Towards a FISH-based karyotype of Rosa L. (Rosaceae)

Kirov, Ilya; Laere, Katrijn Van; Roy, Nadine Van; Khrustaleva, Ludmila

doi:10.3897/compcytogen.v10i4.9536

Cited by 22 publications

(22 citation statements)

References 50 publications

(76 reference statements)

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“…In 5x R. canina (subsect. Caninae) we detected five 18S signals (Figures 2a and S2a), which is in accordance with the presence of one NOR per monoploid (1x = 7) genome in roses (Ma et al, 1997;Fernandez-Romero et al, 2001;Lim et al, 2005;Kirov et al, 2016) 2 and S2). On the contrary, locus loss as an immediate response to hybridization was observed in the synthetic intersectional hybrid R. rubiginosa 9 R. hybrida (Khaitov a et al, 2014).…”

Section: Stability Of Rdna Loci In Reciprocal Dogrose Hybridssupporting

confidence: 83%

“…In 5x R. canina (subsect. Caninae ) we detected five 18S signals (Figures a and S2a), which is in accordance with the presence of one NOR per monoploid (1 x = 7) genome in roses (Ma et al ., ; Fernandez‐Romero et al ., ; Lim et al ., ; Kirov et al ., ). In contrast, 5x R. inodora (subsect.…”

Section: Discussionmentioning

confidence: 97%

“…The fate of rDNA loci has been documented in several polyploid rosaceous genera reporting either the persistence of progenitor rDNA loci regions, for example in Rubus L. Wang et al, 2015) and Sanguisorba L. (Mishima et al, 2002), or frequent losses, for example in Fragaria (Liu and Davis, 2011). In Rosa, one 35S rDNA locus per genome and several small 5S loci have been detected in diploid species (Ma et al, 1997;Fernandez-Romero et al, 2001;Lim et al, 2005;Kirov et al, 2016). In most polyploids, including dogroses, 35S loci are completely retained.…”

Section: Introductionmentioning

confidence: 99%

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The fate of ribosomal RNA genes in spontaneous polyploid dogrose hybrids [Rosa L. sect. Caninae (DC.) Ser.] exhibiting non‐symmetrical meiosis

et al. 2018

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Dogroses represent an exceptional system for studying the effects of genome doubling and hybridization: their asymmetrical meiosis enables recombination in bi-parentally inherited chromosomes but prevents it in maternally inherited ones. We employed fluorescent in situ hybridization, genome skimming, amplicon sequencing of genomic and cDNA as well as conventional cloning of nuclear ribosomal DNA in two phylogenetically distinct pentaploid (2n = 5x = 35) species, Rosa canina and Rosa inodora, and their naturally occurring reciprocal hybrids, Rosa dumalis (5x) and Rosa agrestis (5x, 6x). Both progenitor species differed in composition, meiotic behaviour and expression of rDNA loci: R. canina (five 18S and 5-8 5S loci) was dominated by the Canina ribotypes, but R. inodora (four 18S loci and 7-8 5S loci) by the Rubiginosa ribotype. The co-localized 5S/18S loci occurred on either bivalent-forming (R. canina) or univalent-forming (R. inodora) chromosomes. Ribosomal DNA loci were additively inherited; however, the Canina ribotypes were dominantly expressed, even in genotypes with relatively low copy number of these genes. Moreover, we observed rDNA homogenization towards the paternally transmitted Canina ribotype in 6x R. agrestis. The here-observed variation in arrangement and composition of rDNA types between R. canina and R. inodora suggests the involvement of different genomes in bivalent formation. This results supports the hypothesis that the asymmetrical meiosis arose at least twice by independent ancient hybridization events.

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Section: Stability Of Rdna Loci In Reciprocal Dogrose Hybridssupporting

confidence: 83%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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The fate of ribosomal RNA genes in spontaneous polyploid dogrose hybrids [Rosa L. sect. Caninae (DC.) Ser.] exhibiting non‐symmetrical meiosis

et al. 2018

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“…Fluorescent in situ hybridization-based cytogenetic maps were integrated with genetic maps for a number of cultivated species: rice ( Chen et al, 2002 ), melon ( Gonzalez et al, 2010 ), grapes ( Scalabrin et al, 2010 ), maize ( Wei et al, 2009 ), cotton ( Cui et al, 2015 ), and Rosa wichurana ( Kirov et al, 2014 , 2016 ). In the present study, for the first time, chromosomal localization of the highly conserved fragment belonging to the CesA multigene family, 5S, and 26S rRNA genes was aligned to the integrated genetic/physical map of L. usitatissimum .…”

Section: Discussionmentioning

confidence: 99%

Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA) Genes in Flax (Linum usitatissimum L.)

et al. 2017

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Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase (CesA) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum. Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG) 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.

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“…Mitotic Chromosome slides were prepared with the “SteamDrop” method [67] using young root meristems of R. chinensis ‘Old Blush’. Two oligonucleotide probes (5’-TTGCGTTGTTCTAGTGACATTCATAMRA-3’; 5’-ACCCTAGAAGCGAGAAGTTTGG-TAMRA-3’) were used for FISH, as previously described [68]. DRAWID [69] was used for Chromosome and signal analysis.…”

Section: Methodsmentioning

confidence: 99%

A high-quality sequence ofRosa chinensisto elucidate genome structure and ornamental traits

Hibrand

Ruttink

Hamama

et al. 2018

Preprint

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Rose is the world’s most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits.We produced a haploid rose line from R. chinensis ‘Old Blush’ and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

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Towards a FISH-based karyotype of Rosa L. (Rosaceae)

Cited by 22 publications

References 50 publications

The fate of ribosomal RNA genes in spontaneous polyploid dogrose hybrids [Rosa L. sect. Caninae (DC.) Ser.] exhibiting non‐symmetrical meiosis

The fate of ribosomal RNA genes in spontaneous polyploid dogrose hybrids [Rosa L. sect. Caninae (DC.) Ser.] exhibiting non‐symmetrical meiosis

Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA) Genes in Flax (Linum usitatissimum L.)

A high-quality sequence ofRosa chinensisto elucidate genome structure and ornamental traits

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