Intergenic spacer length variants in Old Portuguese bread wheat cultivars

Carvalho, Ana; Guedes-Pinto, Henrique; Lima-Brito, José

doi:10.1007/s12041-011-0051-4

Cited by 13 publications

(10 citation statements)

References 35 publications

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“…The products obtained in this study were longer than the corresponding products of rRNA regions in wheat described earlier. The changes in length might be caused primarily by differences in the number of subrepeats in the IGS, consistent with the findings of Carvalho et al [30] that polymorphic products are about 3000bp long in wheat. This shows a similar organization of IGS regions in wheat and rye.…”

Section: Discussionsupporting

confidence: 90%

Intergenic Spacer Length Variability in Cultivated, Weedy and Wild Rye Species

2015

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Non-coding rDNA spacers (IGS) can vary substantially in size due to differences in the number of repetitive elements among closely related species. Three pairs of universal primers were used in this study for the amplification of non-coding regions of ribosomal (rRNA) IGS. The amplified IGS products obtained from 19 Secale accessions, which included both cultivated and noncultivated rye and which represented three species and four subspecies of the genus Secale, showed a high level of polymorphism. The PCR results were characterized by multiple bands (1-6), different sizes (750bp-3250bp) and 100% polymorphism. Cluster analysis using the neighborjoining method based on the Dice’s coefficient of genetic similarity showed a division of the studied species into two similarity groups. All the studied Secale cereale ssp. cereale were found to belong to the same similarity group. The variation in the size of the IGS among the species which was detected in this study could be due to dissimilarity between the sequences of their respective repetitive elements or between their tandem repeat numbers. The highly interspecific polymorphisms for the rDNA IGS regions suggested that IGS might be a useful molecular marker in studies of Secale species.

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Section: Discussionsupporting

confidence: 90%

Intergenic Spacer Length Variability in Cultivated, Weedy and Wild Rye Species

2015

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“…The IGS regions of many plants evolve astonishingly quickly (Saghai-Maroof et al , 1984; Borisjuk et al , 1997; Carvalho et al , 2011; Coutinho et al , 2016). For example, in B .…”

Section: Discussionmentioning

confidence: 99%

Gene conversion events and variable degree of homogenization of rDNA loci in cultivars ofBrassica napus

Sochorová

Coriton

Kuderová

et al. 2016

Ann Bot

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Background and aims Brassica napus (AACC, 2n = 38, oilseed rape) is a relatively recent allotetraploid species derived from the putative progenitor diploid species Brassica rapa (AA, 2n = 20) and Brassica oleracea (CC, 2n = 18). To determine the influence of intensive breeding conditions on the evolution of its genome, we analysed structure and copy number of rDNA in 21 cultivars of B. napus, representative of genetic diversity.Methods We used next-generation sequencing genomic approaches, Southern blot hybridization, expression analysis and fluorescence in situ hybridization (FISH). Subgenome-specific sequences derived from rDNA intergenic spacers (IGS) were used as probes for identification of loci composition on chromosomes.Key Results Most B. napus cultivars (18/21, 86 %) had more A-genome than C-genome rDNA copies. Three cultivars analysed by FISH (‘Darmor’, ‘Yudal’ and ‘Asparagus kale’) harboured the same number (12 per diploid set) of loci. In B. napus ‘Darmor’, the A-genome-specific rDNA probe hybridized to all 12 rDNA loci (eight on the A-genome and four on the C-genome) while the C-genome-specific probe showed weak signals on the C-genome loci only. Deep sequencing revealed high homogeneity of arrays suggesting that the C-genome genes were largely overwritten by the A-genome variants in B. napus ‘Darmor’. In contrast, B. napus ‘Yudal’ showed a lack of gene conversion evidenced by additive inheritance of progenitor rDNA variants and highly localized hybridization signals of subgenome-specific probes on chromosomes. Brassica napus ‘Asparagus kale’ showed an intermediate pattern to ‘Darmor’ and ‘Yudal’. At the expression level, most cultivars (95 %) exhibited stable A-genome nucleolar dominance while one cultivar (‘Norin 9’) showed co-dominance.Conclusions The B. napus cultivars differ in the degree and direction of rDNA homogenization. The prevalent direction of gene conversion (towards the A-genome) correlates with the direction of expression dominance indicating that gene activity may be needed for interlocus gene conversion.

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“…sterilis . IGS variability was previously reported in Poaceae between different species [45, 46] and varieties [47] as well as between distinct A . sativa accessions [27].…”

Section: Discussionmentioning

confidence: 83%

45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus

2017

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The genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity–A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5’ external transcribed spacer (5’-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus. In this work, IGS length polymorphisms were detected mainly due to distinct 5’-ETS sequence types resulting from major differences in the number and organization of repeated motifs. Although species with A genome revealed a 5’-ETS organization (A-organization) similar to the one previously described in A. sativa, a distinct organization was unraveled in C genome diploid species (C-organization). Interestingly, such new organization presents a higher similarity with other Poaceae species than A-genome sequences, supporting the hypothesis of C-genome being the ancestral Avena genome. Additionally, polyploid species with both genomes mainly retain the A-genome 5’-ETS organization, confirming the preferential elimination of C-genome sequences in Avena polyploid species. Moreover, 5’-ETS sequences phylogenetic analysis consistently clustered the species studied according to ploidy and genomic constitution supporting the use of ribosomal genes to highlight Avena species evolutive pathways.

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Intergenic spacer length variants in Old Portuguese bread wheat cultivars

Cited by 13 publications

References 35 publications

Intergenic Spacer Length Variability in Cultivated, Weedy and Wild Rye Species

Intergenic Spacer Length Variability in Cultivated, Weedy and Wild Rye Species

Gene conversion events and variable degree of homogenization of rDNA loci in cultivars ofBrassica napus

45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus

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