Use of Tyramide-Fluorescence in situ Hybridization and Chromosome Microdissection for Ascertaining Homology Relationships and Chromosome Linkage Group Associations in Oats

Sanz, M. J.; Loarce, Yolanda; Ferrer, Esther; Fominaya, A.

doi:10.1159/000335641

Cited by 9 publications

(4 citation statements)

References 75 publications

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“…Previously, Tyramide-FISH has been applied to visualize short DNA fragments for large chromosomes of several monocots including onion [53], [92], barley [54], wheat [55] and oat [56]. Despite the difficulty of using rose as a cytogenetic object, we successfully visualized short DNA fragments (1.1–1.7 Kb) of genes using Tyramide-FISH.…”

Section: Discussionmentioning

confidence: 99%

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Anchoring Linkage Groups of the Rosa Genetic Map to Physical Chromosomes with Tyramide-FISH and EST-SNP Markers

Kirov

Laere²,

Riek³

et al. 2014

PLoS ONE

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In order to anchor Rosa linkage groups to physical chromosomes, a combination of the Tyramide-FISH technology and the modern molecular marker system based on High Resolution Melting (HRM) is an efficient approach. Although, Tyramide-FISH is a very promising technique for the visualization of short DNA probes, it is very challenging for plant species with small chromosomes such as Rosa. In this study, we successfully applied the Tyramide-FISH technique for Rosa and compared different detection systems. An indirect detection system exploiting biotinylated tyramides was shown to be the most suitable technique for reliable signal detection. Three gene fragments with a size of 1100 pb–1700 bp (Phenylalanine Ammonia Lyase, Pyrroline-5-Carboxylate Synthase and Orcinol O-Methyl Transferase) have been physically mapped on chromosomes 7, 4 and 1, respectively, of Rosa wichurana. The signal frequency was between 25% and 40%. HRM markers of these 3 gene fragments were used to include the gene fragments on the existing genetic linkage map of Rosa wichurana. As a result, three linkage groups could be anchored to their physical chromosomes. The information was used to check for synteny between the Rosa chromosomes and Fragaria.

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Section: Discussionmentioning

confidence: 99%

“…Tyramide-FISH has been successfully used in human genetics for single-copy gene detection [41], [45]–[52]. In plants, however, Tyramide-FISH has only been used in a few studies [53]–[56].…”

Section: Introductionmentioning

confidence: 99%

Anchoring Linkage Groups of the Rosa Genetic Map to Physical Chromosomes with Tyramide-FISH and EST-SNP Markers

Kirov

Laere²,

Riek³

et al. 2014

PLoS ONE

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“…The sensitivity threshold of common FISH is 10 Kb, while the size of markers is much smaller and they often form several hundred base pairs. Tyramide-(Tyr)-FISH is an approach to increase the sensitivity of FISH [ 20 ] and which has been applied to plant chromosomes [ 11 , 21 , 22 , 23 , 24 , 25 ]. Yet, the method has not become routine because of indistinct in situ hybridization signals for some probes, low detection frequency, and low reproducibility among different laboratories [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps

Kudryavtseva

Ermolaev

Карлов

et al. 2021

IJMS

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In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a challenge. Recently developed optical and Hi-C mapping are aimed at assistance in genome assembly. For high confidence in the genome assembly at chromosome level, more independent approaches are required. The present study is aimed at refining an ultrasensitive Tyr-FISH technique and developing a reliable and simple method of in situ mapping of a short unique DNA sequences on plant chromosomes. We have carefully analyzed the critical steps of the Tyr-FISH to find out the reasons behind the flaws of this technique. The accurate visualization of markers/genes appeared to be significantly dependent on the means of chromosome slide preparation, probe design and labeling, and high stringency washing. Appropriate adjustment of these steps allowed us to detect a short DNA sequence of 1.6 Kb with a frequency of 51.6%. Based on our results, we developed a more reliable and simple protocol for dual-color Tyr-FISH visualization of unique short DNA sequences on plant chromosomes. This new protocol can allow for more accurate determination of the physical distance between markers and can be applied for faster integration of genetic and cytogenetic maps.

