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Wang L, Feng Y, Wang Y, Zhang J, Chen Q, Liu Z, Liu C, He W, Wang H, Yang S, Zhang Y, Luo Y, Tang H, Wang X. Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH. Int J Mol Sci 2022; 23:ijms232113213. [PMID: 36361999 PMCID: PMC9653872 DOI: 10.3390/ijms232113213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
A precise, rapid and straightforward approach to chromosome identification is fundamental for cytogenetics studies. However, the identification of individual chromosomes was not previously possible for Chinese cherry or other Prunus species due to the small size and similar morphology of their chromosomes. To address this issue, we designed a pool of oligonucleotides distributed across specific pseudochromosome regions of Chinese cherry. This oligonucleotide pool was amplified through multiplex PCR with specific internal primers to produce probes that could recognize specific chromosomes. External primers modified with red and green fluorescence tags could produce unique signal barcoding patterns to identify each chromosome concomitantly. The same oligonucleotide pool could also discriminate all chromosomes in other Prunus species. Additionally, the 5S/45S rDNA probes and the oligo pool were applied in two sequential rounds of fluorescence in situ hybridization (FISH) localized to chromosomes and showed different distribution patterns among Prunus species. At the same time, comparative karyotype analysis revealed high conservation among P. pseudocerasus, P. avium, and P. persica. Together, these findings establish this oligonucleotide pool as the most effective tool for chromosome identification and the analysis of genome organization and evolution in the genus Prunus.
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Affiliation(s)
- Lei Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Feng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenshan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Congli Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 410100, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Shaofeng Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
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Blasio F, Prieto P, Pradillo M, Naranjo T. Genomic and Meiotic Changes Accompanying Polyploidization. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11010125. [PMID: 35009128 PMCID: PMC8747196 DOI: 10.3390/plants11010125] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 05/04/2023]
Abstract
Hybridization and polyploidy have been considered as significant evolutionary forces in adaptation and speciation, especially among plants. Interspecific gene flow generates novel genetic variants adaptable to different environments, but it is also a gene introgression mechanism in crops to increase their agronomical yield. An estimate of 9% of interspecific hybridization has been reported although the frequency varies among taxa. Homoploid hybrid speciation is rare compared to allopolyploidy. Chromosome doubling after hybridization is the result of cellular defects produced mainly during meiosis. Unreduced gametes, which are formed at an average frequency of 2.52% across species, are the result of altered spindle organization or orientation, disturbed kinetochore functioning, abnormal cytokinesis, or loss of any meiotic division. Meiotic changes and their genetic basis, leading to the cytological diploidization of allopolyploids, are just beginning to be understood especially in wheat. However, the nature and mode of action of homoeologous recombination suppressor genes are poorly understood in other allopolyploids. The merger of two independent genomes causes a deep modification of their architecture, gene expression, and molecular interactions leading to the phenotype. We provide an overview of genomic changes and transcriptomic modifications that particularly occur at the early stages of allopolyploid formation.
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Affiliation(s)
- Francesco Blasio
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4048, 14080 Cordova, Spain;
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Tomás Naranjo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
- Correspondence:
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Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum. Heredity (Edinb) 2020; 125:212-226. [PMID: 32523055 PMCID: PMC7490355 DOI: 10.1038/s41437-020-0328-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 02/05/2023] Open
Abstract
Naturally occurring autopolyploid species, such as the autotetraploid potato Solanum tuberosum, face a variety of challenges during meiosis. These include proper pairing, recombination and correct segregation of multiple homologous chromosomes, which can form complex multivalent configurations at metaphase I, and in turn alter allelic segregation ratios through double reduction. Here, we present a reference map of meiotic stages in diploid and tetraploid S. tuberosum using fluorescence in situ hybridisation (FISH) to differentiate individual meiotic chromosomes 1 and 2. A diploid-like behaviour at metaphase I involving bivalent configurations was predominant in all three tetraploid varieties. The crossover frequency per bivalent was significantly reduced in the tetraploids compared with a diploid variety, which likely indicates meiotic adaptation to the autotetraploid state. Nevertheless, bivalents were accompanied by a substantial frequency of multivalents, which varied by variety and by chromosome (7-48%). We identified possible sites of synaptic partner switching, leading to multivalent formation, and found potential defects in the polymerisation and/or maintenance of the synaptonemal complex in tetraploids. These findings demonstrate the rise of S. tuberosum as a model for autotetraploid meiotic recombination research and highlight constraints on meiotic chromosome configurations and chiasma frequencies as an important feature of an evolved autotetraploid meiosis.
