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Microarray-based large scale detection of single feature polymorphism in Gossypium hirsutum L
Anukool Srivastava1, Samir V Sawant, Satya Narayan Jena
1Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow 226 001, India. satyanarayan@nbri.res.in.
Journal of Genetics
|December 23, 2015
Summary
This study identified 37,473 single feature polymorphisms (SFPs) in Gossypium hirsutum L. using microarray data, with over 58% validated, revealing key genes involved in cotton fiber development.
Area of Science:
- Plant genetics and genomics
- Agricultural biotechnology
- Cotton breeding
Background:
- Microarrays enable exploration of functional sequence polymorphism in crop cultivars.
- Understanding genetic variations in Gossypium hirsutum L. is crucial for improving fiber quality and yield.
Purpose of the Study:
- To identify single feature polymorphisms (SFPs) in Gossypium hirsutum L. using microarray expression data.
- To validate predicted SFPs and identify genes associated with cotton fiber development.
Main Methods:
- Utilized Affymetrix microarray expression data from five Gossypium hirsutum L. genotypes across six fiber developmental stages.
- Applied statistical analysis (SAM procedure in R) to background-corrected, quantile-normalized log2 intensity values for SFP detection.
- Sequencing on a capillary sequencer was used for validation of randomly selected SFPs.
Main Results:
- Detected a total of 37,473 SFPs among six pairwise genotype combinations.
- Validation confirmed approximately 58.92% of predicted SFPs as true polymorphisms (132 out of 224).
- Identified SFPs associated with genes involved in fatty acid, flavonoid, and auxin biosynthesis pathways.
Conclusions:
- Microarray expression data is a viable method for predicting SFPs in cotton.
- The identified SFPs and associated genes provide valuable targets for cotton breeding and genetic improvement.
- Fatty acid, flavonoid, and auxin biosynthesis pathways play significant roles in cotton fiber development.
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