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Comparative genome analysis between Agrostis stolonifera and members of the Pooideae subfamily, including Brachypodium distachyon.

Araneda L, Sim SC, Bae JJ, Chakraborty N, Curley J, Chang T, Inoue M, Warnke S, Jung G - PLoS ONE (2013)

Bottom Line: In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST).We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon.These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species.

View Article: PubMed Central - PubMed

Affiliation: Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts, United States of America.

ABSTRACT
Creeping bentgrass (Agrostis stolonifera, allotetraploid 2n = 4x = 28) is one of the major cool-season turfgrasses. It is widely used on golf courses due to its tolerance to low mowing and aggressive growth habit. In this study, we investigated genome relationships of creeping bentgrass relative to the Triticeae (a consensus map of Triticum aestivum, T. tauschii, Hordeum vulgare, and H. spontaneum), oat, rice, and ryegrass maps using a common set of 229 EST-RFLP markers. The genome comparisons based on the RFLP markers revealed large-scale chromosomal rearrangements on different numbers of linkage groups (LGs) of creeping bentgrass relative to the Triticeae (3 LGs), oat (4 LGs), and rice (8 LGs). However, we detected no chromosomal rearrangement between creeping bentgrass and ryegrass, suggesting that these recently domesticated species might be closely related, despite their memberships to different Pooideae tribes. In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST). We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon. Also, a total of 24 syntenic blocks based on 678 orthologus loci were identified between these two grass species. The EST orthologs can be utilized in further comparative mapping of Pooideae species. These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species.

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Related in: MedlinePlus

EST-RFLP genetic linkage map of creeping bentgrass.Two different creeping bentgrass diploid genomes are indicated by seven pairs of the homoeologous linkage groups (LGs) followed by “.1” or “.2”. The total map length in cM is shown on the bottom of each LG. The creeping bentgrass, barley, oat and rice cDNA probes used as RFLP markers are indicated as Ast, BCD, CDO and RZ, respectively followed by the probe number. The probe numbers plus ‘.1’, ‘.2’, ‘.3’ or ‘.4’ show duplicate loci detected by the same hybridization probe, which are connected by a dashed black line. Loci connected by a dashed bold blue line are detected between different LGs by the same hybridization probe. The segment on LGs 6.1 and 6.2, spanning three RFLP markers (CDO1380, CDO1158 and CDO534) superimposed by an orange arrow indicates an inversion and translocation between the two homoeologous LGs.
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pone-0079425-g001: EST-RFLP genetic linkage map of creeping bentgrass.Two different creeping bentgrass diploid genomes are indicated by seven pairs of the homoeologous linkage groups (LGs) followed by “.1” or “.2”. The total map length in cM is shown on the bottom of each LG. The creeping bentgrass, barley, oat and rice cDNA probes used as RFLP markers are indicated as Ast, BCD, CDO and RZ, respectively followed by the probe number. The probe numbers plus ‘.1’, ‘.2’, ‘.3’ or ‘.4’ show duplicate loci detected by the same hybridization probe, which are connected by a dashed black line. Loci connected by a dashed bold blue line are detected between different LGs by the same hybridization probe. The segment on LGs 6.1 and 6.2, spanning three RFLP markers (CDO1380, CDO1158 and CDO534) superimposed by an orange arrow indicates an inversion and translocation between the two homoeologous LGs.

Mentions: For comparative genome analysis in this study, we reconstructed a RFLP linkage map of creeping bentgrass using 229 EST-RFLP markers that were previously mapped to 14 linkage groups along with RAPD and AFLP markers [22]. The current map consisting of only RFLP markers provided similar marker order compared to the previous map but was 245 cM shorter in length. In brief, these RFLP markers were generated from 159 RFLP probes including 66 probes (42%) that generated more than 2 duplicated loci per probe (Table 1). A total number of 229 RFLP markers were separated into 14 linkage groups (LGs) at LOD thresholds ranging from 4.0 to 10.0, which were paired into 7 homoeologous LG sets (Figure 1). The numbering of each pair of the homoeologous LGs followed Chakraborty et al. [22]. A total of 865 cM was covered in the current linkage map and the genome coverage varied from 30 cM to 91 cM for each LG. The number of marker per LG ranged from 11 to 22 and an average interval between markers was 3.8 cM in size (Figure 1). Seven probes including Ast5244, Ast39, Ast5343, Ast552, Ast563, BCD98, and CDO99 generated markers that were duplicated within and/or between LGs. The distal end segments of two homoeologous LGs 6.1 and 6.2 showed an evidence of inversion and translocation (Figure 1). The sequences of the 49 bentgrass Ast probes mapped in the current study were BLAST searched, and 39 of them showed similarity to known genes. Moreover 47 and 32 of the Ast probes showed their putative chromosomal locations in rice and wheat, respectively (Table S1).


