Limits...
Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array.

Kim SH, Bhat PR, Cui X, Walia H, Xu J, Wanamaker S, Ismail AM, Wilson C, Close TJ - BMC Plant Biol. (2009)

Bottom Line: Sequencing of putative SFP-containing amplicons from this region and other positions in the genome yielded a validation rate more than 95%.Recombinant inbred line FL478 contains a small (< 1 Mb) segment from the salt tolerant parent in the Saltol region.The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA. kshpaulo@yahoo.co.kr

ABSTRACT

Background: A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification of SNPs or insertion/deletions (INDELs) for high throughput genotyping and high density mapping. Here we applied SFP markers to a lingering question about the source of salt tolerance in a particular rice recombinant inbred line (RIL) derived from a salt tolerant and salt sensitive parent.

Results: Expression data obtained by hybridizing RNA to an oligonucleotide array were analyzed using a statistical method called robustified projection pursuit (RPP). By applying the RPP method, a total of 1208 SFP probes were detected between two presumed parental genotypes (Pokkali and IR29) of a RIL population segregating for salt tolerance. We focused on the Saltol region, a major salt tolerance QTL. Analysis of FL478, a salt tolerant RIL, revealed a small (< 1 Mb) region carrying alleles from the presumed salt tolerant parent, flanked by alleles matching the salt sensitive parent IR29. Sequencing of putative SFP-containing amplicons from this region and other positions in the genome yielded a validation rate more than 95%.

Conclusion: Recombinant inbred line FL478 contains a small (< 1 Mb) segment from the salt tolerant parent in the Saltol region. The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis.

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Chromosome 1 segment associated with a major QTL for salt tolerance. Genetic linkage maps showing the location of Saltol described by Lin et al. (2004) [11] and Bonilla et al. (2002) [8] are shown in (A) and (B), respectively. (C) The segment of pseudomolecule map showing the physical positions of the SKC1 gene [12] and loci with SFPs in the Saltol region. Numbers in parentheses indicate physical positions (Mb) on chromosome 1.
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Figure 4: Chromosome 1 segment associated with a major QTL for salt tolerance. Genetic linkage maps showing the location of Saltol described by Lin et al. (2004) [11] and Bonilla et al. (2002) [8] are shown in (A) and (B), respectively. (C) The segment of pseudomolecule map showing the physical positions of the SKC1 gene [12] and loci with SFPs in the Saltol region. Numbers in parentheses indicate physical positions (Mb) on chromosome 1.

Mentions: We explored the source of the Saltol region in FL478 because several reports demonstrated the importance of this region for salt tolerance, and because our prior report [3] suggested that the Saltol region of FL478 may have originated from the salt sensitive parent. Bonilla et al. (2002) [8] initially delimited Saltol as a QTL controlling three traits (low Na+ absorption, high K+ absorption and low Na+/K+ ratio) within a 15 cM segment of the rice genetic map with peak LOD score > 6.7 (Figure 4). A major QTL for high shoot K+ concentration under salt stress also was identified in the same region [11]. More recently, Ren et al. (2005) identified the SKC1 gene encoding a sodium transporter and demonstrated that it is a determinant of salt tolerance in the Saltol region [12].


Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array.

Kim SH, Bhat PR, Cui X, Walia H, Xu J, Wanamaker S, Ismail AM, Wilson C, Close TJ - BMC Plant Biol. (2009)

Chromosome 1 segment associated with a major QTL for salt tolerance. Genetic linkage maps showing the location of Saltol described by Lin et al. (2004) [11] and Bonilla et al. (2002) [8] are shown in (A) and (B), respectively. (C) The segment of pseudomolecule map showing the physical positions of the SKC1 gene [12] and loci with SFPs in the Saltol region. Numbers in parentheses indicate physical positions (Mb) on chromosome 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697985&req=5

Figure 4: Chromosome 1 segment associated with a major QTL for salt tolerance. Genetic linkage maps showing the location of Saltol described by Lin et al. (2004) [11] and Bonilla et al. (2002) [8] are shown in (A) and (B), respectively. (C) The segment of pseudomolecule map showing the physical positions of the SKC1 gene [12] and loci with SFPs in the Saltol region. Numbers in parentheses indicate physical positions (Mb) on chromosome 1.
Mentions: We explored the source of the Saltol region in FL478 because several reports demonstrated the importance of this region for salt tolerance, and because our prior report [3] suggested that the Saltol region of FL478 may have originated from the salt sensitive parent. Bonilla et al. (2002) [8] initially delimited Saltol as a QTL controlling three traits (low Na+ absorption, high K+ absorption and low Na+/K+ ratio) within a 15 cM segment of the rice genetic map with peak LOD score > 6.7 (Figure 4). A major QTL for high shoot K+ concentration under salt stress also was identified in the same region [11]. More recently, Ren et al. (2005) identified the SKC1 gene encoding a sodium transporter and demonstrated that it is a determinant of salt tolerance in the Saltol region [12].

Bottom Line: Sequencing of putative SFP-containing amplicons from this region and other positions in the genome yielded a validation rate more than 95%.Recombinant inbred line FL478 contains a small (< 1 Mb) segment from the salt tolerant parent in the Saltol region.The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA. kshpaulo@yahoo.co.kr

ABSTRACT

Background: A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification of SNPs or insertion/deletions (INDELs) for high throughput genotyping and high density mapping. Here we applied SFP markers to a lingering question about the source of salt tolerance in a particular rice recombinant inbred line (RIL) derived from a salt tolerant and salt sensitive parent.

Results: Expression data obtained by hybridizing RNA to an oligonucleotide array were analyzed using a statistical method called robustified projection pursuit (RPP). By applying the RPP method, a total of 1208 SFP probes were detected between two presumed parental genotypes (Pokkali and IR29) of a RIL population segregating for salt tolerance. We focused on the Saltol region, a major salt tolerance QTL. Analysis of FL478, a salt tolerant RIL, revealed a small (< 1 Mb) region carrying alleles from the presumed salt tolerant parent, flanked by alleles matching the salt sensitive parent IR29. Sequencing of putative SFP-containing amplicons from this region and other positions in the genome yielded a validation rate more than 95%.

Conclusion: Recombinant inbred line FL478 contains a small (< 1 Mb) segment from the salt tolerant parent in the Saltol region. The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis.

Show MeSH