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Identification of qRBS1, a QTL involved in resistance to bacterial seedling rot in rice.

Mizobuchi R, Sato H, Fukuoka S, Tsushima S, Imbe T, Yano M - Theor. Appl. Genet. (2013)

Bottom Line: Comparison of the levels of BSR in the CSSLs and their recurrent parent, Koshihikari, revealed that a region on chromosome 10 was associated with resistance.The Nona Bokra allele was associated with resistance to BSR.Substitution mapping in the Koshihikari genetic background demonstrated that the QTL, here designated as qRBS1 (quantitative trait locus for RESISTANCE TO BACTERIAL SEEDLING ROT 1), was located in a 393-kb interval (based on the Nipponbare reference genome sequence) defined by simple sequence repeat markers RM24930 and RM24944.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, Japan. ritsuko@affrc.go.jp

ABSTRACT
Bacterial seedling rot (BSR), a destructive disease of rice (Oryza sativa L.), is caused by the bacterial pathogen Burkholderia glumae. To identify QTLs for resistance to BSR, we conducted a QTL analysis using chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bokra (resistant) and Koshihikari (susceptible). Comparison of the levels of BSR in the CSSLs and their recurrent parent, Koshihikari, revealed that a region on chromosome 10 was associated with resistance. Further genetic analyses using an F5 population derived from a cross between a resistant CSSL and Koshihikari confirmed that a QTL for BSR resistance was located on the short arm of chromosome 10. The Nona Bokra allele was associated with resistance to BSR. Substitution mapping in the Koshihikari genetic background demonstrated that the QTL, here designated as qRBS1 (quantitative trait locus for RESISTANCE TO BACTERIAL SEEDLING ROT 1), was located in a 393-kb interval (based on the Nipponbare reference genome sequence) defined by simple sequence repeat markers RM24930 and RM24944.

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Substitution mapping of a QTL controlling resistance to bacterial seedling rot (BSR) on the short arm of chromosome 10 in a set of nine homozygous F4 lines derived from Koshihikari × SL535. (left) Graphical genotypes. Black denotes regions homozygous for Nona Bokra marker alleles; white denotes regions homozygous for Koshihikari marker alleles. The candidate QTL (qRBS1) is indicated at the bottom. (right) The BSR ratio for each of the nine lines. Bars indicate means and error bars indicate SD. Vertical line indicates mean BSR score of Koshihikari. Black indicates a significant difference from Koshihikari at the 5 % level by Dunnett’s test
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Fig4: Substitution mapping of a QTL controlling resistance to bacterial seedling rot (BSR) on the short arm of chromosome 10 in a set of nine homozygous F4 lines derived from Koshihikari × SL535. (left) Graphical genotypes. Black denotes regions homozygous for Nona Bokra marker alleles; white denotes regions homozygous for Koshihikari marker alleles. The candidate QTL (qRBS1) is indicated at the bottom. (right) The BSR ratio for each of the nine lines. Bars indicate means and error bars indicate SD. Vertical line indicates mean BSR score of Koshihikari. Black indicates a significant difference from Koshihikari at the 5 % level by Dunnett’s test

Mentions: To further delimit the candidate genomic region of the QTL for BSR, we genotyped 128 F2 plants derived from a cross between SL535 and Koshihikari and identified nine homozygous lines with recombination near RM474 (Fig. 4). We checked the genome of the lines and the parental cultivars (Koshihikari and Nona Bokra) by the SNP analysis and found that the remaining genome in the lines was identical to that of Koshihikari except for the target region harboring qRBS1 (data not shown). Five lines (Nos. 1, 2, 3, 4, and 6) showed a low BSR ratio (32.2 to 51.7 %), whereas four (Nos. 5, 7, 8, and 9) showed a high BSR ratio (84.1 to 88.3 %; Fig. 4). These two phenotypic groups were associated with genotype classes that were homozygous for the Nona Bokra allele and the Koshihikari allele, respectively (Fig. 4). Together, the genotype and phenotype information clearly delimit the QTL for BSR ratio between SSR markers RM24930 and RM24944 (a 393-kb interval in the Nipponbare genome reference sequence) on chromosome 10 (Fig. 4). We have designated this QTL as qRBS1 (quantitative trait locus for RESISTANCE TO BACTERIAL SEEDLING ROT 1), following the nomenclature recommended by McCouch and CGSNL (Committee on Gene Symbolization 2008). Fig. 4


Identification of qRBS1, a QTL involved in resistance to bacterial seedling rot in rice.

