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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

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

Sung-Hyun Kim¹, Prasanna R Bhat, Xinping Cui

¹Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA. kshpaulo@yahoo.co.kr

BMC Plant Biology

|June 2, 2009

Summary

This summary is machine-generated.

This study identified a small genomic region (< 1 Mb) in rice recombinant inbred line FL478, inherited from its salt-tolerant parent, contributing to salt tolerance. Single Feature Polymorphism (SFP) markers effectively mapped this critical region within the Saltol QTL.

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Area of Science:

Genetics
Plant Biology
Molecular Biology

Background:

Rice exhibits numerous genetic variations influencing traits like abiotic stress tolerance.
Single Feature Polymorphism (SFP) markers enable high-throughput genotyping and high-density mapping.
Investigating the genetic basis of salt tolerance in rice is crucial for crop improvement.

Purpose of the Study:

To pinpoint the genetic source of salt tolerance in a specific rice recombinant inbred line (RIL).
To apply SFP markers for high-resolution mapping of salt tolerance quantitative trait loci (QTL).

Main Methods:

Utilized SFP markers for genotyping a rice RIL population derived from contrasting salt-tolerant and salt-sensitive parents.
Analyzed gene expression data using robustified projection pursuit (RPP) on an oligonucleotide array.
Focused mapping efforts on the Saltol region, a known major salt tolerance QTL.

Main Results:

Detected 1208 SFP probes differentiating parental genotypes (Pokkali and IR29).
Identified a less than 1 Mb region in the salt-tolerant RIL FL478 containing alleles from the salt-tolerant parent within the Saltol region.
Achieved over 95% validation rate for SFP markers through sequencing.

Conclusions:

Rice RIL FL478 possesses a small segment (< 1 Mb) from its salt-tolerant parent within the Saltol region, conferring salt tolerance.
The Affymetrix rice genome array is effective for high-resolution mapping in rice via RNA hybridization and RPP-based SFP analysis.