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Yang Z, Li X, Liao H, Hu L, Peng C, Wang S, Huang X, Bao Z. A Molecular Cytogenetic Map of Scallop (Patinopecten yessoensis). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:731-742. [PMID: 31473865 DOI: 10.1007/s10126-019-09918-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
To consolidate the genetic, physical, and cytogenetic maps of scallop (Patinopecten yessoensis), we constructed a molecular cytogenetic map by localizing 84 fosmid clones that contain different SNP markers from 19 linkage groups (LGs) using fluorescence in situ hybridization (FISH). Among these 84 SNP-anchored clones, 56 clones produced specific and stable signals on one pair of chromosomes. Dual-color FISH assigned 19 LGs to their corresponding chromosomes with 38 SNP-anchored clones as probes. Among these 19 LGs, 17 LGs were assigned to their corresponding one pair of chromosomes, while two clones containing SNPs from LG10 and LG19 were located on two different pairs of chromosomes separately. The orientation of 7 LGs was corrected according to the chromosome location of SNPs within the same LG. In addition, a probe panel of SNP-anchored clones was developed to identify each chromosome of P. yessoensis. The molecular cytogenetic map will facilitate molecular breeding in scallop and enable comparative studies on chromosome evolution of bivalve mollusk.
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Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Post Office Box 11103, 9700 CC, Groningen, Netherlands
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China
| | - Liping Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Yantai Fisheries Research Institute, Yantai, China
| | - Cheng Peng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shenhai Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Jugulam M, Gill BS. Molecular cytogenetics to characterize mechanisms of gene duplication in pesticide resistance. PEST MANAGEMENT SCIENCE 2018; 74:22-29. [PMID: 28714247 DOI: 10.1002/ps.4665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 06/07/2023]
Abstract
Recent advances in molecular cytogenetics empower construction of physical maps to illustrate the precise position of genetic loci on the chromosomes. Such maps provide visible information about the position of DNA sequences, including the distribution of repetitive sequences on the chromosomes. This is an important step toward unraveling the genetic mechanisms implicated in chromosomal aberrations (e.g., gene duplication). In response to stress, such as pesticide selection, duplicated genes provide an immediate adaptive advantage to organisms that overcome unfavorable conditions. Although the significance of gene duplication as one of the important events driving genetic diversity has been reported, the precise mechanisms of gene duplication that contribute to pesticide resistance, especially to herbicides, are elusive. With particular reference to pesticide resistance, we discuss the prospects of application of molecular cytogenetic tools to uncover mechanism(s) of gene duplication, and illustrate hypothetical models that predict the evolutionary basis of gene duplication. The cytogenetic basis of duplicated genes, their stability, as well as the magnitude of selection pressure, can determine the dynamics of the genetic locus (loci) conferring pesticide resistance not only at the population level, but also at the individual level. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Mithila Jugulam
- Department of Agronomy Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Karafiátová M, Bartoš J, Doležel J. Localization of Low-Copy DNA Sequences on Mitotic Chromosomes by FISH. Methods Mol Biol 2017; 1429:49-64. [PMID: 27511166 DOI: 10.1007/978-1-4939-3622-9_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a widely used method to localize DNA sequences on mitotic and meiotic chromosomes and interphase nuclei. It was developed in early 1980s and since then it has contributed to numerous studies and important discoveries. Over the decades, the protocol was modified for ease of use, allowing for localizing multiple probes simultaneously and increasing its sensitivity and specificity. Despite the continuous improvements, the ability to detect short single-copy sequences of only a few kilobases or less, such as genes, remains limited. Here, we provide a detailed protocol for detection of short, single- or low-copy sequences on plant mitotic metaphase chromosomes.
