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High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis.

Ma XF, Jensen E, Alexandrov N, Troukhan M, Zhang L, Thomas-Jones S, Farrar K, Clifton-Brown J, Donnison I, Swaller T, Flavell R - PLoS ONE (2012)

Bottom Line: 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 results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes.In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.

View Article: PubMed Central - PubMed

Affiliation: Ceres, Inc, Thousand Oaks, California, United States of America.

ABSTRACT
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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Related in: MedlinePlus

Graphical representation of the high quality linkage map of M. sinensis.The image is produced with CheckMatrix (http://www.atgc.org/XLinkage/) to validate and verify the quality of the composite map using BIT score (low-left diagonal) and REC score (top-right diagonal). Red color represents tight linkage; yellow represents weak linkage; green to blue represents no linkage. The red along the diagonal, but lack of red off the diagonal, indicate that marker assignments and orders in the 19 linkage groups are supported by both JoinMap and CheckMatrix.
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pone-0033821-g003: Graphical representation of the high quality linkage map of M. sinensis.The image is produced with CheckMatrix (http://www.atgc.org/XLinkage/) to validate and verify the quality of the composite map using BIT score (low-left diagonal) and REC score (top-right diagonal). Red color represents tight linkage; yellow represents weak linkage; green to blue represents no linkage. The red along the diagonal, but lack of red off the diagonal, indicate that marker assignments and orders in the 19 linkage groups are supported by both JoinMap and CheckMatrix.

Mentions: GBS has been used in plants recently, but to the best of our knowledge, this is the first time this technology has been applied in genetic linkage mapping involving a large number of plants for such a large unknown genome species, without any reference sequence of the species itself. Thus, sequence and SNP calling accuracy and mapping quality needed to be carefully addressed. For this study, an independent program, CheckMatrix (http://www.atgc.org/XLinkage/), was used to validate the linkage map (Figure 3). All mapped markers, including segregation distorted markers, were included for CheckMatrix validation. A red color in CheckMatrix represents tight linkage, thus for each linkage a red diagonal should be observed if all markers were in the correct order. Any markers that were found unfit in their positions were remapped using JoinMap with different LOD statistics or removed from the final maps until all marker positions were accepted by both JoinMap and CheckMatrix. After each linkage was verified, a CheckMatrix of all 19 linkage groups was plotted using 25% of the mapped markers of each linkage (Figure 3). Overall results indicated that all markers mapped in the composite map were assigned to correct linkages and placed in the correct order.


High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis.

Ma XF, Jensen E, Alexandrov N, Troukhan M, Zhang L, Thomas-Jones S, Farrar K, Clifton-Brown J, Donnison I, Swaller T, Flavell R - PLoS ONE (2012)

Graphical representation of the high quality linkage map of M. sinensis.The image is produced with CheckMatrix (http://www.atgc.org/XLinkage/) to validate and verify the quality of the composite map using BIT score (low-left diagonal) and REC score (top-right diagonal). Red color represents tight linkage; yellow represents weak linkage; green to blue represents no linkage. The red along the diagonal, but lack of red off the diagonal, indicate that marker assignments and orders in the 19 linkage groups are supported by both JoinMap and CheckMatrix.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3306302&req=5

pone-0033821-g003: Graphical representation of the high quality linkage map of M. sinensis.The image is produced with CheckMatrix (http://www.atgc.org/XLinkage/) to validate and verify the quality of the composite map using BIT score (low-left diagonal) and REC score (top-right diagonal). Red color represents tight linkage; yellow represents weak linkage; green to blue represents no linkage. The red along the diagonal, but lack of red off the diagonal, indicate that marker assignments and orders in the 19 linkage groups are supported by both JoinMap and CheckMatrix.
Mentions: GBS has been used in plants recently, but to the best of our knowledge, this is the first time this technology has been applied in genetic linkage mapping involving a large number of plants for such a large unknown genome species, without any reference sequence of the species itself. Thus, sequence and SNP calling accuracy and mapping quality needed to be carefully addressed. For this study, an independent program, CheckMatrix (http://www.atgc.org/XLinkage/), was used to validate the linkage map (Figure 3). All mapped markers, including segregation distorted markers, were included for CheckMatrix validation. A red color in CheckMatrix represents tight linkage, thus for each linkage a red diagonal should be observed if all markers were in the correct order. Any markers that were found unfit in their positions were remapped using JoinMap with different LOD statistics or removed from the final maps until all marker positions were accepted by both JoinMap and CheckMatrix. After each linkage was verified, a CheckMatrix of all 19 linkage groups was plotted using 25% of the mapped markers of each linkage (Figure 3). Overall results indicated that all markers mapped in the composite map were assigned to correct linkages and placed in the correct order.

Bottom Line: 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 results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes.In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.

View Article: PubMed Central - PubMed

Affiliation: Ceres, Inc, Thousand Oaks, California, United States of America.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus