Differentiation of triticale cultivars through FISH karyotyping of their rye chromosomes

Fradkin, Maia; Ferrari, María Rosa; Espert, Shirley Mary; Ferreira, Víctor; Grassi, Ezequiel; Greizerstein, Eduardo José; Poggio, Lidia

doi:10.1139/gen-2012-0117

Cited by 10 publications

(4 citation statements)

References 17 publications

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“…The ubiquity of repetitive elements in genomes of higher eukaryotes and the fact that they evolve more rapidly than coding sequences make them a unique source of molecular markers to analyze genetic diversity and to study processes of genome evolution and speciation [Koo et al, 2010;Mehrotra and Goyal, 2014;Nybom et al, 2014]. DNA repeats have been used as cytogenetic probes to study the long-range molecular organization of plant genomes [Alkhimova et al, 2004;Cuadrado and Jouve, 2007;Hřibová et al, 2010], to develop molecular karyotypes [Jiang and Gill, 2006;Fradkin et al, 2013;Shibata et al, 2013;Zhang et al, 2013], and to provide comparative analyses of closely related species [Nybom et al, 2014;Dodsworth et al, 2015].…”

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confidence: 99%

Repetitive DNA: A Versatile Tool for Karyotyping in Festuca pratensis Huds.

Křivánková

Kopecký²,

Stočes³

et al. 2017

Cytogenet Genome Res

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FISH is a useful method to identify individual chromosomes in a karyotype and to discover their structural changes accompanying genome evolution and speciation. DNA probes for FISH should be chromosome specific and/or exhibit specific patterns of distribution along each chromosome. Such probes are not available in many plants including meadow fescue (Festuca pratensis Huds.), an important forage grass species. In the present study, various DNA repeats identified in Illumina shotgun sequences specific to chromosome 4F of F. pratensis were used as probes for FISH to develop the molecular karyotype of meadow fescue and to reveal a long-range molecular organization of its chromosomes. Five tandem repeats produced specific patterns on individual chromosomes. Their use in combination with probes for rRNA genes enabled the establishment of the molecular karyotype of meadow fescue. Most of the mobile genetic elements were dispersed along all the chromosomes except for the DNA transposon CACTA, which was localized preferentially to telomeric and subtelomeric regions, and a putative LTR element, which was localized to (peri)centromeric regions. Cytogenetic mapping of the 5 tandem repeats in other accessions of meadow fescue showed a highly similar distribution and confirmed the versatility and robustness of these probes.

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confidence: 99%

Repetitive DNA: A Versatile Tool for Karyotyping in Festuca pratensis Huds.

Křivánková

Kopecký²,

Stočes³

et al. 2017

Cytogenet Genome Res

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“…Unfortunately, BACs are not ideal probes for plant species with large genomes because of the presence of large percentages of repetitive DNA sequences in the clones (Janda et al 2006;Zhang et al 2004). Repeat-based chromosome identification systems have been established in several plant species (Findley et al 2010;Fradkin et al 2013;Kato et al 2004;Lengerova et al 2004;Li et al 2014;Mukai et al 1993;Xiong and Pires 2011). Repeatbased systems reveal polymorphisms for the constituent sequences but are not genotype independent.…”

Section: Discussionmentioning

confidence: 99%

A universal chromosome identification system for maize and wildZeaspecies

Braz

Martins

Zhang

et al. 2020

Preprint

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Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared to other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species. ReferencesAdawy SSM, Stupar RM, Jiang J (2004) Fluorescence in situ hybridization of knob-associated DNA elements analysis reveals multiple loci in one-knob and knobless maize lines. J (2019) Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. P Natl Acad Sci USA 116:1679-1685 Amarillo FIE, Bass HW (2007) A transgenomic cytogenetic sorghum (Sorghum propinquum) bacterial artificial chromosome fluorescence in situ hybridization map of maize (Zea mays L.) pachytene chromosome 9, evidence for regions of genome hyperexpansion.

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“…In previous FISH studies, repetitive sequence probes, such as pSc119.2, pTa535, pTa713, pAs1, and microsatellites like (AAC) 5 , enabled the convenient identification of wheat chromosomes according to distinct probe hybridization patterns [ 17 – 20 ]. Such FISH karyotye has also been conducted in investigations of the diploid Thinopyrun elongatum [ 21 ], Dasypyrum villosum [ 22 ], Agropyron cristatum [ 23 ], Secale cereale [ 24 ], Hordeum vulgare [ 25 ], and Aegilops species, including Ae. markgrafii , Ae.…”

Section: Introductionmentioning

confidence: 99%

Development and application of specific FISH probes for karyotyping Psathyrostachys huashanica chromosomes

et al. 2022

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Background Psathyrostachys huashanica Keng has long been used as a genetic resource for improving wheat cultivar because of its genes mediating the resistance to various diseases (stripe rust, leaf rust, take-all, and powdery mildew) as well as its desirable agronomic traits. However, a high-resolution fluorescence in situ hybridization (FISH) karyotype of P. huashanica remains unavailable. Results To develop chromosome-specific FISH markers for P. huashanica, repetitive sequences, including pSc119.2, pTa535, pTa713, pAs1, (AAC)5, (CTT)12, pSc200, pTa71A-2, and Oligo-44 were used for a FISH analysis. The results indicated that the combination of pSc200, pTa71A-2 and Oligo-44 probes can clearly identify all Ns genomic chromosomes in the two P. huashanica germplasms. The homoeologous relationships between individual P. huashanica chromosomes and common wheat chromosomes were clarified by FISH painting. Marker validation analyses revealed that the combination of pSc200, pTa71A-2, and Oligo-44 for a FISH analysis can distinguish the P. huashanica Ns-genome chromosomes from wheat chromosomes, as well as all chromosomes (except 4Ns) from the chromosomes of diploid wheat relatives carrying St, E, V, I, P and R genomes. Additionally, the probes were applicable for discriminating between the P. huashanica Ns-genome chromosomes in all homologous groups and the corresponding chromosomes in Psathyrostachys juncea and most Leymus species containing the Ns genome. Furthermore, six wheat–P. huashanica chromosome addition lines (i.e., 2Ns, 3Ns, 4Ns, 7Ns chromosomes and chromosomal segments) were characterized using the newly developed FISH markers. Thus, these probes can rapidly and precisely detect P. huashanica alien chromosomes in the wheat background. Conclusions The FISH karyotype established in this study lays a solid foundation for the efficient identification of P. huashanica chromosomes in wheat genetic improvement programs.

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Differentiation of triticale cultivars through FISH karyotyping of their rye chromosomes

Cited by 10 publications

References 17 publications

Repetitive DNA: A Versatile Tool for Karyotyping in<b><i> Festuca pratensis</i></b> Huds.

Repetitive DNA: A Versatile Tool for Karyotyping in<b><i> Festuca pratensis</i></b> Huds.

A universal chromosome identification system for maize and wildZeaspecies

Development and application of specific FISH probes for karyotyping Psathyrostachys huashanica chromosomes

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