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Affiliation(s)
- Miroslava Karafiátová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78374, Olomouc, Czech Republic.
| | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78374, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78374, Olomouc, Czech Republic
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Gaiero P, van de Belt J, Vilaró F, Schranz ME, Speranza P, de Jong H. Collinearity between potato (Solanum tuberosum L.) and wild relatives assessed by comparative cytogenetic mapping. Genome 2016; 60:228-240. [PMID: 28169563 DOI: 10.1139/gen-2016-0150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A major bottleneck to introgressive hybridization is the lack of genome collinearity between the donor (alien) genome and the recipient crop genome. Structural differences between the homeologs may create unbalanced segregation of chromosomes or cause linkage drag. To assess large-scale collinearity between potato and two of its wild relatives (Solanum commersonii and Solanum chacoense), we used BAC-FISH mapping of sequences with known positions on the RH potato map. BAC probes could successfully be hybridized to the S. commersonii and S. chachoense pachytene chromosomes, confirming their correspondence with linkage groups in RH potato. Our study shows that the order of BAC signals is conserved. Distances between BAC signals were quantified and compared; some differences found suggest either small-scale rearrangements or reduction/amplification of repeats. We conclude that S. commersonii and S. chacoense are collinear with cultivated Solanum tuberosum on the whole chromosome scale, making these amenable species for efficient introgressive hybridization breeding.
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Affiliation(s)
- Paola Gaiero
- a Department of Plant Biology, Facultad de Agronomía, Universidad de la República, Garzón 780, PC 12900, Montevideo, Uruguay.,b Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, P.O. Box 16, 6708 PB, Wageningen, the Netherlands
| | - José van de Belt
- b Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, P.O. Box 16, 6708 PB, Wageningen, the Netherlands
| | - Francisco Vilaró
- c Horticulture Unit, National Institute for Agricultural Research, Ruta 48 km 10, Las Brujas, Uruguay
| | - M Eric Schranz
- d Biosystematics Group, Wageningen University, Wageningen, the Netherlands
| | - Pablo Speranza
- a Department of Plant Biology, Facultad de Agronomía, Universidad de la República, Garzón 780, PC 12900, Montevideo, Uruguay
| | - Hans de Jong
- b Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, P.O. Box 16, 6708 PB, Wageningen, the Netherlands
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Iwata-Otsubo A, Lin JY, Gill N, Jackson SA. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis. Chromosome Res 2016; 24:197-216. [PMID: 26758200 PMCID: PMC4856725 DOI: 10.1007/s10577-015-9515-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 11/19/2022]
Abstract
Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.
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Affiliation(s)
- Aiko Iwata-Otsubo
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.,Department of Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Jer-Young Lin
- Department of Agronomy, Purdue University, 170 S. University Street, West Lafayette, IN, USA.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Navdeep Gill
- Department of Agronomy, Purdue University, 170 S. University Street, West Lafayette, IN, USA.,Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
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de Boer JM, Datema E, Tang X, Borm TJA, Bakker EH, van Eck HJ, van Ham RCHJ, de Jong H, Visser RGF, Bachem CWB. Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin. BMC Genomics 2015; 16:374. [PMID: 25958312 PMCID: PMC4470070 DOI: 10.1186/s12864-015-1578-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/24/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In flowering plants it has been shown that de novo genome assemblies of different species and genera show a significant drop in the proportion of alignable sequence. Within a plant species, however, it is assumed that different haplotypes of the same chromosome align well. In this paper we have compared three de novo assemblies of potato chromosome 5 and report on the sequence variation and the proportion of sequence that can be aligned. RESULTS For the diploid potato clone RH89-039-16 (RH) we produced two linkage phase controlled and haplotype-specific assemblies of chromosome 5 based on BAC-by-BAC sequencing, which were aligned to each other and compared to the 52 Mb chromosome 5 reference sequence of the doubled monoploid clone DM 1-3 516 R44 (DM). We identified 17.0 Mb of non-redundant sequence scaffolds derived from euchromatic regions of RH and 38.4 Mb from the pericentromeric heterochromatin. For 32.7 Mb of the RH sequences the correct position and order on chromosome 5 was determined, using genetic markers, fluorescence in situ hybridisation and alignment to the DM reference genome. This ordered fraction of the RH sequences is situated in the euchromatic arms and in the heterochromatin borders. In the euchromatic regions, the sequence collinearity between the three chromosomal homologs is good, but interruption of collinearity occurs at nine gene clusters. Towards and into the heterochromatin borders, absence of collinearity due to structural variation was more extensive and was caused by hemizygous and poorly aligning regions of up to 450 kb in length. In the most central heterochromatin, a total of 22.7 Mb sequence from both RH haplotypes remained unordered. These RH sequences have very few syntenic regions and represent a non-alignable region between the RH and DM heterochromatin haplotypes of chromosome 5. CONCLUSIONS Our results show that among homologous potato chromosomes large regions are present with dramatic loss of sequence collinearity. This stresses the need for more de novo reference assemblies in order to capture genome diversity in this crop. The discovery of three highly diverged pericentric heterochromatin haplotypes within one species is a novelty in plant genome analysis. The possible origin and cytogenetic implication of this heterochromatin haplotype diversity are discussed.
