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Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes

BACKGROUND: The importance of wheat to the world economy, together with progresses in high-throughput next-generation DNA sequencing, have accelerated initiatives of genetic research for wheat improvement. The availability of high density linkage maps is crucial to identify genotype-phenotype associ...

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Autores principales: Colasuonno, Pasqualina, Maria, Mastrangelo Anna, Blanco, Antonio, Gadaleta, Agata
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866978/
https://www.ncbi.nlm.nih.gov/pubmed/24304553
http://dx.doi.org/10.1186/1471-2156-14-114
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author Colasuonno, Pasqualina
Maria, Mastrangelo Anna
Blanco, Antonio
Gadaleta, Agata
author_facet Colasuonno, Pasqualina
Maria, Mastrangelo Anna
Blanco, Antonio
Gadaleta, Agata
author_sort Colasuonno, Pasqualina
collection PubMed
description BACKGROUND: The importance of wheat to the world economy, together with progresses in high-throughput next-generation DNA sequencing, have accelerated initiatives of genetic research for wheat improvement. The availability of high density linkage maps is crucial to identify genotype-phenotype associations, but also for anchoring BAC contigs to genetic maps, a strategy followed for sequencing the wheat genome. RESULTS: Here we report a genetic linkage map in a durum wheat segregating population and the study of mapped DArT markers. The linkage map consists of 126 gSSR, 31 EST-SSR and 351 DArT markers distributed in 24 linkage groups for a total length of 1,272 cM. Through bioinformatic approaches we have analysed 327 DArT clones to reveal their redundancy, syntenic and functional aspects. The DNA sequences of 174 DArT markers were assembled into a non-redundant set of 60 marker clusters. This explained the generation of clusters in very small chromosome regions across genomes. Of these DArT markers, 61 showed highly significant (Expectation < E-10) BLAST similarity to gene sequences in public databases of model species such as Brachypodium and rice. Based on sequence alignments, the analysis revealed a mosaic gene conservation, with 54 and 72 genes present in rice and Brachypodium species, respectively. CONCLUSIONS: In the present manuscript we provide a detailed DArT markers characterization and the basis for future efforts in durum wheat map comparing.
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spelling pubmed-38669782013-12-19 Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes Colasuonno, Pasqualina Maria, Mastrangelo Anna Blanco, Antonio Gadaleta, Agata BMC Genet Research Article BACKGROUND: The importance of wheat to the world economy, together with progresses in high-throughput next-generation DNA sequencing, have accelerated initiatives of genetic research for wheat improvement. The availability of high density linkage maps is crucial to identify genotype-phenotype associations, but also for anchoring BAC contigs to genetic maps, a strategy followed for sequencing the wheat genome. RESULTS: Here we report a genetic linkage map in a durum wheat segregating population and the study of mapped DArT markers. The linkage map consists of 126 gSSR, 31 EST-SSR and 351 DArT markers distributed in 24 linkage groups for a total length of 1,272 cM. Through bioinformatic approaches we have analysed 327 DArT clones to reveal their redundancy, syntenic and functional aspects. The DNA sequences of 174 DArT markers were assembled into a non-redundant set of 60 marker clusters. This explained the generation of clusters in very small chromosome regions across genomes. Of these DArT markers, 61 showed highly significant (Expectation < E-10) BLAST similarity to gene sequences in public databases of model species such as Brachypodium and rice. Based on sequence alignments, the analysis revealed a mosaic gene conservation, with 54 and 72 genes present in rice and Brachypodium species, respectively. CONCLUSIONS: In the present manuscript we provide a detailed DArT markers characterization and the basis for future efforts in durum wheat map comparing. BioMed Central 2013-12-05 /pmc/articles/PMC3866978/ /pubmed/24304553 http://dx.doi.org/10.1186/1471-2156-14-114 Text en Copyright © 2013 Colasuonno et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Colasuonno, Pasqualina
Maria, Mastrangelo Anna
Blanco, Antonio
Gadaleta, Agata
Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes
title Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes
title_full Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes
title_fullStr Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes
title_full_unstemmed Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes
title_short Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes
title_sort description of durum wheat linkage map and comparative sequence analysis of wheat mapped dart markers with rice and brachypodium genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866978/
https://www.ncbi.nlm.nih.gov/pubmed/24304553
http://dx.doi.org/10.1186/1471-2156-14-114
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