 12/11/2022]
|
45
|
Yin S, Ai JS, Shi LH, Wei L, Yuan J, Ouyang YC, Hou Y, Chen DY, Schatten H, Sun QY. Shugoshin1 may play important roles in separation of homologous chromosomes and sister chromatids during mouse oocyte meiosis. PLoS One 2008; 3:e3516. [PMID: 18949044 PMCID: PMC2567865 DOI: 10.1371/journal.pone.0003516] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 10/01/2008] [Indexed: 11/29/2022] Open
Abstract
Background Homologous chromosomes separate in meiosis I and sister chromatids separate in meiosis II, generating haploid gametes. To address the question why sister chromatids do not separate in meiosis I, we explored the roles of Shogoshin1 (Sgo1) in chromosome separation during oocyte meiosis. Methodology/Principal Findings Sgo1 function was evaluated by exogenous overexpression to enhance its roles and RNAi to suppress its roles during two meioses of mouse oocytes. Immunocytochemistry and chromosome spread were used to evaluate phenotypes. The exogenous Sgo1 overexpression kept homologous chromosomes and sister chromatids not to separate in meiosis I and meiosis II, respectively, while the Sgo1 RNAi promoted premature separation of sister chromatids. Conclusions Our results reveal that prevention of premature separation of sister chromatids in meiosis I requires the retention of centromeric Sgo1, while normal separation of sister chromatids in meiosis II requires loss of centromeric Sgo1.
Collapse
Affiliation(s)
- Shen Yin
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Jun-Shu Ai
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Li-Hong Shi
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Liang Wei
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Ju Yuan
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Ying-Chun Ouyang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yi Hou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Da-Yuan Chen
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Qing-Yuan Sun
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| |
Collapse
|