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Yu Z, Cui B, Xiao J, Jiao W, Wang H, Wang Z, Sun L, Song Q, Yuan J, Wang X. Dosage effect genes modulate grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid. J Genet Genomics 2024:S1673-8527(24)00081-X. [PMID: 38670432 DOI: 10.1016/j.jgg.2024.04.010] [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: 09/02/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length, than the tetraploid and diploid parents. To investigate how polyploidization affects grain development at the transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes from genome V of H. villosa. The dosage effect genes overrepresent grain development-related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield.
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Affiliation(s)
- Zhongyu Yu
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Baofeng Cui
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jin Xiao
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Wu Jiao
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Haiyan Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Zongkuan Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Li Sun
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Qingxin Song
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jingya Yuan
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
| | - Xiue Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
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2
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Zhao K, Dong J, Xu J, Bai Y, Yin Y, Long C, Wu L, Lin T, Fan L, Wang Y, Edger PP, Xiong Z. Downregulation of the expression of subgenomic chromosome A7 genes promotes plant height in resynthesized allopolyploid Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:11. [PMID: 38110525 DOI: 10.1007/s00122-023-04510-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/18/2023] [Indexed: 12/20/2023]
Abstract
KEY MESSAGE Homoeolog expression bias and the gene dosage effect induce downregulation of genes on chromosome A7, causing a significant increase in the plant height of resynthesized allopolyploid Brassica napus. Gene expression levels in allopolyploid plants are not equivalent to the simple average of the expression levels in the parents and are associated with several non-additive expression phenomena, including homoeolog expression bias. However, hardly any information is available on the effect of homoeolog expression bias on traits. Here, we studied the effects of gene expression-related characteristics on agronomic traits using six isogenic resynthesized Brassica napus lines across the first ten generations. We found a group of genes located on chromosome A7 whose expression levels were significantly negatively correlated with plant height. They were expressed at significantly lower levels than their homoeologous genes, owing to allopolyploidy rather than inheritance from parents. Homoeolog expression bias resulted in resynthesized allopolyploids with a plant height similar to their female Brassica oleracea parent, but significantly higher than that of the male Brassica rapa parent. Notably, aneuploid lines carrying monosomic and trisomic chromosome A7 had the highest and lowest plant heights, respectively, due to changes in the expression bias of homoeologous genes because of alterations in the gene dosage. These findings suggest that the downregulation of the expression of homoeologous genes on a single chromosome can result in the partial improvement of traits to a significant extent in the nascent allopolyploid B. napus.
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Affiliation(s)
- Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Jing Dong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Junxiong Xu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yanbo Bai
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yuhe Yin
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Chunshen Long
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lei Wu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Tuanrong Lin
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Longqiu Fan
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Yufeng Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Ulanqab, 012000, Inner Mongolia, China
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Feng Q, Yu J, Yu J, Hu M, Gu L, Wang H, Du X, Zhu B, Cai M. Identification and Genome-Wide Gene Expression Perturbation of a Trisomy in Chinese Kale ( Brassica oleracea var. alboglabra). PLANTS (BASEL, SWITZERLAND) 2023; 12:3199. [PMID: 37765363 PMCID: PMC10536521 DOI: 10.3390/plants12183199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Trisomy harbouring an extra copy of the chromosome generally causes a variety of physical and intellectual disabilities in mammals but is an extremely rare and important genetic stock in plants. In this study, a spontaneous trisomy plant in a Chinese kale accession (Brassica oleracea var. alboglabra, CC, 2n = 18) that showed significantly smaller plant architecture when compared to other normal plants was found and subsequently confirmed by cytological analysis in which the chromosome set of 2n = 19 and abnormal chromosome behaviour were observed. Then, based on the gene expression deviation determined by RNA-seq, the extra chromosome copy in this trisomy was identified as chromosome C2 (TC2). Compared to normal plants, TC2 not only showed generally upregulated differentially expressed genes (DEGs) on chromosome C2 (97.21% of 573 DEGs in chromosome C2) but also exhibited a whole-genome expression perturbation, in which 1329 DEGs (69.87% of total DEGs) were observed along two-copy chromosomes (trans-effect). The genes in the high (gene expression value > 100) and medium (100 > gene expression value > 10) groups were more prone to decreased gene expression, but the genes in the low group (10 > gene expression value > 0.1) showed upregulated expression deviation. In addition, GO (Gene ontology) annotation analysis revealed that the upregulated DEGs in the trans-effect group were overrepresented by the genes involved in the response to stress category, while the downregulated DEGs in the trans-effect group were mostly enriched in pathways related to DNA synthesis. In conclusion, we think our results can provide important resources for genetic analysis in B. oleracea and show some novel insights for understanding trisomy plant biology.
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Affiliation(s)
| | | | | | | | | | | | | | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (Q.F.); (J.Y.); (J.Y.); (M.H.); (L.G.); (H.W.); (X.D.)
| | - Mengxian Cai
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (Q.F.); (J.Y.); (J.Y.); (M.H.); (L.G.); (H.W.); (X.D.)
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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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5
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Kawaguchi YW, Tsuchikane Y, Tanaka K, Taji T, Suzuki Y, Toyoda A, Ito M, Watano Y, Nishiyama T, Sekimoto H, Tsuchimatsu T. Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex. Genome Biol Evol 2023; 15:evad115. [PMID: 37348049 PMCID: PMC10407611 DOI: 10.1093/gbe/evad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/17/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Genome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than 2-fold heritable genome size variation among the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale (C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1 segregation analysis. Six de novo assembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in the C. psl. complex, despite its possible detrimental effects.
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Affiliation(s)
- Yawako W Kawaguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Graduate School of Science and Engineering, Chiba University, Chiba, Chiba, Japan
| | - Yuki Tsuchikane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Teruaki Taji
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Yasuyuki Watano
- Graduate School of Science, Chiba University, Chiba, Chiba, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hiroyuki Sekimoto
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo, Japan
| | - Takashi Tsuchimatsu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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6
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Zeng P, Ge X, Li Z. Transcriptional Interactions of Single B-Subgenome Chromosome with C-Subgenome in B. oleracea-nigra Additional Lines. PLANTS (BASEL, SWITZERLAND) 2023; 12:2029. [PMID: 37653946 PMCID: PMC10220956 DOI: 10.3390/plants12102029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 09/02/2023]
Abstract
Serial monosomic alien addition lines (MAALs) provide an ideal system to elucidate the transcriptomic interactions between the alien chromosomes and recipient genome under aneuploidy. Herein, five available Brassica oleracea-nigra MAALs (CCB1, CCB4, CCB5, CCB6, CCB8), their derived B. oleracea plants (non-MAALs), and two parents were analyzed for their gene expressions by using high-throughput technology. Compared to parental B. oleracea, all MAALs showed various numbers of DEGs, but CCB8 gave much higher DEGs; the number of downregulated DEGs was slightly higher than the number of upregulated ones, except for in relation to CCB8. All derived B. oleracea plants also gave certain numbers of DEGs, despite these being much lower than in the respective MAALs. Compared to B. nigra, in all five MAALs more DEGs were downregulated than upregulated. Trans-effects were likely more prevailing than cis-effects, and these DEGs were predominantly associated with material transport by dysregulating the cellular component. Meanwhile, the orthologous genes on alien chromosomes could only play a feeble compensatory role for those gene pairs in C-subgenome, and different levels of the expressed genes had a greater tendency towards downregulation. These results revealed transcriptional aneuploidy response patterns between two genomes and suggested that cis- and trans-mechanisms synergistically regulated alien gene transcriptions after distant hybridization.
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Affiliation(s)
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (P.Z.); (Z.L.)
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7
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Sun S, Liu K, Xue C, Hu Y, Yu H, Qi G, Chen J, Li X, Zhao X, Gong Z. Genome-Wide Effects on Gene Expression Between Parental and Filial Generations of Trisomy 11 and 12 of Rice. RICE (NEW YORK, N.Y.) 2023; 16:17. [PMID: 36964817 PMCID: PMC10039966 DOI: 10.1186/s12284-023-00632-5] [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: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Aneuploid refers to the gene dosage imbalance due to copy number alterations. Aneuploidy is generally harmful to the growth, development and reproduction of organisms according to the numerous research. However, it has rarely been reported on whether aneuploid have a relevant pattern of genome expression between the parental and its offspring generations. In this study, mRNA sequencing analysis was performed on rice (Oryza sativa L.) primary trisomes 11 and 12, same primary trisomes and normal individuals in their filial generation. We systematically summarized the changes in gene expression patterns that occur on cis genes and on trans genes between parental and filial generations. In T11 and T12, the ratio of cis-gene expression showed intermediate type in parents and dosage compensation in filial generations, which maybe due to more genes being downregulated. The trans genes were also affected by aneuploidy and manifested as cis-related. The strains with normal chromosomes in filial generations, there are still aneuploid-sensitive genes differentially expressed in their genomes, indicating that the effect of aneuploidy is far-reaching and could not be easily eliminated. Meanwhile, among these differentially expressed genes, genes with low-expression level were more likely to be upregulated, while genes with medium- and high-expression level were easy to be downregulated. For the different types of rice aneuploid, upregulated genes were mainly associated with genomic imbalance while downregulated genes were mainly influenced by the specific added chromosome. In conclusion, our results provide new insights into the genetic characterization and evolution of biological aneuploidy genomes.
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Affiliation(s)
- Shang Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Kai Liu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Chao Xue
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yingying Hu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Hengxiu Yu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Guoxiao Qi
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jijin Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiya Li
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Xinru Zhao
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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8
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Coombes B, Fellers JP, Grewal S, Rusholme‐Pilcher R, Hubbart‐Edwards S, Yang C, Joynson R, King IP, King J, Hall A. Whole-genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:482-496. [PMID: 35598169 PMCID: PMC9946142 DOI: 10.1111/pbi.13859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/28/2022] [Accepted: 05/15/2022] [Indexed: 05/29/2023]
Abstract
Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterize introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilization of introgression pre-breeding material in wheat breeding programmes.
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Affiliation(s)
| | - John P. Fellers
- USDA–ARS Hard Winter Wheat Genetics Research UnitManhattanKansas66506USA
| | - Surbhi Grewal
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | | | - Stella Hubbart‐Edwards
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | - Cai‐yun Yang
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | | | - Ian P. King
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | - Julie King
- School of BiosciencesThe University of Nottingham, Sutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
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9
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Black JA, Reis-Cunha JL, Cruz AK, Tosi LR. Life in plastic, it's fantastic! How Leishmania exploit genome instability to shape gene expression. Front Cell Infect Microbiol 2023; 13:1102462. [PMID: 36779182 PMCID: PMC9910336 DOI: 10.3389/fcimb.2023.1102462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023] Open
Abstract
Leishmania are kinetoplastid pathogens that cause leishmaniasis, a debilitating and potentially life-threatening infection if untreated. Unusually, Leishmania regulate their gene expression largely post-transcriptionally due to the arrangement of their coding genes into polycistronic transcription units that may contain 100s of functionally unrelated genes. Yet, Leishmania are capable of rapid and responsive changes in gene expression to challenging environments, often instead correlating with dynamic changes in their genome composition, ranging from chromosome and gene copy number variations to the generation of extrachromosomal DNA and the accumulation of point mutations. Typically, such events indicate genome instability in other eukaryotes, coinciding with genetic abnormalities, but for Leishmania, exploiting these products of genome instability can provide selectable substrates to catalyse necessary gene expression changes by modifying gene copy number. Unorthodox DNA replication, DNA repair, replication stress factors and DNA repeats are recognised in Leishmania as contributors to this intrinsic instability, but how Leishmania regulate genome plasticity to enhance fitness whilst limiting toxic under- or over-expression of co-amplified and co-transcribed genes is unclear. Herein, we focus on fresh, and detailed insights that improve our understanding of genome plasticity in Leishmania. Furthermore, we discuss emerging models and factors that potentially circumvent regulatory issues arising from polycistronic transcription. Lastly, we highlight key gaps in our understanding of Leishmania genome plasticity and discuss future studies to define, in higher resolution, these complex regulatory interactions.
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Affiliation(s)
- Jennifer A. Black
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil,The Wellcome Centre for Integrative Parasitology, School of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom,*Correspondence: Luiz. R.O. Tosi, ; Jennifer A. Black,
| | | | - Angela. K. Cruz
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz. R.O. Tosi
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil,*Correspondence: Luiz. R.O. Tosi, ; Jennifer A. Black,
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10
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Wang B, Lv R, Zhang Z, Yang C, Xun H, Liu B, Gong L. Homoeologous exchange enables rapid evolution of tolerance to salinity and hyper-osmotic stresses in a synthetic allotetraploid wheat. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7488-7502. [PMID: 36055762 DOI: 10.1093/jxb/erac355] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The link between polyploidy and enhanced adaptation to environmental stresses could be a result of polyploidy itself harbouring higher tolerance to adverse conditions, or polyploidy possessing higher evolvability than diploids under stress conditions. Natural polyploids are inherently unsuitable to disentangle these two possibilities. Using selfed progenies of a synthetic allotetraploid wheat AT3 (AADD) along with its diploid parents, Triticum urartu TMU38 (AA) and Aegilops tauschii TQ27 (DD), we addressed the foregoing issue under abiotic salinity and hyper-osmotic (drought-like) stress. Under short duration of both stresses, euploid plants of AT3 showed intermediate tolerance of diploid parents; under life-long duration of both stresses, tolerant individuals to either stress emerged from selfed progenies of AT3, but not from comparable-sized diploid parent populations. Tolerance to both stresses were conditioned by the same two homoeologous exchanges (HEs; 2DS/2AS and 3DL/3AL), and at least one HE needed to be at the homozygous state. Transcriptomic analyses revealed that hyper-up-regulation of within-HE stress responsive genes of the A sub-genome origin is likely responsible for the dual-stress tolerant phenotypes. Our results suggest that HE-mediated inter-sub-genome rearrangements can be an important mechanism leading to adaptive evolution in allopolyploids as well as a promising target for genetic manipulation in crop improvement.
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Affiliation(s)
- Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruili Lv
- 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
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongwei Xun
- 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
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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11
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Zhang Z, Xun H, Lv R, Gou X, Ma X, Li J, Zhao J, Li N, Gong L, Liu B. Effects of homoeologous exchange on gene expression and alternative splicing in a newly formed allotetraploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1267-1282. [PMID: 35763523 DOI: 10.1111/tpj.15886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Homoeologous exchange (HE) is a major mechanism generating post-polyploidization genetic variation with important evolutionary consequences. However, the direct impacts of HE on gene expression and transcript diversity in allopolyploids without the intertwined evolutionary processes remain to be fully understood. Here, we analyzed high-throughput RNA-seq data of young leaves from plant groups of a synthetic allotetraploid wheat (AADD), which contained variable numbers of HEs. We aimed to investigate if and to which extent HE directly impacts gene expression and alternative splicing (AS). We found that HE impacts expression of genes located within HE regions primarily via a cis-acting dosage effect, which led to significant changes in the total expression level of homoeologous gene pairs, especially for homoeologs whose original expression was biased. In parallel, HE also influences expression of a large number of genes residing in non-HE regions by trans-regulation leading to convergent expression of homoeologs. Intriguingly, when taking the original relative homoeolog expression states into account, homoeolog pairs under trans-effect are more prone to manifesting a convergent response to the HEs whereas those under cis-regulation tended to show further exacerbated subgenome-biased expression. Moreover, HE-induced quantitative, largely individual-specific, changes of AS events were detected. Similar to homoeologous expression, homoeo-AS events under trans-effect were more responsive to HE. HE therefore exerts multifaceted immediate effects on gene expression and, to a less extent, on individualized transcript diversity in nascent allopolyploidy.
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Affiliation(s)
- Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Hongwei Xun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - 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
| | - Xintong Ma
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ning Li
- 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
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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12
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Hao M, Zhang L, Huang L, Ning S, Yuan Z, Jiang B, Yan Z, Wu B, Zheng Y, Liu D. 渗入杂交与小麦杂种优势. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Consequences of Chromosome Loss: Why Do Cells Need Each Chromosome Twice? Cells 2022; 11:cells11091530. [PMID: 35563836 PMCID: PMC9101035 DOI: 10.3390/cells11091530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
Aneuploidy is a cellular state with an unbalanced chromosome number that deviates from the usual euploid status. During evolution, elaborate cellular mechanisms have evolved to maintain the correct chromosome content over generations. The rare errors often lead to cell death, cell cycle arrest, or impaired proliferation. At the same time, aneuploidy can provide a growth advantage under selective conditions in a stressful, frequently changing environment. This is likely why aneuploidy is commonly found in cancer cells, where it correlates with malignancy, drug resistance, and poor prognosis. To understand this “aneuploidy paradox”, model systems have been established and analyzed to investigate the consequences of aneuploidy. Most of the evidence to date has been based on models with chromosomes gains, but chromosome losses and recurrent monosomies can also be found in cancer. We summarize the current models of chromosome loss and our understanding of its consequences, particularly in comparison to chromosome gains.
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Abstract
Aneuploidy, a genomic alternation characterized by deviations in the copy number of chromosomes, affects organisms from early development through to aging. Although it is a main cause of human pregnancy loss and a hallmark of cancer, how aneuploidy affects cellular function has been elusive. The last two decades have seen rapid advances in the understanding of the causes and consequences of aneuploidy at the molecular and cellular levels. These studies have uncovered effects of aneuploidy that can be beneficial or detrimental to cells and organisms in an environmental context-dependent and karyotype-dependent manner. Aneuploidy also imposes general stress on cells that stems from an imbalanced genome and, consequently, also an imbalanced proteome. These insights provide the fundamental framework for understanding the impact of aneuploidy in genome evolution, human pathogenesis and drug resistance.
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15
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Interaction of Male Specific Lethal complex and genomic imbalance on global gene expression in Drosophila. Sci Rep 2021; 11:19679. [PMID: 34608252 PMCID: PMC8490464 DOI: 10.1038/s41598-021-99268-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/20/2021] [Indexed: 02/04/2023] Open
Abstract
The inverse dosage effect caused by chromosome number variations shows global consequences in genomic imbalance including sexual dimorphism and an X chromosome-specific response. To investigate the relationship of the MSL complex to genomic imbalance, we over-expressed MSL2 in autosomal and sex chromosomal aneuploids, and analyzed the different transcriptomes. Some candidate genes involved in regulatory mechanisms have also been tested during embryogenesis using TSA-FISH. Here we show that the de novo MSL complex assembled on the X chromosomes in females further reduced the global expression level on the basis of 2/3 down-regulation caused by the inverse dosage effect in trisomy through epigenetic modulations rather than induced dosage compensation. Plus, the sexual dimorphism effect in unbalanced genomes was further examined due to the pre-existing of the MSL complex in males. All these results demonstrate the dynamic functions of the MSL complex on global gene expression in different aneuploid genomes.
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Abstract
How cells exposed to one stress are later able to better survive other types of stress is not well understood. In eukaryotic organisms, physiological and pathological stresses can disturb endoplasmic reticulum (ER) function, resulting in “ER stress.” Here, we found that exposure to tunicamycin, an inducer of ER stress, resulted in the acquisition of a specific aneuploidy, chromosome 2 trisomy (Chr2x3), in Candida albicans. Importantly, the resulting aneuploidy also conferred cross-tolerance to caspofungin, a first-line echinocandin antifungal, as well as to hydroxyurea, a common chemotherapeutic agent. Exposure to a range of tunicamycin concentrations induced similar ER stress responses. Extra copies of one Chr2 gene, MKK2, affected both tunicamycin and caspofungin tolerance, while at least 3 genes on chromosome 2 (ALG7, RTA2, and RTA3) affected only tunicamycin and not caspofungin responses. Other Chr2 genes (RNR1 and RNR21) affected hydroxyurea tolerance but neither tunicamycin nor caspofungin tolerance. Deletion of components of the protein kinase C (PKC) or calcineurin pathways affected tolerance to both tunicamycin and caspofungin, supporting the idea that the ER stress response and echinocandin tolerance are regulated by overlapping stress response pathways. Thus, antifungal drug tolerance can arise rapidly via ER stress-induced aneuploidy.
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Taagen E, Tanaka J, Gul A, Sorrells ME. Positional-based cloning 'fail-safe' approach is overpowered by wheat chromosome structural variation. THE PLANT GENOME 2021; 14:e20106. [PMID: 34197040 DOI: 10.1002/tpg2.20106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
Positional-based cloning is a foundational method for understanding the genes and gene networks that control valuable agronomic traits such as grain yield components. In this study, we sought to positionally clone the causal genetic variant of a 1000-grain weight (TGW) quantitative trait loci (QTL) on wheat (Triticum aestivum L.) chromosome arm 5AL. We developed heterogenous inbred families (HIFs) (>5,000 plants) for enhanced genotypic resolution and fine-mapped the QTL to a 10-Mbp region. The transcriptome of developing grains from positive and negative control HIF haplotypes revealed presence-absence chromosome arm 5AS structural variation and unexpectedly no differential expression of genes within the chromosome arm 5AL candidate region. Evaluation of genomic, transcriptomic, and phenotypic data, and predicted function of genes, identified that the 5AL QTL was the result of strong linkage disequilibrium (LD) with chromosome arm 5AS presence or absence (HIF r2 = 0.91). Structural variation is common in wheat, and our results highlight that the redundant polyploid genome's masking of such variation is a significant barrier to positional cloning. We propose recommendations for more efficient and robust detection of structural variation, including transitioning from a single nucleotide polymorphism (SNP) to a haplotype-based approach to identify positional cloning targets. We also present nine candidate genes for grain yield components based on chromosome arm 5AS presence or absence, which may unveil hidden variation of homoeolog dosage-dependent genes across the group five chromosome short arms. Taken together, our discovery demonstrates the phenotypic resiliency of polyploid genomic structural variation and highlights a considerable challenge to routine positional cloning in wheat.
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Affiliation(s)
- Ella Taagen
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - James Tanaka
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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18
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Shao Y, Pan Q, Zhang D, Kang L, Li Z. Global gene expression perturbations in rapeseed due to the introduction of alien radish chromosomes. J Genet 2021. [DOI: 10.1007/s12041-021-01276-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Jiao Z, Zhu X, Li H, Liu Z, Huang X, Wu N, An J, Li J, Zhang J, Jiang Y, Li Q, Qi Z, Niu J. Cytological and molecular characterizations of a novel 2A nullisomic line derived from a widely-grown wheat cultivar Zhoumai 18 conferring male sterility. PeerJ 2020; 8:e10275. [PMID: 33194433 PMCID: PMC7605228 DOI: 10.7717/peerj.10275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/08/2020] [Indexed: 11/20/2022] Open
Abstract
A dwarf, multi-pistil and male sterile dms mutant was previously reported by us. However, the genetic changes in this dms are unclear. To examine the genetic changes, single nucleotide polymorphism (SNP) association, chromosome counting, and high-resolution chromosome fluorescence in situ hybridization (FISH) techniques were employed. By comparing tall plants (T) with dwarf plants (D) in the offspring of dms mutant plants, SNP association analysis indicated that most SNPs were on chromosome 2A. There were three types in offspring of dms plants, with 42, 41 and 40 chromosomes respectively. High-resolution chromosome painting analysis demonstrated that T plants had all 42 wheat chromosomes; the medium plants (M) had 41 chromosomes, lacking one chromosome 2A; while D plants had 40 wheat chromosomes, and lacked both 2A chromosomes. These data demonstrated that dms resulted from a loss of chromosome 2A. We identified 23 genes on chromosome 2A which might be involved in the development of stamens or pollen grains. These results lay a solid foundation for further analysis of the molecular mechanisms of wheat male sterility. Because D plants can be used as a female parent to cross with other wheat genotypes, dms is a unique germplasm for any functional study of chromosome 2A and wheat breeding specifically targeting genes on 2A.
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Affiliation(s)
- Zhixin Jiao
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Xinxin Zhu
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Huijuan Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Zhitao Liu
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China.,Sichuan Academy of Agricultural Sciences, Crop Research Institue, Chengdu, Sichuan, China
| | - Xinyi Huang
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Nan Wu
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Junhang An
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Junchang Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Jing Zhang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Yumei Jiang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Qiaoyun Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Zengjun Qi
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Jishan Niu
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
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20
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Gou X, Lv R, Wang C, Fu T, Sha Y, Gong L, Zhang H, Liu B. Balanced Genome Triplication in Wheat Causes Premature Growth Arrest and an Upheaval of Genome-Wide Gene Regulation. Front Genet 2020; 11:687. [PMID: 32733539 PMCID: PMC7360807 DOI: 10.3389/fgene.2020.00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/04/2020] [Indexed: 11/13/2022] Open
Abstract
Polyploidy, or whole genome duplication (WGD), is a driving evolutionary force across the tree of life and has played a pervasive role in the evolution of the plant kingdom. It is generally believed that a major genetic attribute contributing to the success of polyploidy is increased gene and genome dosage. The evolution of polyploid wheat has lent support to this scenario. Wheat has evolved at three ploidal levels: diploidy, tetraploidy, and hexaploidy. Ample evidence testifies that the evolutionary success, be it with respect to evolvability, natural adaptability, or domestication has dramatically increased with each elevation of the ploidal levels. A long-standing question is what would be the outcome if a further elevation of ploidy is superimposed on hexaploid wheat? Here, we characterized a spontaneously occurring nonaploid wheat individual in selfed progenies of synthetic hexaploid wheat and compared it with its isogenic hexaploid siblings at the phenotypic, cytological, and genome-wide gene-expression levels. The nonaploid manifested severe defects in growth and development, albeit with a balanced triplication of the three wheat subgenomes. Transcriptomic profiling of the second leaf of nonaploid, taken at a stage when phenotypic abnormality was not yet discernible, already revealed significant dysregulation in global-scale gene expression with ca. 25.2% of the 49,436 expressed genes being differentially expressed genes (DEGs) at a twofold change cutoff relative to the hexaploid counterpart. Both up- and downregulated DEGs were identified in the nonaploid vs. hexaploid, including 457 genes showing qualitative alteration, i.e., silencing or activation. Impaired functionality at both cellular and organismal levels was inferred from gene ontology analysis of the DEGs. Homoeologous expression analysis of 9,574 sets of syntenic triads indicated that, compared with hexaploid, the proportions showing various homeologous expression patterns were highly conserved in the nonaploid although gene identity showed moderate reshuffling among some of the patterns in the nonaploid. Together, our results suggest hexaploidy is likely the upper limit of ploidy level in wheat; crossing this threshold incurs severe ploidy syndrome that is preceded by disruptive dysregulation of global gene expression.
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Affiliation(s)
- Xiaowan Gou
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Key Laboratory of Molecular Epigenetics, Northeast Normal University, Changchun, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics, Northeast Normal University, Changchun, China
| | - Changyi Wang
- Key Laboratory of Molecular Epigenetics, Northeast Normal University, Changchun, China
| | - Tiansi Fu
- Key Laboratory of Molecular Epigenetics, Northeast Normal University, Changchun, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics, Northeast Normal University, Changchun, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics, Northeast Normal University, Changchun, China
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics, Northeast Normal University, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics, Northeast Normal University, Changchun, China
- *Correspondence: Bao Liu,
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21
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Bhanbhro N, Xiao B, Han L, Lu H, Wang H, Yang C. Adaptive strategy of allohexaploid wheat to long-term salinity stress. BMC PLANT BIOLOGY 2020; 20:210. [PMID: 32397960 PMCID: PMC7216640 DOI: 10.1186/s12870-020-02423-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/30/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Most studies of crop salinity tolerance are conducted under short-term stress condition within one growth stage. Understanding of the mechanisms of crop response to long-term salinity stress (LSS) is valuable for achieving the improvement of crop salinity tolerance. In the current study, we exposed allohexaploid wheat seeds to LSS conditions from germination stage to young seedling stage for 30 days. To elucidate the adaptive strategy of allohexaploid wheat to LSS, we analyzed chloroplast ultrastructure, leaf anatomy, transcriptomic profiling and concentrations of plant hormones and organic compatible solutes, comparing stressed and control plants. RESULTS Transcriptomic profiling and biochemical analysis showed that energy partitioning between general metabolism maintenance and stress response may be crucial for survival of allohexaploid wheat under LSS. Under LSS, wheat appeared to shift energy from general maintenance to stress response through stimulating the abscisic acid (ABA) pathway and suppressing gibberellin and jasmonic acid pathways in the leaf. We further distinguished the expression status of the A, B, and D homeologs of any gene triad, and also surveyed the effects of LSS on homeolog expression bias for salinity-tolerant triads. We found that LSS had similar effects on expression of the three homeologs for most salinity-tolerant triads. However, in some of these triads, LSS induced different effects on the expression of the three homeologs. CONCLUSIONS The shift of the energy from general maintenance to stress response may be important for wheat LSS tolerance. LSS influences homeolog expression bias of salinity-tolerant triads.