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Affiliation(s)
- Jan M de Boer
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: Averis Seeds B.V., Valtherblokken Zuid 40, 7876 TC, Valthermond, The Netherlands.
| | - Erwin Datema
- Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands.
| | - Xiaomin Tang
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: Department of Biology, Colorado State University, Fort Collins, USA.
| | - Theo J A Borm
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Erin H Bakker
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Herman J van Eck
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Roeland C H J van Ham
- Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands.
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Christian W B Bachem
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
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Construction of cytogenetic map of Gossypium herbaceum chromosome 1 and its integration with genetic maps. Mol Cytogenet 2015; 8:2. [PMID: 25628758 PMCID: PMC4307992 DOI: 10.1186/s13039-015-0106-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/08/2015] [Indexed: 12/14/2022] Open
Abstract
Background Cytogenetic map can provide not only information of the genome structure, but also can build a solid foundation for genetic research. With the developments of molecular and cytogenetic studies in cotton (Gossypium), the construction of cytogenetic map is becoming more and more imperative. Results A cytogenetic map of chromosome 1 (A101) of Gossypium herbaceum (A1) which includes 10 bacterial artificial chromosome (BAC) clones was constructed by using fluorescent in situ hybridization (FISH). Meanwhile, comparison and analysis were made for the cytogenetic map of chromosome 1 (A101) of G. herbaceum with four genetic linkage maps of chromosome 1 (Ah01) of G. hirsutum ((AD)1) and one genetic linkage map of chromosome 1 of (A101) G. arboreum (A2). The 10 BAC clones were also used to be localized on G. raimondii (D5) chromosome 1 (D501), and 2 of them showed clear unique hybridized signals. Furthermore, these 2 BAC clones were also shown localized on chromosome 1 of both A sub-genome and D sub-genome of G. hirsutum. Conclusion The comparison of the cytogenetic map with genetic linkage maps showed that most of the identified marker-tagged BAC clones appearing same orders in different maps except three markers showing different positions, which might indicate chromosomal segmental rearrangements. The positions of the 2 BAC clones which were localized on Ah01 and Dh01 chromosomes were almost the same as that on A101 and D501 chromosomes. The corresponding anchored SSR markers of these 2 BAC clones were firstly found to be localized on chromosome D501 (Dh01) as they were not seen mapped like this in any genetic map reported.
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Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome. Mol Genet Genomics 2014; 289:1307-19. [PMID: 25106953 DOI: 10.1007/s00438-014-0891-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 07/18/2014] [Indexed: 10/24/2022]
Abstract
One of the most powerful technologies in unraveling the organization of a eukaryotic plant genome is high-resolution Fluorescent in situ hybridization of repeats and single copy DNA sequences on pachytene chromosomes. This technology allows the integration of physical mapping information with chromosomal positions, including centromeres, telomeres, nucleolar-organizing region, and euchromatin and heterochromatin. In this report, we established chromosomal positions of different repeat fractions of the potato genomic DNA (Cot100, Cot500 and Cot1000) on the chromosomes. We also analysed various repeat elements that are unique to potato including the moderately repetitive P5 and REP2 elements, where the REP2 is part of a larger Gypsy-type LTR retrotransposon and cover most chromosome regions, with some brighter fluorescing spots in the heterochromatin. The most abundant tandem repeat is the potato genomic repeat 1 that covers subtelomeric regions of most chromosome arms. Extensive multiple alignments of these repetitive sequences in the assembled RH89-039-16 potato BACs and the draft assembly of the DM1-3 516 R44 genome shed light on the conservation of these repeats within the potato genome. The consensus sequences thus obtained revealed the native complete transposable elements from which they were derived.
