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Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers.

Molnár I, Šimková H, Leverington-Waite M, Goram R, Cseh A, Vrána J, Farkas A, Doležel J, Molnár-Láng M, Griffiths S - PLoS ONE (2013)

Bottom Line: A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat.The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin.The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary.

ABSTRACT
Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS) markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.

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Differences in the yield of a 173 bp PCR product of the X1N marker amplified from the genomic DNA and subgenomic DNA samples from peaks I–IV on the flow karyotype of Aegilops umbellulata (MvGB470).
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pone-0070844-g001: Differences in the yield of a 173 bp PCR product of the X1N marker amplified from the genomic DNA and subgenomic DNA samples from peaks I–IV on the flow karyotype of Aegilops umbellulata (MvGB470).

Mentions: Of the 140 COS markers, 133 showed PCR products in the wheat genotypes (Chinese Spring, Mv9kr1 and Mv25) or in at least one of the eight Aegilops genotypes, while seven markers did not amplify any product. The 133 markers resulted in 822 PCR products (range: 1–5 PCR products/marker/genotype, mean: 2.04 PCR products; Table S5) with different sizes on the eight genotypes of the four Aegilops species, 492 (59.85%) of which showed size polymorphism relative to wheat, while 330 (40.15%) were non-polymorphic. Out of the 492 polymorphic PCR products, 295 (59.95%) products of 89 COS markers could not be unambiguously assigned to Aegilops chromosomes because a relevant wheat-Aegilops addition line bearing the polymorphic locus was not available and the locus was located in a subgenomic DNA sample representing more chromosomes. 197 (40.04%) polymorphic PCR products were assigned to Aegilops chromosomes. The majority of these (159 products) were assigned using wheat-Aegilops introgression lines, while the others could be assigned using flow-sorted chromosomes (Table S6). Because each of the Aegilops chromosomes has a major location in one of the peaks on a flow-karyotype (Table 1), the yield of PCR products was different on the peak-specific subgenomic DNA samples of the species. Therefore, the highest PCR yield was observed in the peak where the locus-carrying chromosome has its major location (Figure 1). For example, the marker X1N, specific for group 1 chromosomes of wheat, produced a 173 bp PCR amplicon with continuously decreasing yield in the Ae. umbellulata flow karyotype peaks I, II, III and IV (no amplicon in peak IV) (Figure 1), where the 1U chromosome content was 98.9%, 25.8%, 4.32% and 0%, respectively (Table 1). Based on the yield differences between the subgenomic samples, 25 polymorphic PCR products were also located on Aegilops chromosomes, while the genomic positions of 13 fragments were identified simultaneously by introgression lines and by subgenomic DNA samples. Of the 330 non-polymorphic PCR products, 35 could also be assigned using subgenomic DNA samples.


Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers.

Molnár I, Šimková H, Leverington-Waite M, Goram R, Cseh A, Vrána J, Farkas A, Doležel J, Molnár-Láng M, Griffiths S - PLoS ONE (2013)

Differences in the yield of a 173 bp PCR product of the X1N marker amplified from the genomic DNA and subgenomic DNA samples from peaks I–IV on the flow karyotype of Aegilops umbellulata (MvGB470).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3733919&req=5

pone-0070844-g001: Differences in the yield of a 173 bp PCR product of the X1N marker amplified from the genomic DNA and subgenomic DNA samples from peaks I–IV on the flow karyotype of Aegilops umbellulata (MvGB470).
Mentions: Of the 140 COS markers, 133 showed PCR products in the wheat genotypes (Chinese Spring, Mv9kr1 and Mv25) or in at least one of the eight Aegilops genotypes, while seven markers did not amplify any product. The 133 markers resulted in 822 PCR products (range: 1–5 PCR products/marker/genotype, mean: 2.04 PCR products; Table S5) with different sizes on the eight genotypes of the four Aegilops species, 492 (59.85%) of which showed size polymorphism relative to wheat, while 330 (40.15%) were non-polymorphic. Out of the 492 polymorphic PCR products, 295 (59.95%) products of 89 COS markers could not be unambiguously assigned to Aegilops chromosomes because a relevant wheat-Aegilops addition line bearing the polymorphic locus was not available and the locus was located in a subgenomic DNA sample representing more chromosomes. 197 (40.04%) polymorphic PCR products were assigned to Aegilops chromosomes. The majority of these (159 products) were assigned using wheat-Aegilops introgression lines, while the others could be assigned using flow-sorted chromosomes (Table S6). Because each of the Aegilops chromosomes has a major location in one of the peaks on a flow-karyotype (Table 1), the yield of PCR products was different on the peak-specific subgenomic DNA samples of the species. Therefore, the highest PCR yield was observed in the peak where the locus-carrying chromosome has its major location (Figure 1). For example, the marker X1N, specific for group 1 chromosomes of wheat, produced a 173 bp PCR amplicon with continuously decreasing yield in the Ae. umbellulata flow karyotype peaks I, II, III and IV (no amplicon in peak IV) (Figure 1), where the 1U chromosome content was 98.9%, 25.8%, 4.32% and 0%, respectively (Table 1). Based on the yield differences between the subgenomic samples, 25 polymorphic PCR products were also located on Aegilops chromosomes, while the genomic positions of 13 fragments were identified simultaneously by introgression lines and by subgenomic DNA samples. Of the 330 non-polymorphic PCR products, 35 could also be assigned using subgenomic DNA samples.

Bottom Line: A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat.The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin.The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary.

ABSTRACT
Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS) markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.

Show MeSH