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Affiliation(s)
- Nadeem Bhanbhro
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Binbin Xiao
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Han
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huiying Lu
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huan Wang
- Department of Agronomy, Jilin Agricultural University, Changchun, 130118, China
| | - Chunwu Yang
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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22
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Zeng D, Guan J, Luo J, Zhao L, Li Y, Chen W, Zhang L, Ning S, Yuan Z, Li A, Zheng Y, Mao L, Liu D, Hao M. A transcriptomic view of the ability of nascent hexaploid wheat to tolerate aneuploidy. BMC PLANT BIOLOGY 2020; 20:97. [PMID: 32131739 PMCID: PMC7057484 DOI: 10.1186/s12870-020-2309-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/24/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND In contrast to most animal species, polyploid plant species are quite tolerant of aneuploidy. Here, the global transcriptome of four aneuploid derivatives of a synthetic hexaploid wheat line was acquired, with the goal of characterizing the relationship between gene copy number and transcript abundance. RESULTS For most of the genes mapped to the chromosome involved in aneuploidy, the abundance of transcripts reflected the gene copy number. Aneuploidy had a greater effect on the strength of transcription of genes mapped to the chromosome present in a noneuploid dose than on that of genes mapped elsewhere in the genome. Overall, changing the copy number of one member of a homeologous set had little effect on the abundance of transcripts generated from the set of homeologs as a whole, consistent with the tolerance of aneuploidy exhibited by allopolyploids, whether in the form of a chromosomal deficit (monosomy) or chromosomal excess (trisomy). CONCLUSIONS Our findings shed new light on the genetic regulation of homeoallele transcription and contribute to a deeper understanding of allopolyploid genome evolution, with implications for the breeding of polyploid crops.
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Affiliation(s)
- Deying Zeng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Jiantao Guan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiangtao Luo
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, 610066, Sichuan, China
| | - Laibin Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Yazhou Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Wenshuai Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Shunzong Ning
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Zhongwei Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Aili Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Long Mao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China.
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23
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Wei J, Cao H, Liu JD, Zuo JH, Fang Y, Lin CT, Sun RZ, Li WL, Liu YX. Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq. Funct Integr Genomics 2019; 19:919-932. [PMID: 31168755 DOI: 10.1007/s10142-019-00693-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 03/21/2019] [Accepted: 05/17/2019] [Indexed: 11/28/2022]
Abstract
Bread wheat (Triticum aestivum L.) is an allohexaploid, and the transcriptional characteristics of the wheat embryo and endosperm during grain development remain unclear. To analyze the transcriptome, we performed isoform sequencing (Iso-Seq) for wheat grain and RNA sequencing (RNA-Seq) for the embryo and de-embryonated kernels. The differential regulation between the embryo and de-embryonated kernels was found to be greater than the difference between the two time points for each tissue. Exactly 2264 and 4790 tissue-specific genes were found at 14 days post-anthesis (DPA), while 5166 and 3784 genes were found at 25 DPA in the embryo and de-embryonated kernels, respectively. Genes expressed in the embryo were more likely to be related to nucleic acid and enzyme regulation. In de-embryonated kernels, genes were rich in substance metabolism and enzyme activity functions. Moreover, 4351, 4641, 4516, and 4453 genes with the A, B, and D homoeoloci were detected for each of the four tissues. Expression characteristics suggested that the D genome may be the largest contributor to the transcriptome in developing grain. Among these, 48, 66, and 38 silenced genes emerged in the A, B, and D genomes, respectively. Gene ontology analysis showed that silenced genes could be inclined to different functions in different genomes. Our study provided specific gene pools of the embryo and de-embryonated kernels and a homoeolog expression bias model on a large scale. This is helpful for providing new insights into the molecular physiology of wheat.
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Affiliation(s)
- Jun Wei
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing-Dong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing-Hong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Fang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chih-Ta Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Run-Ze Sun
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wen-Long Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,Science and Technology Daily, Beijing, 100093, China
| | - Yong-Xiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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24
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Bin Z, Qi P, Dongao H, Pan Z, Bowei C, Xianhong G, Zaiyun L. Transcriptional Aneuploidy Responses of Brassica rapa- oleracea Monosomic Alien Addition Lines (MAALs) Derived From Natural Allopolyploid B. napus. Front Genet 2019; 10:67. [PMID: 30815011 PMCID: PMC6381038 DOI: 10.3389/fgene.2019.00067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 01/28/2019] [Indexed: 01/21/2023] Open
Abstract
Establishing the whole set of aneuploids, for one naturally evolved allopolyploid species, provides a unique opportunity to elucidate the transcriptomic response of the constituent subgenomes to serial aneuploidy. Previously, the whole set of monosomic alien addition lines (MAALs, C1-C9) with each of the nine C subgenome chromosomes, added to the extracted A subgenome, was developed in the context of the allotetraploid Brassica napus donor “Oro,” after the restitution of the ancestral B. rapa (RBR Oro) was realized. Herein, transcriptomic analysis using high-throughput technology was conducted to detect gene expression alterations in these MAALs and RBR. Compared to diploid RBR, the genes of all of the MAALs showed various degrees of dysregulated expressions that resulted from cis effects and more prevailing trans effects. In addition, the trans-effect on gene expression in MAALs increased with higher levels of homology between the recipient A subgenome and additional C subgenome chromosomes, instead of gene numbers of extra chromosomes. A total of 10 trans-effect dysregulated genes, among all pairwise comparisons, were mainly involved in the function of transporter activity. Furthermore, highly expressed genes were more prone to downregulation and vice-versa, suggesting a common trend for transcriptional pattern responses to aneuploidy. These results provided a comprehensive insight of the impact of gene expression of individual chromosomes, in one subgenome, on another intact subgenome for one allopolyploid with a long evolutionary history.
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Affiliation(s)
- Zhu Bin
- School of Life Sciences, Guizhou Normal University, Guiyang, China.,National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Pan Qi
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huo Dongao
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, China
| | - Zeng Pan
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Cai Bowei
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ge Xianhong
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Zaiyun
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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25
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Phenotypic, cytogenetic, and molecular marker analysis of Brassica napus introgressants derived from an intergeneric hybridization with Orychophragmus. PLoS One 2019; 14:e0210518. [PMID: 30629679 PMCID: PMC6328085 DOI: 10.1371/journal.pone.0210518] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/23/2018] [Indexed: 01/09/2023] Open
Abstract
Aneuploids of a single species that have lost or gained different chromosomes are useful for genomic analysis. The polyploid nature of many crops including oilseed rape (Brassica napus) allows these plants to tolerate the loss of individual chromosomes from homologous pairs, thus facilitating the development of aneuploid lines. Here, we selected 39 lines from advanced generations of an intergeneric hybridization between Brassica rapa and Orychophragmus violaceus with accidental pollination by B. napus. The lines showed a wide spectrum of phenotypic variations, with some traits specific to O. violaceus. Most lines had the same chromosome number (2n = 38) as B. napus. However, we also identified B. napus nulli-tetrasomics with 22 A-genome and 16 C-genome chromosomes and lines with the typical B. napus complement of 20 A-genome and 18 C-genome chromosomes, as revealed by FISH analysis using a C-genome specific probe. Other lines had 2n = 37 or 39 chromosomes, with variable numbers of A- or C-genome chromosomes. The formation of quadrivalents by four A-genome chromosomes with similar shapes suggests that they were derived from the same chromosome. The frequent homoeologous pairing between chromosomes of the A and C genomes points to their non-diploidized meiotic behavior. Sequence-related amplified polymorphism (SRAP) analysis revealed substantial genomic changes of the lines compared to B. rapa associated with O. violaceus specific DNA bands, but only a few genes were identified in these bands by DNA sequencing. These novel B. napus aneuploids and introgressants represent unique tools for studies of Brassica genetics and for Brassica breeding projects.
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26
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Zhang R, Geng S, Qin Z, Tang Z, Liu C, Liu D, Song G, Li Y, Zhang S, Li W, Gao J, Han X, Li G. The genome-wide transcriptional consequences of the nullisomic-tetrasomic stocks for homoeologous group 7 in bread wheat. BMC Genomics 2019; 20:29. [PMID: 30630423 PMCID: PMC6327598 DOI: 10.1186/s12864-018-5421-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/27/2018] [Indexed: 11/16/2022] Open
Abstract
Background Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants lacking two and adding two of six homoeologous chromosomes. These plants can grow normally, but with significantly morphological variations because the adding two chromosomes or the remaining four chromosomes compensate for those absent. Despite these interesting phenomena, detailed molecular mechanisms underlying dosage deletion and compensation in these useful genetic materials have not been determined. Results By sequencing the transcriptomes of leaves in two-week-old seedlings, we showed that the profiles of differentially expressed genes between NT stocks for homoeologous group 7 and the parent hexaploid Chinese Spring (CS) occurred throughout the whole genome with a subgenome and chromosome preference. The deletion effect of nulli-chromosomes was compensated partly by the tetra-chromosomes via the dose level of expressed genes, according to the types of homoeologous genes. The functions of differentially regulated genes primarily focused on carbon metabolic process, photosynthesis process, hormone metabolism, and responding to stimulus, and etc., which might be related to the defective phenotypes that included reductions in plant height, flag leaf length, spikelet number, and kernels per spike. Conclusions The perturbation of the expression levels of transcriptional genes among the NT stocks for homoeologous group 7 demonstrated the gene dosage effect of the subgenome at the genome-wide level. The gene dosage deletion and compensation can be used as a model to elucidate the functions of the subgenomes in modern polyploid plants. Electronic supplementary material The online version of this article (10.1186/s12864-018-5421-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rongzhi Zhang
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China.
| | - Shuaifeng Geng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhengrui Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zongxiang Tang
- Agronomy College, Sichuan Agricultural University, Wenjiang, Chengdu, 610054, China
| | - Cheng Liu
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Dongfeng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Guoqi Song
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Yulian Li
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Shujuan Zhang
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Wei Li
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Jie Gao
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Xiaodong Han
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China
| | - Genying Li
- Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, National Engineering Laboratory for Wheat & Maize, Institute of Crop Science, Shandong Academy of Agricultural Sciences (SAAS), #202, Road of Gongyebei, Jinan, 250100, China.
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27
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Wang H, Hu Z, Huang K, Han Y, Zhao A, Han H, Song L, Fan C, Li R, Xin M, Peng H, Yao Y, Sun Q, Ni Z. Three genomes differentially contribute to the seedling lateral root number in allohexaploid wheat: evidence from phenotype evolution and gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:976-987. [PMID: 29932270 DOI: 10.1111/tpj.14005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 06/09/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Common wheat is an allohexaploid (BBAADD) that originated from the hybridization and polyploidization of the diploid Aegilops tauschii (DD) with the allotetraploid Triticum turgidum (BBAA). Phenotypic changes often arise with the formation and evolution of allopolyploid wheat, but little is known about the evolution of root traits in different wheat species with varying ploidy levels. Here, we reported that the lateral root number on the primary root (LRNPR) of synthetic and natural allohexaploid wheats (BBAADD) is significantly higher than that of their allotetraploid (BBAA) and diploid (AA and SS) progenitors, but is much lower than that of their diploid (DD) progenitors. The expression of the wheat gene TaLBD16, an ortholog of the Arabidopsis LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16), which is involved in lateral root development in Arabidopsis, was positively correlated with the LRNPR in diploid and allopolyploid wheats. In natural and synthetic allohexaploid wheats, the transcript of the TaLBD16 from the D genome (TaLBD16-D) was relatively more abundant compared with TaLBD16-A and TaLBD16-B. Consistent with the observed variation in LRNPR, the divergence in the expression of TaLBD16 homoeologous genes occurred before the formation of polyploidy wheat. Collectively, our observations indicate that the D genome played a crucial role in the increased lateral root number of allohexaploid wheats compared with their allotetraploid progenitors, and that TaLBD16-D was one of the key genes involved in the formation of lateral root number during wheat evolution.
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Affiliation(s)
- Huifang Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ke Huang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yao Han
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Haiming Han
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Long Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chaofeng Fan
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Run Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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28
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Deng X, Sha Y, Lv Z, Wu Y, Zhang A, Wang F, Liu B. The Capacity to Buffer and Sustain Imbalanced D-Subgenome Chromosomes by the BBAA Component of Hexaploid Wheat Is an Evolved Dominant Trait. FRONTIERS IN PLANT SCIENCE 2018; 9:1149. [PMID: 30131821 PMCID: PMC6090280 DOI: 10.3389/fpls.2018.01149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Successful generation of pentaploid wheat (genome, BBAAD) via interspecific hybridization between tetraploid wheat (BBAA) and hexaploid wheat (BBAADD) holds great promise to mutually exchange desirable traits between the two cultivated wheat species, as well as providing a novel facet for evolutionary studies of polyploid wheat. Taking advantage of the viable and fertile nature of an extracted tetraploid wheat (ETW) with a BBAA genome that is virtually identical with the BBAA component of a hexaploid common wheat, and a synthetic hexaploid wheat, we constructed four pentaploid wheats with several distinct yet complementary features, of which harboring homozygous BBAA subgenomes is a common feature. By using a combined FISH/GISH method that enables diagnosing all individual wheat chromosomes, we precisely karyotyped a larger number of cohorts from the immediate progenies of each of the four pentaploid wheats. We found that the BBAA component of hexaploid common wheat possesses a significantly stronger capacity to buffer and sustain imbalanced D genome chromosomes and appears to harbor more structural chromosome variations than the BBAA genome of tetraploid wheat. We also document that this stronger capacity of the hexaploid BBAA subgenomes behaves as a genetically controlled dominant trait. Our findings bear implications to the known greater than expected level of genetic diversity in, and the remarkable adaptability of, hexaploid common wheat as a staple crop of global significance, as well as in using pentaploidy as intermediates for reciprocal introgression of useful traits between tetraploid and hexaploid wheat cultivars.
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Affiliation(s)
- Xin Deng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhenling Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Fang Wang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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29
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Wu Y, Sun Y, Sun S, Li G, Wang J, Wang B, Lin X, Huang M, Gong Z, Sanguinet KA, Zhang Z, Liu B. Aneuploidization under segmental allotetraploidy in rice and its phenotypic manifestation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1273-1285. [PMID: 29478186 PMCID: PMC5945760 DOI: 10.1007/s00122-018-3077-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/15/2018] [Indexed: 05/24/2023]
Abstract
We report a repertoire of diverse aneuploids harbored by a newly synthesized segmental allotetraploid rice population with fully sequenced sub-genomes and demonstrate their retention features and phenotypic consequences. Aneuploidy, defined as unequal numbers of different chromosomes, is a large-effect genetic variant and may produce diverse cellular and organismal phenotypes. Polyploids are more permissive to chromosomal content imbalance than their diploid and haploid counterparts, and therefore, may enable more in-depth investigation of the phenotypic consequences of aneuploidy. Based on whole-genome resequencing, we identify that ca. 40% of the 312 selfed individual plants sampled from an early generation rice segmental allotetraploid population are constitutive aneuploids harboring 55 distinct aneuploid karyotypes. We document that gain of a chromosome is more prevalent than loss of a chromosome, and the 12 rice chromosomes have distinct tendencies to be in an aneuploid state. These properties of aneuploidy are constrained by multiple factors including the number of genes residing on the chromosome and predicted functional connectivity with other chromosomes. Two broad categories of aneuploidy-associated phenotypes are recognized: those shared by different aneuploids, and those associated with aneuploidy of a specific chromosome. A repertoire of diverse aneuploids in the context of a segmental allotetraploid rice genome with fully sequenced sub-genomes provides a tractable resource to explore the roles of aneuploidy in nascent polyploid genome evolution and helps to decipher the mechanisms conferring karyotypic stabilization on the path to polyploid speciation and towards artificial construction of novel polyploid crops.
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Affiliation(s)
- Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Yue Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuai Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie 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
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Meng Huang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Zhiyun Gong
- Agricultural College, Yangzhou University, Yangzhou, 225009, China
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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30
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Zhu J, Tsai HJ, Gordon MR, Li R. Cellular Stress Associated with Aneuploidy. Dev Cell 2018; 44:420-431. [PMID: 29486194 DOI: 10.1016/j.devcel.2018.02.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 01/10/2023]
Abstract
Aneuploidy, chromosome stoichiometry that deviates from exact multiples of the haploid compliment of an organism, exists in eukaryotic microbes, several normal human tissues, and the majority of solid tumors. Here, we review the current understanding about the cellular stress states that may result from aneuploidy. The topics of aneuploidy-induced proteotoxic, metabolic, replication, and mitotic stress are assessed in the context of the gene dosage imbalance observed in aneuploid cells. We also highlight emerging findings related to the downstream effects of aneuploidy-induced cellular stress on the immune surveillance against aneuploid cells.
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Affiliation(s)
- Jin Zhu
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hung-Ji Tsai
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Molly R Gordon
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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