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High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis

We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics inf...

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Autores principales: Ma, Xue-Feng, Jensen, Elaine, Alexandrov, Nickolai, Troukhan, Maxim, Zhang, Liping, Thomas-Jones, Sian, Farrar, Kerrie, Clifton-Brown, John, Donnison, Iain, Swaller, Timothy, Flavell, Richard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306302/
https://www.ncbi.nlm.nih.gov/pubmed/22439001
http://dx.doi.org/10.1371/journal.pone.0033821
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author Ma, Xue-Feng
Jensen, Elaine
Alexandrov, Nickolai
Troukhan, Maxim
Zhang, Liping
Thomas-Jones, Sian
Farrar, Kerrie
Clifton-Brown, John
Donnison, Iain
Swaller, Timothy
Flavell, Richard
author_facet Ma, Xue-Feng
Jensen, Elaine
Alexandrov, Nickolai
Troukhan, Maxim
Zhang, Liping
Thomas-Jones, Sian
Farrar, Kerrie
Clifton-Brown, John
Donnison, Iain
Swaller, Timothy
Flavell, Richard
author_sort Ma, Xue-Feng
collection PubMed
description We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.
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spelling pubmed-33063022012-03-21 High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis Ma, Xue-Feng Jensen, Elaine Alexandrov, Nickolai Troukhan, Maxim Zhang, Liping Thomas-Jones, Sian Farrar, Kerrie Clifton-Brown, John Donnison, Iain Swaller, Timothy Flavell, Richard PLoS One Research Article We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus. Public Library of Science 2012-03-16 /pmc/articles/PMC3306302/ /pubmed/22439001 http://dx.doi.org/10.1371/journal.pone.0033821 Text en Ma et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Ma, Xue-Feng
Jensen, Elaine
Alexandrov, Nickolai
Troukhan, Maxim
Zhang, Liping
Thomas-Jones, Sian
Farrar, Kerrie
Clifton-Brown, John
Donnison, Iain
Swaller, Timothy
Flavell, Richard
High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis
title High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis
title_full High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis
title_fullStr High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis
title_full_unstemmed High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis
title_short High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis
title_sort high resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid miscanthus sinensis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306302/
https://www.ncbi.nlm.nih.gov/pubmed/22439001
http://dx.doi.org/10.1371/journal.pone.0033821
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