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Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar 'Koshihikari'.

Yonemaru J, Choi SH, Sakai H, Ando T, Shomura A, Yano M, Wu J, Fukuoka S - Breed. Sci. (2015)

Bottom Line: Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively.Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers.The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.

View Article: PubMed Central - PubMed

Affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.

ABSTRACT
Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar 'Koshihikari' was performed to extract regions containing large indels (10-51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between 'Koshihikari' and other diverse cultivars, we subtracted the indel regions detected in 'Koshihikari' from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.

No MeSH data available.


Numbers of indel markers shared between various numbers of cultivars. Common cultivars are defined as those sharing the same primer sequences for the indel markers.
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f1-65_249: Numbers of indel markers shared between various numbers of cultivars. Common cultivars are defined as those sharing the same primer sequences for the indel markers.

Mentions: As a result of designing primers, about half of the indel regions were eliminated. Few indel markers were detected between ‘Koshihikari’ and ‘Nipponbare’ (752 markers), so the removal of these markers did not greatly influence the number of indel markers. In total, we selected 121,248 indel markers (with redundancy) and 36,766 indel markers (without redundancy) for the 10 other cultivars (i.e., non-’Koshihikari’ cultivars). In terms of marker efficiency, the available markers to detect indels that were common to all 10 cultivars but not ‘Koshihikari’ were effective but few (283 markers, Fig. 1). The largest number was observed for solitary indel regions, which represent indel markers common to ‘Koshihikari’ and only one other cultivar (12,198 markers). The number of indel markers decreased as the number of cultivars sharing the same primer sequences (termed here “common cultivars”) increased (Fig. 1).


Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar 'Koshihikari'.

Yonemaru J, Choi SH, Sakai H, Ando T, Shomura A, Yano M, Wu J, Fukuoka S - Breed. Sci. (2015)

Numbers of indel markers shared between various numbers of cultivars. Common cultivars are defined as those sharing the same primer sequences for the indel markers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482175&req=5

f1-65_249: Numbers of indel markers shared between various numbers of cultivars. Common cultivars are defined as those sharing the same primer sequences for the indel markers.
Mentions: As a result of designing primers, about half of the indel regions were eliminated. Few indel markers were detected between ‘Koshihikari’ and ‘Nipponbare’ (752 markers), so the removal of these markers did not greatly influence the number of indel markers. In total, we selected 121,248 indel markers (with redundancy) and 36,766 indel markers (without redundancy) for the 10 other cultivars (i.e., non-’Koshihikari’ cultivars). In terms of marker efficiency, the available markers to detect indels that were common to all 10 cultivars but not ‘Koshihikari’ were effective but few (283 markers, Fig. 1). The largest number was observed for solitary indel regions, which represent indel markers common to ‘Koshihikari’ and only one other cultivar (12,198 markers). The number of indel markers decreased as the number of cultivars sharing the same primer sequences (termed here “common cultivars”) increased (Fig. 1).

Bottom Line: Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively.Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers.The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.

View Article: PubMed Central - PubMed

Affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.

ABSTRACT
Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar 'Koshihikari' was performed to extract regions containing large indels (10-51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between 'Koshihikari' and other diverse cultivars, we subtracted the indel regions detected in 'Koshihikari' from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.

No MeSH data available.