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PCR-based INDEL markers co-dominant between Oryza sativa, japonica cultivars and closely-related wild Oryza species.

Niihama M, Mochizuki M, Kurata N, Nonomura K - Breed. Sci. (2015)

Bottom Line: We confirmed that up to 155 of 188 markers developed for detection of japonica-indica INDELs could also detect INDELs between rice cultivars and wild AA-species accessions.Percentages of applicable markers were higher in O. rufipogon accessions (61.7 to 85.6%), and lower in accessions of other four AA species (39.8 to 51.4%).These markers were distributed throughout the rice chromosomes, and will be useful for genotyping of CSSLs and other genetic resources derived from crosses between rice cultivars and closely related wild species.

View Article: PubMed Central - PubMed

Affiliation: Plant Genetics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540 , Japan.

ABSTRACT
Wild relatives genetically close to cultivars are precious genetic resources for plant breeding. Oryza rufipogon, O. barthii, O. glumaepatula, O. meridionalis and O. longistaminata are such wild species, and are also categorized as AA genome species based on their structural similarities. Chromosome segment substitution lines (CSSLs) are a powerful resource in breeding and genetics, and numerous rice CSSLs have been produced. This study aimed to develop DNA markers for evaluation of CSSLs directly by PCR and subsequent gel electrophoresis. We confirmed that up to 155 of 188 markers developed for detection of japonica-indica INDELs could also detect INDELs between rice cultivars and wild AA-species accessions. Percentages of applicable markers were higher in O. rufipogon accessions (61.7 to 85.6%), and lower in accessions of other four AA species (39.8 to 51.4%). These markers were distributed throughout the rice chromosomes, and will be useful for genotyping of CSSLs and other genetic resources derived from crosses between rice cultivars and closely related wild species.

No MeSH data available.


Different INDEL patterns among cultivars and AA genome wild rice species. Three independent INDEL markers, chr09.0755, chr10.0007 and chr12.2774, were used for example. C1; class I marker, C2; class II marker, C3; class III marker, CO; class “Others” (See the text and Table 1). Nip (j), Kas (i) and T65 (j) indicate standard rice cultivars, Nipponbare (japonica), Kasalath (indica) and Taichung 65 (japonica), respectively.
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f1-65_357: Different INDEL patterns among cultivars and AA genome wild rice species. Three independent INDEL markers, chr09.0755, chr10.0007 and chr12.2774, were used for example. C1; class I marker, C2; class II marker, C3; class III marker, CO; class “Others” (See the text and Table 1). Nip (j), Kas (i) and T65 (j) indicate standard rice cultivars, Nipponbare (japonica), Kasalath (indica) and Taichung 65 (japonica), respectively.

Mentions: Fourteen accessions of five wild Oryza species were used: O. rufipogon (accession Nos. W0106, W0120, W0137, W1551, W1681), O. barthii (W0049, W1605), O. glumaepatula (W1169, W1171), O. meridionalis (W1297, W2103), and O. longistaminata (W1413, W1508, W1624) (Table 1). Seeds of all accessions were prepared from the wild Oryza collection conserved at the National Institute of Genetics (NIG) (Nonomura et al. 2010). The japonica cultivars Nipponbare and Taichung 65 (T65), and the indica cv. Kasalath were used as standards of cultivated species (Fig. 1, Supplemental Table 1). All plants were grown in the field of NIG, Mishima, Japan.


PCR-based INDEL markers co-dominant between Oryza sativa, japonica cultivars and closely-related wild Oryza species.

Niihama M, Mochizuki M, Kurata N, Nonomura K - Breed. Sci. (2015)

Different INDEL patterns among cultivars and AA genome wild rice species. Three independent INDEL markers, chr09.0755, chr10.0007 and chr12.2774, were used for example. C1; class I marker, C2; class II marker, C3; class III marker, CO; class “Others” (See the text and Table 1). Nip (j), Kas (i) and T65 (j) indicate standard rice cultivars, Nipponbare (japonica), Kasalath (indica) and Taichung 65 (japonica), respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542938&req=5

f1-65_357: Different INDEL patterns among cultivars and AA genome wild rice species. Three independent INDEL markers, chr09.0755, chr10.0007 and chr12.2774, were used for example. C1; class I marker, C2; class II marker, C3; class III marker, CO; class “Others” (See the text and Table 1). Nip (j), Kas (i) and T65 (j) indicate standard rice cultivars, Nipponbare (japonica), Kasalath (indica) and Taichung 65 (japonica), respectively.
Mentions: Fourteen accessions of five wild Oryza species were used: O. rufipogon (accession Nos. W0106, W0120, W0137, W1551, W1681), O. barthii (W0049, W1605), O. glumaepatula (W1169, W1171), O. meridionalis (W1297, W2103), and O. longistaminata (W1413, W1508, W1624) (Table 1). Seeds of all accessions were prepared from the wild Oryza collection conserved at the National Institute of Genetics (NIG) (Nonomura et al. 2010). The japonica cultivars Nipponbare and Taichung 65 (T65), and the indica cv. Kasalath were used as standards of cultivated species (Fig. 1, Supplemental Table 1). All plants were grown in the field of NIG, Mishima, Japan.

Bottom Line: We confirmed that up to 155 of 188 markers developed for detection of japonica-indica INDELs could also detect INDELs between rice cultivars and wild AA-species accessions.Percentages of applicable markers were higher in O. rufipogon accessions (61.7 to 85.6%), and lower in accessions of other four AA species (39.8 to 51.4%).These markers were distributed throughout the rice chromosomes, and will be useful for genotyping of CSSLs and other genetic resources derived from crosses between rice cultivars and closely related wild species.

View Article: PubMed Central - PubMed

Affiliation: Plant Genetics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540 , Japan.

ABSTRACT
Wild relatives genetically close to cultivars are precious genetic resources for plant breeding. Oryza rufipogon, O. barthii, O. glumaepatula, O. meridionalis and O. longistaminata are such wild species, and are also categorized as AA genome species based on their structural similarities. Chromosome segment substitution lines (CSSLs) are a powerful resource in breeding and genetics, and numerous rice CSSLs have been produced. This study aimed to develop DNA markers for evaluation of CSSLs directly by PCR and subsequent gel electrophoresis. We confirmed that up to 155 of 188 markers developed for detection of japonica-indica INDELs could also detect INDELs between rice cultivars and wild AA-species accessions. Percentages of applicable markers were higher in O. rufipogon accessions (61.7 to 85.6%), and lower in accessions of other four AA species (39.8 to 51.4%). These markers were distributed throughout the rice chromosomes, and will be useful for genotyping of CSSLs and other genetic resources derived from crosses between rice cultivars and closely related wild species.

No MeSH data available.