ArticleBMC plant biology2009
Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array.
Article in BMC plant biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 42 citations in OpenAlex.
- DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials.Rice (New York, N.Y.) · 2022Article
- Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines.Frontiers in plant science · 2021Article
- Assessing trait contribution and mapping novel QTL for salinity tolerance using the Bangladeshi rice landrace Capsule.Rice (New York, N.Y.) · 2019Article
- Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice.Rice (New York, N.Y.) · 2017Article
- Transcription dynamics of Saltol QTL localized genes encoding transcription factors, reveals their differential regulation in contrasting genotypes of rice.Functional & integrative genomics · 2017Article
- Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.).Journal of genetics · 2013Article
- Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat.Plant physiology · 2013Article
- Salinity tolerance, Na+ exclusion and allele mining of HKT1;5 in Oryza sativa and O. glaberrima: many sources, many genes, one mechanism?BMC plant biology · 2013Article
- Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.).BMC genomics · 2012Article
- Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application.Plant physiology · 2011Article
- High-throughput identification of genetic markers using representational oligonucleotide microarray analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays.BMC genomics · 2010Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA 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.
resultsExpression 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%.
conclusionRecombinant 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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