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“…In plants, Sandery et al (1991) first applied the microdissection technique toward isolating B-chromosomes from rye ( Secale cereale Linnaeus, 1753) and were able to identify a DNA sequence on these rye B-chromosomes. With the development of PCR, microdissection techniques have widely been used with genetic studies of Secale cereale ( Houben et al 1996 ; Zhou et al 1999 ), Triticum aestivum Linnaeus, 1753 ( Hu et al 2004 ), Zea mays Linnaeus, 1753 ( Stein et al 1998 ), Avena sativa Linnaeus, 1753 ( Chen and Armstrong 1995 ; Sanz et al 2012 ), Gossypium arboreum Linnaeus, 1753 ( Renhai et al 2012 ), Citrus grandis Osbeck, 1757 ( Huang et al 2004a , b ), Silene latifolia Poiret, 1789 ( Hobza et al 2004 , 2007 ), Populus tremula Linnaeus, 1753 ( Zhang et al 2005 ), an addition line of wheat- Thinopyrum intermedium Barkworth & Dewey, 1985 ( Deng et al 2013a ) and Spinacia oleracea Linnaeus, 1753 ( Deng et al 2013b ). Chromosome microdissection and cloning are powerful tools that combine cytogenetics with molecular genetics and have played an important role in research on genome structure ( Fominaya et al 2005 ; Hobza and Vyskot 2007 ).…”

Section: Introductionmentioning

confidence: 99%

Use of laser microdissection for the construction of Humulus japonicus Siebold et Zuccarini, 1846 (Cannabaceae) sex chromosome-specific DNA library and cytogenetics analysis

Yakovin¹,

Divashuk²,

Razumova³

et al. 2014

CCG

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Dioecy is relatively rare among plant species, and distinguishable sex chromosomes have been reported in few dioecious species. The multiple sex chromosome system (XX/XY1Y2) of Humulus japonicus Siebold et Zuccarini, 1846 differs from that of other members of the family Cannabaceae, in which the XX/XY chromosome system is present. Sex chromosomes of Humulus japonicus were isolated from meiotic chromosome spreads of males by laser microdissection with the P.A.L.M. MicroLaser system. The chromosomal DNA was directly amplified by degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR). Fast fluorescence in situ hybridization (FAST-FISH) using a labeled, chromosome-specific DOP-PCR product as a probe showed preferential hybridization to sex chromosomes. In addition, the DOP-PCR product was used to construct a short-insert, Humulus japonicus sex chromosomes-specific DNA library. The randomly sequenced clones showed that about 12% of them have significant homology to Humulus lupulus and 88% to Cannabis sativa Linnaeus, 1753 sequences from GenBank database. Forty-four percent of the sequences show homology to plant retroelements. It was concluded that laser microdissection is a useful tool for isolating the DNA of sex chromosomes of Humulus japonicus and for the construction of chromosome-specific DNA libraries for the study of the structure and evolution of sex chromosomes. The results provide the potential for identifying unique or sex chromosome-specific sequence elements in Humulus japonicus and could aid in the identification of sex chromosome-specific repeat and coding regions through chromosome isolation and genome complexity reduction.

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Use of Tyramide-Fluorescence in situ Hybridization and Chromosome Microdissection for Ascertaining Homology Relationships and Chromosome Linkage Group Associations in Oats

Cited by 9 publications

References 75 publications

Anchoring Linkage Groups of the Rosa Genetic Map to Physical Chromosomes with Tyramide-FISH and EST-SNP Markers

Anchoring Linkage Groups of the Rosa Genetic Map to Physical Chromosomes with Tyramide-FISH and EST-SNP Markers

A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps

Use of laser microdissection for the construction of Humulus japonicus Siebold et Zuccarini, 1846 (Cannabaceae) sex chromosome-specific DNA library and cytogenetics analysis

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