1
|
Mason AS, Rousseau-Gueutin M, Morice J, Bayer PE, Besharat N, Cousin A, Pradhan A, Parkin IAP, Chèvre AM, Batley J, Nelson MN. Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis. Genetics 2016; 202:513-23. [PMID: 26614742 PMCID: PMC4788232 DOI: 10.1534/genetics.115.183210] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/23/2015] [Indexed: 11/18/2022] Open
Abstract
Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.
Collapse
Affiliation(s)
- Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia
| | | | - Jérôme Morice
- IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France
| | - Philipp E Bayer
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia
| | - Naghmeh Besharat
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia
| | - Anouska Cousin
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia
| | - Aneeta Pradhan
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada
| | - Anne-Marie Chèvre
- IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France
| | - Jacqueline Batley
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia
| | - Matthew N Nelson
- School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom
| |
Collapse
|
2
|
Cseh A, Kruppa K, Molnár I, Rakszegi M, Doležel J, Molnár-Láng M. Characterization of a new 4BS.7HL wheat–barley translocation line using GISH, FISH, and SSR markers and its effect on the β-glucan content of wheat. Genome 2011; 54:795-804. [DOI: 10.1139/g11-044] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A spontaneous interspecific Robertsonian translocation was revealed by genomic in situ hybridization (GISH) in the progenies of a monosomic 7H addition line originating from a new wheat ‘Asakaze komugi’ × barley ‘Manas’ hybrid. Fluorescence in situ hybridization (FISH) with repetitive DNA sequences (Afa family, pSc119.2, and pTa71) allowed identification of all wheat chromosomes, including wheat chromosome arm 4BS involved in the translocation. FISH using barley telomere- and centromere-specific repetitive DNA probes (HvT01 and (AGGGAG)n) confirmed that one of the arms of barley chromosome 7H was involved in the translocation. Simple sequence repeat (SSR) markers specific to the long (L) and short (S) arms of barley chromosome 7H identified the translocated chromosome segment as 7HL. Further analysis of the translocation chromosome clarified the physical position of genetically mapped SSRs within 7H, with a special focus on its centromeric region. The presence of the HvCslF6 gene, responsible for (1,3;1,4)-β-d-glucan production, was revealed in the centromeric region of 7HL. An increased (1,3;1,4)-β-d-glucan level was also detected in the translocation line, demonstrating that the HvCslF6 gene is of potential relevance for the manipulation of wheat (1,3;1,4)-β-d-glucan levels.
Collapse
Affiliation(s)
- A. Cseh
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
| | - K. Kruppa
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
| | - I. Molnár
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
| | - M. Rakszegi
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
| | - J. Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
| | - M. Molnár-Láng
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
| |
Collapse
|
3
|
Alwala S, Kimbeng CA, Williams WP, Kang MS. Molecular Markers Associated with Resistance toAspergillus flavusin Maize Grain: QTL and Discriminant Analyses. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/15228860701879067] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Sreedhar Alwala
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Collins A. Kimbeng
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - W. P. Williams
- USDA- ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS, USA
| | - Manjit S. Kang
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
- Vice Chancellor, Punjab Agricultural University, Ludhiana, 141 004, India
| |
Collapse
|
4
|
Pouilly N, Delourme R, Alix K, Jenczewski E. Repetitive sequence-derived markers tag centromeres and telomeres and provide insights into chromosome evolution in Brassica napus. Chromosome Res 2008; 16:683-700. [PMID: 18535916 DOI: 10.1007/s10577-008-1219-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 03/17/2008] [Accepted: 03/17/2008] [Indexed: 10/22/2022]
Abstract
Centromeres and telomeres are obvious markers on chromosomes but their location on genetic maps is difficult to determine, which hampers many basic and applied research programmes. In this study, we used the characteristic distribution of five Brassica repeated sequences to generate physically anchored molecular markers tentatively tagging Brassica centromeres (84 markers) and telomeres (31 markers). These markers were mapped to the existing oilseed rape genetic map. Clusters of centromere-related loci were observed on 14 linkage groups; in addition to previous reports, we could thus provide information about the most likely position of centromeres on 17 of the 19 B. napus linkage groups. The location of centromeres on linkage groups usually matches their position on chromosomes and coincides with sites of evolutionary breakage between chromosomes. Most telomere sequence-derived markers mapped interstitially or in the proximity of centromeres; this result echoes previous reports on many eukaryote genomes and may reflect different forms of chromosome evolution. Seven telomere sequence-derived markers were located at the outermost positions of seven linkage groups and therefore probably tagged telomeres.
