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Sequence characterization, in silico mapping and cytosine methylation analysis of markers linked to apospory in Paspalum notatum.

Podio M, Rodríguez MP, Felitti S, Stein J, Martínez EJ, Siena LA, Quarin CL, Pessino SC, Ortiz JP - Genet. Mol. Biol. (2012)

Bottom Line: Approximately 5 kb corresponding to different markers were characterized through the global sequencing procedure.A more refined analysis based on sequence information indicated synteny with segments of chromosomes 2 and 12 of rice and chromosomes 3 and 5 of maize.Although both target sequences were methylated no methylation polymorphisms associated with the mode of reproduction were detected.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Santa Fe, Argentina. ; Instituto de Botánica del Nordeste, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Corrientes, Argentina.

ABSTRACT
In previous studies we reported the identification of several AFLP, RAPD and RFLP molecular markers linked to apospory in Paspalum notatum. The objective of this work was to sequence these markers, obtain their flanking regions by chromosome walking and perform an in silico mapping analysis in rice and maize. The methylation status of two apospory-related sequences was also assessed using methylation-sensitive RFLP experiments. Fourteen molecular markers were analyzed and several protein-coding sequences were identified. Copy number estimates and RFLP linkage analysis showed that the sequence PnMAI3 displayed 2-4 copies per genome and linkage to apospory. Extension of this marker by chromosome walking revealed an additional protein-coding sequence mapping in silico in the apospory-syntenic regions of rice and maize. Approximately 5 kb corresponding to different markers were characterized through the global sequencing procedure. A more refined analysis based on sequence information indicated synteny with segments of chromosomes 2 and 12 of rice and chromosomes 3 and 5 of maize. Two loci associated with apomixis locus were tested in methylation-sensitive RFLP experiments using genomic DNA extracted from leaves. Although both target sequences were methylated no methylation polymorphisms associated with the mode of reproduction were detected.

No MeSH data available.


Related in: MedlinePlus

In silico mapping of apospory-specific sequences in the rice and maize genomes. Paspalum notatum and rice sequences were located on rice (Os) and maize (Zm) chromosomes by using the BLASTn tool available at GRAMENE. The relative position of each marker was determined based on the physical position of the orthologous sequences listed in Table 3. Rice RFLP clones from rice chromosomes 2 and 12 that generated markers completely linked to apospory in the species were included as reference points.
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f2-gmb-35-827: In silico mapping of apospory-specific sequences in the rice and maize genomes. Paspalum notatum and rice sequences were located on rice (Os) and maize (Zm) chromosomes by using the BLASTn tool available at GRAMENE. The relative position of each marker was determined based on the physical position of the orthologous sequences listed in Table 3. Rice RFLP clones from rice chromosomes 2 and 12 that generated markers completely linked to apospory in the species were included as reference points.

Mentions: All sequences derived from the P. notatum apospory-specific markers were mapped in silico onto the rice and maize genomes in order to determine the location of orthologous sequences in both model species. Rice RFLP clones previously associated with apospory were also included as reference points (Table 3). Putative orthologues to PnMA243 and PnMAM3 were found located on rice chromosome 2, close to the apospory-related markers C560 and C932. PnMA764 aligned with a genomic sequence of rice chromosome 12 and maize chromosome 5, near to the apospory-related rice clones C1069 and C932, respectively. Apospory-related sequences mapping onto rice chromosomes 2 and 12 and maize chromosomes 3 and 5 covered approximately 10 Mbp and 30 Mbp, respectively (Figure 2). The rest of the sequences analyzed mapped on maize chromosomes 1 (C454), 4 (PnMA243, PnMAJ5 and C560) and 6 (PnMAJ5) (Table 3).


Sequence characterization, in silico mapping and cytosine methylation analysis of markers linked to apospory in Paspalum notatum.

Podio M, Rodríguez MP, Felitti S, Stein J, Martínez EJ, Siena LA, Quarin CL, Pessino SC, Ortiz JP - Genet. Mol. Biol. (2012)

In silico mapping of apospory-specific sequences in the rice and maize genomes. Paspalum notatum and rice sequences were located on rice (Os) and maize (Zm) chromosomes by using the BLASTn tool available at GRAMENE. The relative position of each marker was determined based on the physical position of the orthologous sequences listed in Table 3. Rice RFLP clones from rice chromosomes 2 and 12 that generated markers completely linked to apospory in the species were included as reference points.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3526092&req=5

f2-gmb-35-827: In silico mapping of apospory-specific sequences in the rice and maize genomes. Paspalum notatum and rice sequences were located on rice (Os) and maize (Zm) chromosomes by using the BLASTn tool available at GRAMENE. The relative position of each marker was determined based on the physical position of the orthologous sequences listed in Table 3. Rice RFLP clones from rice chromosomes 2 and 12 that generated markers completely linked to apospory in the species were included as reference points.
Mentions: All sequences derived from the P. notatum apospory-specific markers were mapped in silico onto the rice and maize genomes in order to determine the location of orthologous sequences in both model species. Rice RFLP clones previously associated with apospory were also included as reference points (Table 3). Putative orthologues to PnMA243 and PnMAM3 were found located on rice chromosome 2, close to the apospory-related markers C560 and C932. PnMA764 aligned with a genomic sequence of rice chromosome 12 and maize chromosome 5, near to the apospory-related rice clones C1069 and C932, respectively. Apospory-related sequences mapping onto rice chromosomes 2 and 12 and maize chromosomes 3 and 5 covered approximately 10 Mbp and 30 Mbp, respectively (Figure 2). The rest of the sequences analyzed mapped on maize chromosomes 1 (C454), 4 (PnMA243, PnMAJ5 and C560) and 6 (PnMAJ5) (Table 3).

Bottom Line: Approximately 5 kb corresponding to different markers were characterized through the global sequencing procedure.A more refined analysis based on sequence information indicated synteny with segments of chromosomes 2 and 12 of rice and chromosomes 3 and 5 of maize.Although both target sequences were methylated no methylation polymorphisms associated with the mode of reproduction were detected.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Santa Fe, Argentina. ; Instituto de Botánica del Nordeste, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Corrientes, Argentina.

ABSTRACT
In previous studies we reported the identification of several AFLP, RAPD and RFLP molecular markers linked to apospory in Paspalum notatum. The objective of this work was to sequence these markers, obtain their flanking regions by chromosome walking and perform an in silico mapping analysis in rice and maize. The methylation status of two apospory-related sequences was also assessed using methylation-sensitive RFLP experiments. Fourteen molecular markers were analyzed and several protein-coding sequences were identified. Copy number estimates and RFLP linkage analysis showed that the sequence PnMAI3 displayed 2-4 copies per genome and linkage to apospory. Extension of this marker by chromosome walking revealed an additional protein-coding sequence mapping in silico in the apospory-syntenic regions of rice and maize. Approximately 5 kb corresponding to different markers were characterized through the global sequencing procedure. A more refined analysis based on sequence information indicated synteny with segments of chromosomes 2 and 12 of rice and chromosomes 3 and 5 of maize. Two loci associated with apomixis locus were tested in methylation-sensitive RFLP experiments using genomic DNA extracted from leaves. Although both target sequences were methylated no methylation polymorphisms associated with the mode of reproduction were detected.

No MeSH data available.


Related in: MedlinePlus