Application of retrotransposon-based Inter-SINE Amplified Polymorphism (ISAP) markers for the differentiation of common poplar genotypes

Reiche, Birgit; Kögler, Anja; Morgenstern, Kristin; Brückner, Marie; Weber, B.; Heitkam, Tony; Seibt, Kathrin M.; Tröber, Ute; Meyer, Matthias; Wolf, Heino; Schmidt, Thomas; Krabel, Doris

doi:10.1139/cjfr-2020-0209

Cited by 3 publications

(2 citation statements)

References 50 publications

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“…Regarding their applicability, the retrotransposons identified here may provide suitable targets for the development of molecular markers in assisted breeding programs [19][20][21][22][23]. We suggest targeting retrotransposons that are most abundant and for which high transcription implies closeness to genes.…”

Section: Macrocarpon Leaves and Shoot Tipsmentioning

confidence: 98%

“…Especially transposable elements (TEs) play a major role in genome evolution and contribute largely to the generation of polymorphisms between genotypes [14][15][16][17][18]. Hence, TEs can also be applied as molecular markers for the differentiation of accessions and to inform plant breeding programs [19][20][21][22][23]. Thus, the correct annotation and characterization of repetitive sequences, particularly TEs, are a prerequisite for an enriched genome assembly as well as for subsequent genome characterization and valorization [10][11][12].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

Sultana

Menzel

Seibt

et al. 2022

JBR

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BACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts. OBJECTIVE: Exemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages. METHODS: Graph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed. RESULTS: We provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsy in silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions. CONCLUSIONS: We conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.

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Section: Macrocarpon Leaves and Shoot Tipsmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

Sultana

Menzel

Seibt

et al. 2022

JBR

View full text Add to dashboard Cite

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Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Amiteye

2021

Heliyon

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The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR-or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.

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Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

Sultana

Menzel

Seibt

et al. 2021

Preprint

Self Cite

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BACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts. OBJECTIVE: Exemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages. METHODS: Graph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed. RESULTS: We provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsyin silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions. CONCLUSIONS: We conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.

show abstract

Application of retrotransposon-based Inter-SINE Amplified Polymorphism (ISAP) markers for the differentiation of common poplar genotypes

Cited by 3 publications

References 50 publications

Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

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