Collapse
Affiliation(s)
- Nicolas Pouilly
- INRA, Agrocampus Rennes, Université Rennes 1, UMR 118 Amélioration des Plantes et Biotechnologies Végétales, Le Rheu Cedex, France
| | | | | | | |
Collapse
|
5
|
Okagaki RJ, Jacobs MS, Stec AO, Kynast RG, Buescher E, Rines HW, Vales MI, Riera-Lizarazu O, Schneerman M, Doyle G, Friedman KL, Staub RW, Weber DF, Kamps TL, Amarillo IFE, Chase CD, Bass HW, Phillips RL. Maize centromere mapping: a comparison of physical and genetic strategies. ACTA ACUST UNITED AC 2008; 99:85-93. [PMID: 18216028 DOI: 10.1093/jhered/esm111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Centromere positions on 7 maize chromosomes were compared on the basis of data from 4 to 6 mapping techniques per chromosome. Centromere positions were first located relative to molecular markers by means of radiation hybrid lines and centric fission lines recovered from oat-maize chromosome addition lines. These centromere positions were then compared with new data from centric fission lines recovered from maize plants, half-tetrad mapping, and fluorescence in situ hybridizations and to data from earlier studies. Surprisingly, the choice of mapping technique was not the critical determining factor. Instead, on 4 chromosomes, results from all techniques were consistent with a single centromere position. On chromosomes 1, 3, and 6, centromere positions were not consistent even in studies using the same technique. The conflicting centromere map positions on chromosomes 1, 3, and 6 could be explained by pericentric inversions or alternative centromere positions on these chromosomes.
Collapse
Affiliation(s)
- Ron J Okagaki
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108-6026, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Luce AC, Sharma A, Mollere OSB, Wolfgruber TK, Nagaki K, Jiang J, Presting GG, Dawe RK. Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-polymerase chain reaction. Genetics 2006; 174:1057-61. [PMID: 16951073 PMCID: PMC1602074 DOI: 10.1534/genetics.106.060467] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Centromeres are difficult to map even in species where genetic resolution is excellent. Here we show that junctions between repeats provide reliable single-copy markers for recombinant inbred mapping within centromeres and pericentromeric heterochromatin. Repeat junction mapping was combined with anti-CENH3-mediated ChIP to provide a definitive map position for maize centromere 8.
Collapse
Affiliation(s)
- Amy C Luce
- Department of Plant Biology, University of Georgia, Georgia 30602, USA
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Abstract
An isochromosome was found in the maize HiII Parent B line during somatic karyotyping with a multiprobe fluorescence in situ hybridization (FISH) system. Cytological analyses showed that it pairs with the short arm of chromosome 8 during the pachytene stage of meiosis. The chromosome 8 short arm origin of this isochromosome was also confirmed by FISH at mitotic metaphase. Knob heterochromatin signals were present at the short arms of chromosome 8 when subjected to prolonged exposure and also observed at both ends of the isochromosome. This isochromosome can be a univalent or a trivalent by pairing with the normal chromosome 8 short arms during meiosis. At anaphase and telophase, the isochromosome lagged behind other chromosomes. It had a transmission rate of 17%–20% from both male and female gametes. One plant homozygous for the isochromosome contained 2 isochromosomes that differed in the quantity of their CentC centromere repeat sequence. Both variations of the isochromosome were transmitted to the next generation. Because the 2 isochromosomes should be identical by descent, these observations document a radical change in copy number of the centromere repeat array within 1 generation. Plants with 1 isochromosome were not normal as compared with the original HiII Parent B plants. Those that contained a pair of this isochromosome (6 total copies of 8S) were even more abnormal and had reduced fertility. The results indicate the ability of the somatic karyotyping system to recognize and characterize chromosomal aberrations.Key words: maize, isochromosome, FISH, karyotyping, chromosomal aberration.
Collapse
Affiliation(s)
- Weichang Yu
- Division of Biological Sciences, University of Missouri-Columbia, 65211, USA
| | | | | | | |
Collapse
|