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Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Šimková H. Advances in plant chromosome genomics. Biotechnol Adv 2014; 32:122-36. [DOI: 10.1016/j.biotechadv.2013.12.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 01/09/2023]
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Iacia AAS, Pinto-Maglio CAF. Mapping pachytene chromosomes of coffee using a modified protocol for fluorescence in situ hybridization. AOB PLANTS 2013; 5:plt040. [PMID: 24244840 PMCID: PMC3828664 DOI: 10.1093/aobpla/plt040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
Fluorescence in situ hybridization (FISH) is the most direct method for physically mapping DNA sequences on chromosomes. Fluorescence in situ hybridization mapping of meiotic chromosomes during the pachytene stage is an important tool in plant cytogenetics, because it provides high-resolution measurements of physical distances. Fluorescence in situ hybridization mapping of coffee pachytene chromosomes offers significant advantages compared with FISH mapping of somatic chromosomes, because pachytene chromosomes are 30 times longer and provide additional cytological markers. However, the application of this technique to pachytene chromosomes has been complicated by problems in making preparations of meiotic chromosomes and by difficulties in the application of standard FISH protocols. We have been able to overcome most of these obstacles in applying the FISH technique to the pachytene chromosomes of coffee plants. Digesting the external callose layer surrounding the pollen mother cells (PMCs) in conjunction with other procedures permitted suitable pachytene chromosomes to be obtained by increasing cell permeability, which allowed the probe sequences to enter the cells. For the first time, hybridization signals were registered on coffee pachytene chromosomes using the FISH technique with a repetitive sequence as a probe. We obtained slides on which 80 % of the PMCs had hybridization signals, resulting in FISH labelling with high efficiency. The procedure does not seem to be dependent on the genotype, because hybridization signals were detected in genetically different coffee plants. These findings enhance the possibilities for high-resolution physical mapping of coffee chromosomes.
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Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3-GENES GENOMES GENETICS 2013; 3:2031-47. [PMID: 24062527 PMCID: PMC3815063 DOI: 10.1534/g3.113.007153] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker−based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”.
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Karafiátová M, Bartoš J, Kopecký D, Ma L, Sato K, Houben A, Stein N, Doležel J. Mapping nonrecombining regions in barley using multicolor FISH. Chromosome Res 2013; 21:739-51. [DOI: 10.1007/s10577-013-9380-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 12/22/2022]
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Sun J, Zhang Z, Zong X, Huang S, Li Z, Han Y. A high-resolution cucumber cytogenetic map integrated with the genome assembly. BMC Genomics 2013; 14:461. [PMID: 23834562 PMCID: PMC3710503 DOI: 10.1186/1471-2164-14-461] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/05/2013] [Indexed: 01/05/2023] Open
Abstract
Background High-resolution cytogenetic map can provide not only important biological information on genome organization but also solid foundation for genetic and genomic research. The progress in the molecular and cytogenetic studies has created the basis for developing the cytogenetic map in cucumber (Cucumis sativus L.). Results Here, the cytogenetic maps of four cucumber chromosomes (chromosomes 1, 3–5) were constructed by fluorescence in situ hybridization (FISH) analysis on cucumber pachytene chromosomes. Together with our previously constructed cytogenetic maps of three cucumber chromosomes (chromosomes 2, 6–7), cucumber has a complete cytogenetic map with 76 anchoring points between the genetic, the cytogenetic and the draft genome assembly maps. To compare our pachytene FISH map directly to the genetic linkage and draft genome assembly maps, we used a standardized map unit—relative map position (RMP) to produce the comparative map alignments. The alignments allowed a global view of the relationship of genetic and physical distances along each cucumber chromosome, and accuracy and coverage of the draft genome assembly map. Conclusions We demonstrated a good correlation between positions of the markers in the linkage and physical maps, and essentially complete coverage of chromosome arms by the draft genome assembly. Our study not only provides essential information for the improvement of sequence assembly but also offers molecular tools for cucumber genomics research, comparative genomics and evolutionary study.
