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The r-X1 deletion induces terminal deficiencies in the maize B chromosome. Chromosome Res 2021; 29:351-360. [PMID: 34480269 DOI: 10.1007/s10577-021-09671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 10/20/2022]
Abstract
In addition to causing the nondisjunction of maize B and normal A chromosomes at the second megaspore division during embryo sac development, the r-X1 deletion results in terminal deficiencies (TDs) in various A chromosomal arms, but whether the r-X1 deletion also induces TDs of the maize B chromosome remains unknown. To answer this question, the chromosomal composition in the r-X1-containing progeny of r-X1/R-r female parents carrying two standard B chromosomes was determined. Nine of 104 (8.7%) examined kernels contained a smaller telocentric B chromosome, and one of these (designated Bdef-1) was further identified as a TD with a breakpoint in the third distal heterochromatic region of the B chromosome. Thus, the results indicated that the r-X1 deletion could also induce TDs of the maize B chromosome during megaspore divisions. The Bdef-1 chromosome lacked nondisjunctional behavior, and this behavior was restored by the presence of the B chromosome in the cell. A transmission analysis of the Bdef-1 chromosome revealed that loss of the distal portion of the B chromosome reduced female but not male transmission of the B chromosome. Furthermore, the Bdef-1 chromosome was used to more finely map B-derived miRNA genes on the B chromosome. Our results indicate that the r-X1 deletion results in TDs of the B chromosome in maize, and the r-X1 deletion system can thus be used to generate a series of terminally truncated B chromosomes that may be used to map features of the B chromosome, including genes and properties related to B chromosome functions.
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Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution. Proc Natl Acad Sci U S A 2021; 118:2104254118. [PMID: 34088847 PMCID: PMC8201846 DOI: 10.1073/pnas.2104254118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
B chromosomes are enigmatic elements in thousands of plant and animal genomes that persist in populations despite being nonessential. They circumvent the laws of Mendelian inheritance but the molecular mechanisms underlying this behavior remain unknown. Here we present the sequence, annotation, and analysis of the maize B chromosome providing insight into its drive mechanism. The sequence assembly reveals detailed locations of the elements involved with the cis and trans functions of its drive mechanism, consisting of nondisjunction at the second pollen mitosis and preferential fertilization of the egg by the B-containing sperm. We identified 758 protein-coding genes in 125.9 Mb of B chromosome sequence, of which at least 88 are expressed. Our results demonstrate that transposable elements in the B chromosome are shared with the standard A chromosome set but multiple lines of evidence fail to detect a syntenic genic region in the A chromosomes, suggesting a distant origin. The current gene content is a result of continuous transfer from the A chromosomal complement over an extended evolutionary time with subsequent degradation but with selection for maintenance of this nonvital chromosome.
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Novel B-chromosome-specific transcriptionally active sequences are present throughout the maize B chromosome. Mol Genet Genomics 2019; 295:313-325. [PMID: 31729549 DOI: 10.1007/s00438-019-01623-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
Supernumerary B chromosomes are dispensable parts of the nuclear genome and occur in all eukaryotic groups. They differ from the normal A chromosomes in morphology, genetic behavior, and inheritance. Because they are nonessential for individual development, B chromosomes are considered to be genetically inert and to lack functional genes. However, the maize B chromosome carries control elements that direct its behavior and affects A chromosomes during cell division. Therefore, the maize B chromosome might contain genic regions that differ from the genic regions of A chromosomes. Yet, only a few B-specific transcript sequences have been isolated. To identify more B-specific transcriptionally active sequences, we constructed de novo transcriptome assemblies for maize B73 inbred lines with 0B (+0B) and 2B (+2B). Comparative analysis of the B73 + 0B and B73 + 2B assemblies revealed that unigenes annotated to 201 gene ontology terms were differentially expressed. Using RT-PCR analysis of novel transcript sequences specific to B73 + 2B, we identified 32 novel B-related transcript sequences, and most sequences showed consistent B-specific transcription in different inbred lines. Moreover, 20 of those novel B-related transcript sequences were further confirmed to be located only on the B chromosome by genomic PCR analysis. A total of 19 novel B-specific transcript sequences were mapped to various positions along the B chromosome using B-10L translocations. Taken together, our results suggest that the maize B chromosome indeed affects the expression of A-located genes and that a substantial amount of novel B-specific transcriptionally active sequences are present throughout the maize B chromosome. Therefore, the maize B chromosome seems not to be genetically inert.
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Huang YH, Peng SF, Lin YP, Cheng YM. The maize B chromosome is capable of expressing microRNAs and altering the expression of microRNAs derived from A chromosomes. Chromosome Res 2019; 28:129-138. [PMID: 31712937 DOI: 10.1007/s10577-019-09620-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 11/30/2022]
Abstract
Supernumerary B chromosomes (Bs) are nonessential chromosomes that are considered genetically inert. However, the maize B carries control elements that direct its behavior, such as that of nondisjunction, during the second pollen mitosis, and affects normal A chromosomes during cell division. Recently, the maize B has been found to contain transcriptionally active sequences and to affect the transcription of genes on A chromosomes. To better understand the regulatory mechanisms underlying the maize B, we constructed two small RNA libraries from maize B73 inbred lines with and without Bs. The sequencing results revealed that 18 known microRNAs (miRNAs) were significantly differentially expressed in response to the presence of the B, and most target mRNAs were characterized as transcription factors. Moreover, three novel B-derived miRNAs were identified via stem-loop reverse transcriptase-polymerase chain reaction (RT-PCR)-based analysis, and all showed consistent B-specific expression in almost all analyzed inbred lines and in all tissue types, including leaves, roots, and pollen grains. By the use of B-10L translocations, the three B-derived miRNAs were mapped to specific B regions. The results from this study suggest that the maize B can express miRNAs and affect the expression of A-derived miRNAs, which could regulate the expression of A-located genes.
