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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Published on: July 28, 2017
Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP
Ximei Li1, Daojun Yuan, Hantao Wang
1National Key Laboratory of Crop Genetic Improvement & National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, Hubei, China.
Genome
|June 8, 2012
Summary
Single-strand conformation polymorphism (SSCP) analysis successfully identified polymorphism in monomorphic simple sequence repeat (SSR) markers in cotton. This method enhances the utility of existing SSR primers for genetic mapping and marker-assisted breeding.
Area of Science:
- Plant genetics and breeding
- Molecular markers
- Cotton genomics
Background:
- Simple sequence repeat (SSR) markers are crucial in plant genetics but often fail to show polymorphism in cotton.
- Traditional SSR genotyping methods are limited as they only detect product size differences, missing potential polymorphisms.
Purpose of the Study:
- To investigate the utility of single-strand conformation polymorphism (SSCP) analysis for detecting polymorphism in monomorphic SSR markers in cotton.
- To increase the efficiency and application of existing SSR primers in cotton genetic studies.
Main Methods:
- Monomorphic SSRs from two cotton mapping parents ('Emian22' and 3-79) were analyzed using SSCP.
- Polymorphic loci identified by SSCP were further analyzed for sequence variations.
- Genetic mapping was performed using the identified polymorphic loci.
Main Results:
- SSCP analysis revealed polymorphism in 158 out of 4194 monomorphic SSR primer pairs (3.77%), identifying 174 polymorphic loci.
- Sequence analysis confirmed that polymorphisms were due to base transitions or transversions, aligning with SSCP principles.
- SSCP identified specific SSR motifs (AT/TA, GAA/CTT) as more polymorphic in dinucleotides and trinucleotides, respectively.
- 160 loci were integrated into an interspecific BC(1) linkage map, with 5 associated with quantitative trait loci (QTLs) for cotton fiber quality.
Conclusions:
- SSCP analysis is an effective method to uncover hidden polymorphism in monomorphic SSR markers in cotton.
- This technique significantly enhances the utilization of existing SSR resources for genetic mapping and identifying genes related to important traits like fiber quality.
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