Exploiting repetitive sequences and BAC clones in Festuca pratensis karyotyping

Majka, Joanna; Książczyk, Tomasz; Kiełbowicz-Matuk, Agnieszka; Kopecký, David; Kosmala, Arkadiusz

doi:10.1371/journal.pone.0179043

Cited by 8 publications

(7 citation statements)

References 53 publications

(57 reference statements)

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“…In large plant genomes that are saturated with ubiquitous repeats, the BAC–FISH-based approach either fails or is technically challenging and only partially successful in providing landmarks that are reproducibly diagnostic for individual chromosomes ( Ma et al , 2010 ; Majka et al , 2017 ). However, as has already been demonstrated for several taxa, it is considerably more effective in plants with small and preferably sequenced genomes and also often in their close relatives, e.g.…”

Section: Discussionmentioning

confidence: 99%

Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum

et al. 2018

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Background and AimsThe Brachypodium genus represents a useful model system to study grass genome organization. Palaeogenomic analyses (e.g. Murat F, Armero A, Pont C, Klopp C, Salse J. 2017. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics49: 490–496) have identified polyploidization and dysploidy as the prime mechanisms driving the diversity of plant karyotypes and nested chromosome fusions (NCFs) crucial for shaping grass chromosomes. This study compares the karyotype structure and evolution in B. distachyon (genome Bd), B. stacei (genome Bs) and in their putative allotetraploid B. hybridum (genomes BdBs).Methods Brachypodium chromosomes were measured and identified using multicolour fluorescence in situ hybridization (mcFISH). For higher resolution, comparative chromosome barcoding was developed using sets of low-repeat, physically mapped B. distachyon-derived bacterial artificial chromosome (BAC) clones.Key ResultsAll species had rather small chromosomes, and essentially all in the Bs genome were morphometrically indistinguishable. Seven BACs combined with two rDNA-based probes provided unambiguous and reproducible chromosome discrimination. Comparative chromosome barcoding revealed NCFs that contributed to the reduction in the x = 12 chromosome number that has been suggested for the intermediate ancestral grass karyotype. Chromosome Bd3 derives from two NCFs of three ancestral chromosomes (Os2, Os8, Os10). Chromosome Bs6 shows an ancient Os8/Os10 NCF, whilst Bs4 represents Os2 only. Chromosome Bd4 originated from a descending dysploidy that involves two NCFs of Os12, Os9 and Os11. The specific distribution of BACs along Bs9 and Bs5, in both B. stacei and B. hybridum, suggests a Bs genome-specific Robertsonian rearrangement.ConclusionsmcFISH-based karyotyping identifies all chromosomes in Brachypodium annuals. Comparative chromosome barcoding reveals rearrangements responsible for the diverse organization of Bd and Bs genomes and provides new data regarding karyotype evolution since the split of the two diploids. The fact that no chromosome rearrangements were observed in B. hybridum compared with the karyotypes of its phylogenetic ancestors suggests prolonged genome stasis after the formation of the allotetraploid.

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Section: Discussionmentioning

confidence: 99%

Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum

et al. 2018

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“…Roots from plants growing in a greenhouse were excised and pretreated in ice-cold water for 24 h, fixed in 3:1 (v/v) ethanol:glacial acetic acid and then stored at − 20 °C until required. Mitotic chromosome preparations were made using the excised roots, according to the procedure described in Majka et al [71]. The high-quality slides were frozen and stored at 4 °C until used.…”

Section: Methodsmentioning

confidence: 99%

Cytogenetic and molecular genotyping in the allotetraploid Festuca pratensis × Lolium perenne hybrids

et al. 2019

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Background Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium ( Festulolium ) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids can merge in their genomes agronomically important characteristics. However, in polyploid plants, especially in allopolyploids, the hybridization of divergent genomes could contribute to various abnormalities, such as variability in chromosome number, structural rearrangements, and/or disorders in inheritance patterns. Here we studied these issues in allotetraploid Festuca pratensis × Lolium perenne hybrids. Results Cytogenetic procedures, including fluorescent in situ hybridization, genomic in situ hybridization, and molecular markers – inter-simple sequence repeats (ISSR) were exploited. This cytogenetic approach indicated the dynamics in the number and distribution of ribosomal RNA genes and structural rearrangements for both parental genomes ( Festuca and Lolium ) in hybrid karyotypes. The separate analysis of F. pratensis and L. perenne chromosomes in hybrid plants (F 2 -F 3 generations of F. pratensis × L. perenne ) revealed the asymmetrical level of rearrangements. Recognized structural changes were mainly located in the distal part of chromosome arms, and in chromosomes bearing ribosomal DNA, they were more frequently mapped in arms without this sequence. Based on the ISSR markers distribution, we found that the tetrasomic type of inheritance was characteristic for the majority of ISSR loci, but the disomic type was also observed. Nonetheless, no preference in the transmission of either Festuca or Lolium alleles to the following generations of allotetraploid F. pratensis × L. perenne hybrid was observed. Conclusion Our study reports cytogenetic and molecular genotyping of the F. pratensis × L. perenne hybrid and its following F 2 -F 3 progenies. The analysis of 137 allotetraploid F. pratensis × L. perenne hybrids revealed the higher level of recombination in chromosomes derived from F. pratensis genome. The results of ISSR markers indicated a mixed model of inheritance, which may be characteristic for these hybrids. Electronic supplementary material The online versio...

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“…Root tips were collected from the water culture hydroponic system. Metaphase accumulation and fixation procedures were carried out according to Majka et al ( 2017a ). Root meristems were digested with a mixture of enzymes containing 20% ( v / v ) pectinase (Sigma), 1% ( w / v ) cellulose (Calbiochem), and 1% ( w / v ) cellulase “Onozuka R-10” (Serva) at 37 °C and squashed in a drop of 60% acetic acid.…”

Section: Methodsmentioning

confidence: 99%

Karyotype reshufflings of Festuca pratensis × Lolium perenne hybrids

et al. 2017

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Many different processes have an impact on the shape of plant karyotype. Recently, cytogenetic examination of Lolium species has revealed the occurrence of spontaneous fragile sites (FSs) associated with 35S rDNA regions. The FSs are defined as the chromosomal regions that are sensitive to forming gaps or breaks on chromosomes. The shape of karyotype can also be determined by interstitial telomeric sequences (ITSs), what was recognized for the first time in this paper in chromosomes of Festuca pratensis × Lolium perenne hybrids. Both FSs and ITSs can contribute to genome instabilities and chromosome rearrangements. To evaluate whether these cytogenetic phenomena have an impact on karyotype reshuffling observed in Festuca × Lolium hybrids, we examined F1 F. pratensis × L. perenne plants and generated F2-F9 progeny by fluorescent in situ hybridization (FISH) using rDNA sequences, telomere and centromere probes, as well as by genomic in situ hybridization (GISH). Analyses using a combination of FISH and GISH revealed that intergenomic rearrangements did not correspond to FSs but overlapped with ITSs for several analyzed genotypes. It suggests that internal telomeric repeats can affect the shape of F. pratensis × L. perenne karyotypes. However, other factors that are involved in rearrangements and have a more crucial impact could exist, but they are still unknown.Electronic supplementary materialThe online version of this article (10.1007/s00709-017-1161-5) contains supplementary material, which is available to authorized users.

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Exploiting repetitive sequences and BAC clones in Festuca pratensis karyotyping

Cited by 8 publications

References 53 publications

Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum

Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum

Cytogenetic and molecular genotyping in the allotetraploid Festuca pratensis × Lolium perenne hybrids

Karyotype reshufflings of Festuca pratensis × Lolium perenne hybrids

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