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Affiliation(s)
- Jianying Sun
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
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17
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Gan Y, Liu F, Peng R, Wang C, Li S, Zhang X, Wang Y, Wang K. Individual chromosome identification, chromosomal collinearity and genetic-physical integrated map in Gossypium darwinii and four D genome cotton species revealed by BAC-FISH. Genes Genet Syst 2013; 87:233-41. [PMID: 23229310 DOI: 10.1266/ggs.87.233] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The study was conducted on the individual chromosome identification in Gossypium darwinii (A(d)D(d)), G. klotzschianum (D(3k)), G. davidsonii (D(3d)), G. armourianum (D(2-1)) and G. aridum (D(4)) using a multi-probe fluorescence of in situ hybridization (FISH) system. Comparative analysis on their genetic maps with that of physical maps was made as well. The FISH probes used contained two sets of bacterial artificial chromosome (BAC) clones [one is specific to 26 individual chromosomes from A and D subgenomes of G. hirsutum (A(h) and D(h)) while the other is a D genome centromere-specific BAC clone 150D24], 45S and 5S rDNA clones. The results showed that all A(d) chromosomes were marked with the 13 A(h) chromosome-specific BAC clones, whilst all D(d), D(3k), D(3d), D(2-1) and D(4) chromosomes and chromosomal arms were identified with the 13 D(h) chromosome-specific BAC clones and the D genome centromere-specific BAC. According to the homology within D subgenomes which are between A (D) genome and A (D) subgenome, the systematic nomenclature for individual chromosome in the five species was established. The chromosomes of A (D) subgenomes in G. darwinii were named as A(d)01-A(d)13 (D(d)01-D(d)13). The chromosomes in D(3k), D(3d), D(2-1) and D(4) were named as D(3k)01-D(3k)13, D(3d)01-D(3d)13, D(2-1)01-D(2-1)13 and D(4)01-D(4)13, respectively. Based on the successful identification for individual chromosomes, 45S and 5S rDNA were located to the special chromosomes and chromosomal arms for all five species. And there appeared chromosomal collinearity from the BAC clones among different species by comparing BACs positions, which suggested that the majority of chromosome segment homology may exist between D genomes and D subgenome. Moreover, as the genetic map and physical map were integrated, the orientations of genetic maps for D(d) and D genomes of diploid cotton were established. The orientations of some of chromosomes in genetic maps (D(d)03, D(d)04, D(d)06, D(d)09, D(d)10 and D(d)12) were found switched. The SSR marker in the middle of linkage group 04 was corrected at nearby the end of chromosome 04 by FISH. The study will be helpful to establish a theoretical basis using the wild gene bank to exploit more genes aiming for cotton breeding and will provide powerful evidences both for the evolution of Gossypium and assembling the sequences of the obtained and as well the on-going whole genome sequencing projects of cotton.
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Affiliation(s)
- Yimei Gan
- State Key Laboratory of Cotton Biology (China)/Cotton Research Institute of Chinese Academy of Agricultural Science, China
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18
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Interstitial telomeric repeats are enriched in the centromeres of chromosomes in Solanum species. Chromosome Res 2012; 21:5-13. [PMID: 23250588 DOI: 10.1007/s10577-012-9332-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Revised: 11/27/2012] [Accepted: 12/06/2012] [Indexed: 01/05/2023]
Abstract
Interstitial telomeric repeats (ITRs) were reported in a number of animal and plant species. Most ITRs are organized as short tandem arrays and are likely evolutionary relics derived from chromosomal rearrangements and DNA repairs. However, megabase-sized ITR arrays were reported in Solanum species. Here, we report a fluorescence in situ hybridization (FISH) survey of ITRs in all representative diploid Solanum species, including potato, tomato, and eggplant. FISH revealed massive amplification of ITRs in the centromeric regions of chromosomes from the Solanum species containing the B and P genomes. A significant proportion of the ITR FISH signals was mapped within the primary constrictions of the pachytene chromosomes of Solanum pinnatisectum (B genome). In addition, some ITR sites overlapped with St49, a satellite repeat enriched in centromeric DNA sequences associated with CENH3 nucleosomes, in both A and B genome Solanum species. These results show that some ITR subfamilies have been amplified and invaded in the functional centromeres of chromosomes in Solanum species.
