Precise Centromere Mapping Using a Combination of Repeat Junction Markers and Chromatin Immunoprecipitation–Polymerase Chain Reaction

Luce, Amy C.; Sharma, Anupma; Mollere, Oliver S. B.; Wolfgruber, Thomas; Nagaki, Kiyotaka; Jiang, Jiming; Presting, Gernot G.; Dawe, R. Kelly

doi:10.1534/genetics.106.060467

Cited by 29 publications

(22 citation statements)

References 21 publications

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“…The centromere, as marked by the CentC cluster, is located between tda66d at 9S.03 and cdo17 at 9L.03. This position is close to but not the same as that determined by Luce et al (2006), using a CenH3-based method of centromere mapping. Placing centromeres on the genetic map is an indirect form of linkage mapping and it is further complicated by the dynamic nature of centromeres and their epigenetic specification Lee et al 2005;Luce et al 2006).…”

Section: Discussionsupporting

confidence: 68%

A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescencein SituHybridization Map of Maize (Zea maysL.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

Amarillo

Bass

2007

Genetics

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A cytogenetic FISH map of maize pachytene-stage chromosome 9 was produced with 32 maize markerselected sorghum BACs as probes. The genetically mapped markers used are distributed along the linkage maps at an average spacing of 5 cM. Each locus was mapped by means of multicolor direct FISH with a fluorescently labeled probe mix containing a whole-chromosome paint, a single sorghum BAC clone, and the centromeric sequence, CentC. A maize-chromosome-addition line of oat was used for bright unambiguous identification of the maize 9 fiber within pachytene chromosome spreads. The locations of the sorghum BAC-FISH signals were determined, and each new cytogenetic locus was assigned a centiMcClintock position on the short (9S) or long (9L) arm. Nearly all of the markers appeared in the same order on linkage and cytogenetic maps but at different relative positions on the two. The CentC FISH signal was localized between cdo17 (at 9L.03) and tda66 (at 9S.03). Several regions of genome hyperexpansion on maize chromosome 9 were found by comparative analysis of relative marker spacing in maize and sorghum. This transgenomic cytogenetic FISH map creates anchors between various maps of maize and sorghum and creates additional tools and information for understanding the structure and evolution of the maize genome.

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Section: Discussionsupporting

confidence: 68%

A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescencein SituHybridization Map of Maize (Zea maysL.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

Amarillo

Bass

2007

Genetics

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“…ISBPs and RJMs are based on unique and genome‐specific insertion junctions generated by transposable elements that contribute to approximately 80% of the wheat genome (Dvořák, ). TE junctions are randomly distributed along chromosomes, present in both hetero‐ and euchromatin and thus suitable for high‐density RH mapping of the entire genome including centromeres and pericentromeric heterochromatin‐rich regions (Luce et al ., ). Most notably, the highest map resolution was previously obtained in centromere near bins employing RH mapping technique in combination with ISBP markers (Kobayashi et al ., ).…”

Section: Discussionmentioning

confidence: 97%

High‐resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTLQfhs.ifa‐5A

Buerstmayr

Steiner

Wagner

et al. 2017

Plant Biotechnology Journal

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SummaryThe Qfhs.ifa‐5A allele, contributing to enhanced Fusarium head blight resistance in wheat, resides in a low‐recombinogenic region of chromosome 5A close to the centromere. A near‐isogenic RIL population segregating for the Qfhs.ifa‐5A resistance allele was developed and among 3650 lines as few as four recombined within the pericentromeric C‐5AS1‐0.40 bin, yielding only a single recombination point. Genetic mapping of the pericentromeric region using a recombination‐dependent approach was thus not successful. To facilitate fine‐mapping the physically large Qfhs.ifa‐5A interval, two gamma‐irradiated deletion panels were generated: (i) seeds of line NIL3 carrying the Qfhs.ifa‐5A resistance allele in an otherwise susceptible background were irradiated and plants thereof were selfed to obtain deletions in homozygous state and (ii) a radiation hybrid panel was produced using irradiated pollen of the wheat line Chinese Spring (CS) for pollinating the CS‐nullisomic5Atetrasomic5B. In total, 5157 radiation selfing and 276 radiation hybrid plants were screened for deletions on 5AS and plants containing deletions were analysed using 102 5AS‐specific markers. Combining genotypic information of both panels yielded an 817‐fold map improvement (cR/cM) for the centromeric bin and was 389‐fold increased across the Qfhs.ifa‐5A interval compared to the genetic map, with an average map resolution of 0.77 Mb/cR. We successfully proved that the RH mapping technique can effectively resolve marker order in low‐recombining regions, including pericentromeric intervals, and simultaneously allow developing an in vivo panel of sister lines differing for induced deletions across the Qfhs.ifa‐5A interval that can be used for phenotyping.

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“…PCR-based repeat-junction markers have been used to investigate haplotype variations of TE insertions Devos et al, 2005;Luce et al, 2006;You et al, 2010), but this method is only suitable for analyses of a limited numbers of TE families. Sequencing and recent resequencing of many plant genomes have provided unprecedented opportunities to investigate genome-wide TE insertions within a recent evolutionary time frame and at a population level.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean

et al. 2012

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Preferential accumulation of transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), in recombination-suppressed pericentromeric regions seems to be a general pattern of TE distribution in flowering plants.However, whether such a pattern was formed primarily by preferential TE insertions into pericentromeric regions or by selection against TE insertions into euchromatin remains obscure. We recently investigated TE insertions in 31 resequenced wild and cultivated soybean (Glycine max) genomes and detected 34,154 unique nonreference TE insertions mappable to the reference genome. Our data revealed consistent distribution patterns of the nonreference LTR-RT insertions and those present in the reference genome, whereas the distribution patterns of the nonreference DNA TE insertions and the accumulated ones were significantly different. The densities of the nonreference LTR-RT insertions were found to negatively correlate with the rates of local genetic recombination, but no significant correlation between the densities of nonreference DNA TE insertions and the rates of local genetic recombination was detected. These observations suggest that distinct insertional preferences were primary factors that resulted in different levels of effectiveness of purifying selection, perhaps as an effect of local genomic features, such as recombination rates and gene densities that reshaped the distribution patterns of LTR-RTs and DNA TEs in soybean.

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Precise Centromere Mapping Using a Combination of Repeat Junction Markers and Chromatin Immunoprecipitation–Polymerase Chain Reaction

Cited by 29 publications

References 21 publications

A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescencein SituHybridization Map of Maize (Zea maysL.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescencein SituHybridization Map of Maize (Zea maysL.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

High‐resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTLQfhs.ifa‐5A

Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean

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