Comparative genome analysis between Agrostis stolonifera and members of the Pooideae subfamily, including Brachypodium distachyon.

Araneda L, Sim SC, Bae JJ, Chakraborty N, Curley J, Chang T, Inoue M, Warnke S, Jung G - PLoS ONE (2013)

EST-RFLP genetic linkage map of creeping bentgrass.Two different creeping bentgrass diploid genomes are indicated by seven pairs of the homoeologous linkage groups (LGs) followed by “.1” or “.2”. The total map length in cM is shown on the bottom of each LG. The creeping bentgrass, barley, oat and rice cDNA probes used as RFLP markers are indicated as Ast, BCD, CDO and RZ, respectively followed by the probe number. The probe numbers plus ‘.1’, ‘.2’, ‘.3’ or ‘.4’ show duplicate loci detected by the same hybridization probe, which are connected by a dashed black line. Loci connected by a dashed bold blue line are detected between different LGs by the same hybridization probe. The segment on LGs 6.1 and 6.2, spanning three RFLP markers (CDO1380, CDO1158 and CDO534) superimposed by an orange arrow indicates an inversion and translocation between the two homoeologous LGs.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3823605&req=5

pone-0079425-g001: EST-RFLP genetic linkage map of creeping bentgrass.Two different creeping bentgrass diploid genomes are indicated by seven pairs of the homoeologous linkage groups (LGs) followed by “.1” or “.2”. The total map length in cM is shown on the bottom of each LG. The creeping bentgrass, barley, oat and rice cDNA probes used as RFLP markers are indicated as Ast, BCD, CDO and RZ, respectively followed by the probe number. The probe numbers plus ‘.1’, ‘.2’, ‘.3’ or ‘.4’ show duplicate loci detected by the same hybridization probe, which are connected by a dashed black line. Loci connected by a dashed bold blue line are detected between different LGs by the same hybridization probe. The segment on LGs 6.1 and 6.2, spanning three RFLP markers (CDO1380, CDO1158 and CDO534) superimposed by an orange arrow indicates an inversion and translocation between the two homoeologous LGs.
Mentions: For comparative genome analysis in this study, we reconstructed a RFLP linkage map of creeping bentgrass using 229 EST-RFLP markers that were previously mapped to 14 linkage groups along with RAPD and AFLP markers [22]. The current map consisting of only RFLP markers provided similar marker order compared to the previous map but was 245 cM shorter in length. In brief, these RFLP markers were generated from 159 RFLP probes including 66 probes (42%) that generated more than 2 duplicated loci per probe (Table 1). A total number of 229 RFLP markers were separated into 14 linkage groups (LGs) at LOD thresholds ranging from 4.0 to 10.0, which were paired into 7 homoeologous LG sets (Figure 1). The numbering of each pair of the homoeologous LGs followed Chakraborty et al. [22]. A total of 865 cM was covered in the current linkage map and the genome coverage varied from 30 cM to 91 cM for each LG. The number of marker per LG ranged from 11 to 22 and an average interval between markers was 3.8 cM in size (Figure 1). Seven probes including Ast5244, Ast39, Ast5343, Ast552, Ast563, BCD98, and CDO99 generated markers that were duplicated within and/or between LGs. The distal end segments of two homoeologous LGs 6.1 and 6.2 showed an evidence of inversion and translocation (Figure 1). The sequences of the 49 bentgrass Ast probes mapped in the current study were BLAST searched, and 39 of them showed similarity to known genes. Moreover 47 and 32 of the Ast probes showed their putative chromosomal locations in rice and wheat, respectively (Table S1).

Bottom Line: In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST).We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon.These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species.

View Article: PubMed Central - PubMed

Affiliation: Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts, United States of America.

ABSTRACT
Creeping bentgrass (Agrostis stolonifera, allotetraploid 2n = 4x = 28) is one of the major cool-season turfgrasses. It is widely used on golf courses due to its tolerance to low mowing and aggressive growth habit. In this study, we investigated genome relationships of creeping bentgrass relative to the Triticeae (a consensus map of Triticum aestivum, T. tauschii, Hordeum vulgare, and H. spontaneum), oat, rice, and ryegrass maps using a common set of 229 EST-RFLP markers. The genome comparisons based on the RFLP markers revealed large-scale chromosomal rearrangements on different numbers of linkage groups (LGs) of creeping bentgrass relative to the Triticeae (3 LGs), oat (4 LGs), and rice (8 LGs). However, we detected no chromosomal rearrangement between creeping bentgrass and ryegrass, suggesting that these recently domesticated species might be closely related, despite their memberships to different Pooideae tribes. In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST). We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon. Also, a total of 24 syntenic blocks based on 678 orthologus loci were identified between these two grass species. The EST orthologs can be utilized in further comparative mapping of Pooideae species. These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species.

Show MeSH
Related in: MedlinePlus