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Paesold S, Borchardt D, Schmidt T, Dechyeva D. A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome-arm identification, integration of genetic linkage groups and analysis of major repeat family distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:600-11. [PMID: 22775355 DOI: 10.1111/j.1365-313x.2012.05102.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We developed a reference karyotype for B. vulgaris which is applicable to all beet cultivars and provides a consistent numbering of chromosomes and genetic linkage groups. Linkage groups of sugar beet were assigned to physical chromosome arms by FISH (fluorescent in situ hybridization) using a set of 18 genetically anchored BAC (bacterial artificial chromosome) markers. Genetic maps of sugar beet were correlated to chromosome arms, and North-South orientation of linkage groups was established. The FISH karyotype provides a technical platform for genome studies and can be applied for numbering and identification of chromosomes in related wild beet species. The discrimination of all nine chromosomes by BAC probes enabled the study of chromosome-specific distribution of the major repetitive components of sugar beet genome comprising pericentromeric, intercalary and subtelomeric satellites and 18S-5.8S-25S and 5S rRNA gene arrays. We developed a multicolor FISH procedure allowing the identification of all nine sugar beet chromosome pairs in a single hybridization using a pool of satellite DNA probes. Fiber-FISH was applied to analyse five chromosome arms in which the furthermost genetic marker of the linkage group was mapped adjacently to terminal repetitive sequences on pachytene chromosomes. Only on two arms telomere arrays and the markers are physically linked, hence these linkage groups can be considered as terminally closed making the further identification of distal informative markers difficult. The results support genetic mapping by marker localization, the anchoring of contigs and scaffolds for the annotation of the sugar beet genome sequence and the analysis of the chromosomal distribution patterns of major families of repetitive DNA.
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MESH Headings
- Beta vulgaris/genetics
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Plant/genetics
- DNA Probes/genetics
- DNA, Plant/analysis
- DNA, Plant/genetics
- DNA, Satellite/analysis
- DNA, Satellite/genetics
- Genetic Linkage
- Genetic Markers
- Genome, Plant
- In Situ Hybridization, Fluorescence/methods
- Karyotype
- Pachytene Stage
- Physical Chromosome Mapping/methods
- RNA, Ribosomal/analysis
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/analysis
- RNA, Ribosomal, 5.8S/genetics
- Reference Standards
- Tandem Repeat Sequences
- Telomere/genetics
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Affiliation(s)
- Susanne Paesold
- Institute of Botany, Dresden University of Technology, Zellescher Weg 20b, 01217 Dresden, Germany
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20
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Gan Y, Chen D, Liu F, Wang C, Li S, Zhang X, Wang Y, Peng R, Wang K. Individual chromosome assignment and chromosomal collinearity in Gossypium thurberi, G. trilobum and D subgenome of G. barbadense revealed by BAC-FISH. Genes Genet Syst 2012; 86:165-74. [PMID: 21952206 DOI: 10.1266/ggs.86.165] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The experiment on individual chromosome assignments and chromosomal diversity was conducted using a multi-probe fluorescence in situ hybridization (FISH) system in D subgenome of tetraploid Gossypium barbadense (D(b)), G. thurberi (D(1)) and G. trilobum (D(8)), which the later two were the possible subgenome donors of tetraploid cottons. The FISH probes contained a set of bacterial artificial chromosome (BAC) clones specific to 13 individual chromosomes from D subgenome of G. hirsutum (D(h)), a D genome centromere-specific BAC clone 150D24, 45S and 5S ribosomal DNA (rDNA) clones, respectively. All tested chromosome orientations were confirmed by the centromere-specific BAC probe. In D(1) and D(8), four 45S rDNA loci were found assigning at the end of the short arm of chromosomes 03, 07, 09 and 11, while one 5S rDNA locus was successfully marked at pericentromeric region of the short arm of chromosome 09. In D(b), three 45S rDNA loci and two 5S rDNA loci were found out. Among them, two 45S rDNA loci were located at the terminal of the short arm of chromosomes D(b)07 and D(b)09, whilst one 5S rDNA locus was found situating near centromeric region of the short arm of chromosome D(b)09. The positions of the BAC clones specific to the 13 individual chromosomes from D(h) were compared between D(1), D(8) and D(b). The result showed the existence of chromosomal collinearity within D(1) and D(8), and as well between them and D(b). The results will serve as a base for understanding chromosome structure of cotton and polyploidy evolution of cotton genome and will provide bio-information for assembling the sequences of finished and the on-going cotton whole genome sequencing projects.
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Affiliation(s)
- Yimei Gan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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21
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de Boer JM, Borm TJA, Jesse T, Brugmans B, Wiggers-Perebolte L, de Leeuw L, Tang X, Bryan GJ, Bakker J, van Eck HJ, Visser RGF. A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome. BMC Genomics 2011; 12:594. [PMID: 22142254 PMCID: PMC3261212 DOI: 10.1186/1471-2164-12-594] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 12/05/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). RESULTS First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. CONCLUSIONS The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
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Affiliation(s)
- Jan M de Boer
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalstesteeg 1, 6708 PD Wageningen, The Netherlands.