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Affiliation(s)
- Yen-Hua Huang
- Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan
| | - Shu-Fen Peng
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Yao-Pin Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ya-Ming Cheng
- Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan.
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Huang W, Du Y, Zhao X, Jin W. B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.). BMC PLANT BIOLOGY 2016; 16:88. [PMID: 27083560 PMCID: PMC4833949 DOI: 10.1186/s12870-016-0775-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/11/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND The dispensable maize (Zea mays L.) B chromosome is highly heterochromatic and widely believed to be devoid of functional genes. Although low-copy B chromosome causes no obvious phenotype variation, its existence might influence A genome gene expression. Previous studies suggested that B chromosomes are evolved from standard chromosomes; therefore, they might contain genic regions showing homology with A chromosome sequences. RESULTS Our data suggested that maize B chromosome influences the A-genome transcription with stronger effect associated with an increase in copy number of B chromosome. In total 130 differently expressed genes were detected in comparison between with and without B chromosome lines. These differentially expressed genes are mainly involved in cell metabolism and nucleotide binding. Using Starter + B, we amplified ten B chromosome loci with high sequence similarity to A-genome genes. Fluorescence in situ hybridization (FISH) confirmed that at least four ~5 kb-sized genes are located on the B chromosome. In addition, through de novo assembly of the reads not unmapped to maize B73 reference genome together with PCR validation, we found three B-located LTR; in particular, one of them, the 3.2 kb comp75688, is expressed in a B-dosage dependent manner. CONCLUSION We found that in the presence of maize B chromosome, the transcription of A genome genes was altered, with more impact by the increase of the B chromosome number. The B-located transcriptionally active genes showed high similarity to their A-genome homologues, and retrotransposons on B chromosome also have partial homologous to A genome sequences. Our data shed more lights on the genome structure and evolution of the maize B chromosome.
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Affiliation(s)
- Wei Huang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yan Du
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xin Zhao
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Weiwei Jin
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
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Cheng YM, Feng YR, Lin YP, Peng SF. Cytomolecular characterization and origin of de novo formed maize B chromosome variants. Chromosome Res 2016; 24:183-95. [PMID: 26748511 DOI: 10.1007/s10577-015-9516-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/20/2015] [Accepted: 12/29/2015] [Indexed: 10/22/2022]
Abstract
B chromosomes are dispensable elements that occur in many species, including maize. The maize B chromosome is acrocentric and highly heterochromatic and undergoes nondisjunction during the second pollen mitosis. In this study, we determined the genetic behavior and organization of two naturally occurring B chromosome variants (designated B(ta) and B(tb)). The morphology and genetic behavior of the B(ta) chromosome were similar to those of the typical B chromosome, but the B(ta) chromosome contained a deletion in the first heterochromatin region and had higher transmission frequencies through both male and female parents. The B(tb) chromosome was reduced in size, consisted primarily of heterochromatin, and had a lower transmission frequency. The B(tb) chromosome lacked nondisjunctional behavior, which was restored by the presence of normal B chromosomes in the cell. Furthermore, the B(tb) chromosome contained two centromeric regions, only one of which was active. The organization of these two naturally occurring B chromosome variants was also determined using fluorescence in situ hybridization with B-associated sequences and by amplification of B-specific molecular markers to create possible evolutionary models.
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Affiliation(s)
- Ya-Ming Cheng
- Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan.
| | - Ying-Ru Feng
- Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan
| | - Yao-Pin Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Fen Peng
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
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Mei Z, Zhou B, Wei C, Cheng J, Imani S, Chen H, Fu J. Genetic Authentication of Gardenia jasminoides Ellis var. grandiflora Nakai by Improved RAPD-Derived DNA Markers. Molecules 2015; 20:20219-29. [PMID: 26569205 PMCID: PMC6331946 DOI: 10.3390/molecules201119687] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/18/2015] [Accepted: 11/03/2015] [Indexed: 11/19/2022] Open
Abstract
The evergreen shrub, Gardenia jasminoides Ellis var. grandiflora Nakai is one of the most popular garden-plants, with significant ornamental importance. Here, we have cloned improved random amplified polymorphic DNA (RAPD) derived fragments into T-vector, and developed sequence-characterized amplified region (SCAR) markers. These markers have been deposited in GenBank database with the accession numbers KP641310, KP641311, KP641312 and KP641313 respectively. The BLAST search of database confirmed the novelty of these markers. The four SCAR markers, namely ZZH11, ZZH31, ZZH41 and ZZH51 can specifically recognize the genetic materials of G. jasminoides from other plant species. Moreover, SCAR marker ZZH31 can be used to distinguish G. jasminoides Ellis var. grandiflora Nakai from other G. jasminoides on the market. Together, this study has developed four stably molecular SCAR markers by improved RAPD-derived DNA markers for the genetic identification and authentication, and for ecological conservation of medicinal and ornamental plant G. jasminoides.
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Affiliation(s)
- Zhiqiang Mei
- Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou 646000, China.
| | - Boxu Zhou
- Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou 646000, China.
| | - Chunli Wei
- Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou 646000, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR) 999078, China.
| | - Jingliang Cheng
- Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou 646000, China.
| | - Saber Imani
- Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou 646000, China.
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran 14359-44711, Iran.
| | - Hanchun Chen
- Department of Biochemistry, School of Life Sciences & the State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China.
| | - Junjiang Fu
- Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou 646000, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR) 999078, China.
- Judicial Authentication Center, Sichuan Medical University, Luzhou 646000, China.
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