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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.


Related in: MedlinePlus

Distribution of applicable INDEL markers, polymorphic between cv. T65 and closely-related wild rice species; (A) O. rufipogon (acc. No. W0106), (B) O. barthii (W0049), (C) O. glumaepatula (W1169), (D) O. meridionalis (W1297), and (E) O. longistaminata (W1413). The marker names were omitted, but corresponded to those registered in Supplemental Table 2 in the order from the top to the bottom of each chromosome. Centromere positions were indicated by arrowheads.
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f2-65_357: Distribution of applicable INDEL markers, polymorphic between cv. T65 and closely-related wild rice species; (A) O. rufipogon (acc. No. W0106), (B) O. barthii (W0049), (C) O. glumaepatula (W1169), (D) O. meridionalis (W1297), and (E) O. longistaminata (W1413). The marker names were omitted, but corresponded to those registered in Supplemental Table 2 in the order from the top to the bottom of each chromosome. Centromere positions were indicated by arrowheads.

Mentions: The applicable marker rates were higher in O. rufipogon accessions. The rates differed intraspecifically among the four accessions we used; the highest was 155 markers (85.6%) in W1551 and the lowest was 111 markers (61.7%) in W0137 (Table 1). The high application rate in this species was largely because it had the fewest class III markers. This is not surprising because O. rufipogon is widely accepted as an ancestral progenitor of O. sativa cultivars (Vaughan and Morishima 2003). These applicable markers were distributed through all rice chromosomes (Fig. 2A), and were sufficient for genotyping of CSSLs and other AA genome-derived genetic resources.


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)

Distribution of applicable INDEL markers, polymorphic between cv. T65 and closely-related wild rice species; (A) O. rufipogon (acc. No. W0106), (B) O. barthii (W0049), (C) O. glumaepatula (W1169), (D) O. meridionalis (W1297), and (E) O. longistaminata (W1413). The marker names were omitted, but corresponded to those registered in Supplemental Table 2 in the order from the top to the bottom of each chromosome. Centromere positions were indicated by arrowheads.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2-65_357: Distribution of applicable INDEL markers, polymorphic between cv. T65 and closely-related wild rice species; (A) O. rufipogon (acc. No. W0106), (B) O. barthii (W0049), (C) O. glumaepatula (W1169), (D) O. meridionalis (W1297), and (E) O. longistaminata (W1413). The marker names were omitted, but corresponded to those registered in Supplemental Table 2 in the order from the top to the bottom of each chromosome. Centromere positions were indicated by arrowheads.
Mentions: The applicable marker rates were higher in O. rufipogon accessions. The rates differed intraspecifically among the four accessions we used; the highest was 155 markers (85.6%) in W1551 and the lowest was 111 markers (61.7%) in W0137 (Table 1). The high application rate in this species was largely because it had the fewest class III markers. This is not surprising because O. rufipogon is widely accepted as an ancestral progenitor of O. sativa cultivars (Vaughan and Morishima 2003). These applicable markers were distributed through all rice chromosomes (Fig. 2A), and were sufficient for genotyping of CSSLs and other AA genome-derived genetic resources.

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.


Related in: MedlinePlus