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22
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Zatloukalová P, Hřibová E, Kubaláková M, Suchánková P, Simková H, Adoración C, Kahl G, Millán T, Doležel J. Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes. Chromosome Res 2011; 19:729-39. [PMID: 21947955 DOI: 10.1007/s10577-011-9235-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 08/20/2011] [Accepted: 08/23/2011] [Indexed: 11/29/2022]
Abstract
Cultivated chickpea is the third most important legume after field bean and garden pea worldwide. Despite considerable breeding towards improved yield and resistance to biotic and abiotic stresses, the production of chickpea remained stagnant, but molecular tools are expected to increase the impact of current improvement programs. As a first step towards this goal, various genetic linkage maps have been established and markers linked to resistance genes been identified. However, until now, only one linkage group (LG) has been assigned to a specific chromosome. In the present work, mitotic chromosomes were sorted using flow cytometry and used as template for PCR with primers designed for genomic regions flanking microsatellites. These primers amplify sequence-tagged microsatellite site markers. This approach confirmed the assignment of LG8 to the smallest chromosome H. For the first time, LG5 was linked to the largest chromosome A, LG4 to a medium-sized chromosome E, while LG3 was anchored to the second largest chromosome B. Chromosomes C and D could not be flow-sorted separately and were jointly associated to LG6 and LG7. By the same token, chromosomes F and G were anchored to LG1 and LG2. To establish a set of preferably diagnostic cytogenetic markers, the genomic distribution of various probes was verified using FISH. Moreover, a partial genomic bacterial artificial chromosome (BAC) library was constructed and putative single/low-copy BAC clones were mapped cytogenetically. As a result, two clones were identified localizing specifically to chromosomes E and H, for which no cytogenetic markers were yet available.
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Affiliation(s)
- Pavlína Zatloukalová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Sokolovská 6, 77200 Olomouc, Czech Republic
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23
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Genome sequence and analysis of the tuber crop potato. Nature 2011; 475:189-95. [PMID: 21743474 DOI: 10.1038/nature10158] [Citation(s) in RCA: 1198] [Impact Index Per Article: 92.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 05/03/2011] [Indexed: 02/03/2023]
Abstract
Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.
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Comparative FISH mapping of Daucus species (Apiaceae family). Chromosome Res 2011; 19:493-506. [DOI: 10.1007/s10577-011-9202-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 03/10/2011] [Accepted: 03/13/2011] [Indexed: 10/18/2022]
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25
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Lesniewska K, Książkiewicz M, Nelson MN, Mahé F, Aïnouche A, Wolko B, Naganowska B. Assignment of 3 Genetic Linkage Groups to 3 Chromosomes of Narrow-Leafed Lupin. J Hered 2010; 102:228-36. [DOI: 10.1093/jhered/esq107] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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26
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Achenbach UC, Tang X, Ballvora A, de Jong H, Gebhardt C. Comparison of the chromosome maps around a resistance hot spot on chromosome 5 of potato and tomato using BAC-FISH painting. Genome 2010; 53:103-10. [PMID: 20140028 DOI: 10.1139/g09-086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Potato chromosome 5 harbours numerous genes for important qualitative and quantitative traits, such as resistance to the root cyst nematode Globodera pallida and the late blight fungus, Phytophthora infestans. The genes make up part of a "hot spot" for resistances to various pathogens covering a genetic map length of 3 cM between markers GP21 and GP179. We established the physical size and position of this region on chromosome 5 in potato and tomato using fluorescence in situ hybridization (FISH) on pachytene chromosomes. Five potato bacterial artificial chromosome (BAC) clones with the genetically anchored markers GP21, R1-contig (proximal end), CosA, GP179, and StPto were selected, labeled with different fluorophores, and hybridized in a five-colour FISH experiment. Our results showed the location of the BAC clones in the middle of the long arm of chromosome 5 in both potato and tomato. Based on chromosome measurements, we estimate the physical size of the GP21-GP179 interval at 0.85 Mb and 1.2 Mb in potato and tomato, respectively. The GP21-GP179 interval is part of a genome segment known to have inverted map positions between potato and tomato.
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Affiliation(s)
- Ute C Achenbach
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Köln, Germany
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