Mizobuchi R, Sato H, Fukuoka S, Tsushima S, Imbe T, Yano M - Theor. Appl. Genet. (2013)

Substitution mapping of a QTL controlling resistance to bacterial seedling rot (BSR) on the short arm of chromosome 10 in a set of nine homozygous F4 lines derived from Koshihikari × SL535. (left) Graphical genotypes. Black denotes regions homozygous for Nona Bokra marker alleles; white denotes regions homozygous for Koshihikari marker alleles. The candidate QTL (qRBS1) is indicated at the bottom. (right) The BSR ratio for each of the nine lines. Bars indicate means and error bars indicate SD. Vertical line indicates mean BSR score of Koshihikari. Black indicates a significant difference from Koshihikari at the 5 % level by Dunnett’s test
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig4: Substitution mapping of a QTL controlling resistance to bacterial seedling rot (BSR) on the short arm of chromosome 10 in a set of nine homozygous F4 lines derived from Koshihikari × SL535. (left) Graphical genotypes. Black denotes regions homozygous for Nona Bokra marker alleles; white denotes regions homozygous for Koshihikari marker alleles. The candidate QTL (qRBS1) is indicated at the bottom. (right) The BSR ratio for each of the nine lines. Bars indicate means and error bars indicate SD. Vertical line indicates mean BSR score of Koshihikari. Black indicates a significant difference from Koshihikari at the 5 % level by Dunnett’s test
Mentions: To further delimit the candidate genomic region of the QTL for BSR, we genotyped 128 F2 plants derived from a cross between SL535 and Koshihikari and identified nine homozygous lines with recombination near RM474 (Fig. 4). We checked the genome of the lines and the parental cultivars (Koshihikari and Nona Bokra) by the SNP analysis and found that the remaining genome in the lines was identical to that of Koshihikari except for the target region harboring qRBS1 (data not shown). Five lines (Nos. 1, 2, 3, 4, and 6) showed a low BSR ratio (32.2 to 51.7 %), whereas four (Nos. 5, 7, 8, and 9) showed a high BSR ratio (84.1 to 88.3 %; Fig. 4). These two phenotypic groups were associated with genotype classes that were homozygous for the Nona Bokra allele and the Koshihikari allele, respectively (Fig. 4). Together, the genotype and phenotype information clearly delimit the QTL for BSR ratio between SSR markers RM24930 and RM24944 (a 393-kb interval in the Nipponbare genome reference sequence) on chromosome 10 (Fig. 4). We have designated this QTL as qRBS1 (quantitative trait locus for RESISTANCE TO BACTERIAL SEEDLING ROT 1), following the nomenclature recommended by McCouch and CGSNL (Committee on Gene Symbolization 2008). Fig. 4

Bottom Line: Comparison of the levels of BSR in the CSSLs and their recurrent parent, Koshihikari, revealed that a region on chromosome 10 was associated with resistance.The Nona Bokra allele was associated with resistance to BSR.Substitution mapping in the Koshihikari genetic background demonstrated that the QTL, here designated as qRBS1 (quantitative trait locus for RESISTANCE TO BACTERIAL SEEDLING ROT 1), was located in a 393-kb interval (based on the Nipponbare reference genome sequence) defined by simple sequence repeat markers RM24930 and RM24944.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, Japan. ritsuko@affrc.go.jp

ABSTRACT
Bacterial seedling rot (BSR), a destructive disease of rice (Oryza sativa L.), is caused by the bacterial pathogen Burkholderia glumae. To identify QTLs for resistance to BSR, we conducted a QTL analysis using chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bokra (resistant) and Koshihikari (susceptible). Comparison of the levels of BSR in the CSSLs and their recurrent parent, Koshihikari, revealed that a region on chromosome 10 was associated with resistance. Further genetic analyses using an F5 population derived from a cross between a resistant CSSL and Koshihikari confirmed that a QTL for BSR resistance was located on the short arm of chromosome 10. The Nona Bokra allele was associated with resistance to BSR. Substitution mapping in the Koshihikari genetic background demonstrated that the QTL, here designated as qRBS1 (quantitative trait locus for RESISTANCE TO BACTERIAL SEEDLING ROT 1), was located in a 393-kb interval (based on the Nipponbare reference genome sequence) defined by simple sequence repeat markers RM24930 and RM24944.

Show MeSH
Related in: MedlinePlus