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A Robust and Rapid Candidate Gene Mapping Pipeline Based on M2 Populations
Huangkai Zhou1,2, Kuanqiang Tang1,2, Guang Li1,2
1Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China.
Frontiers in Plant Science
|June 21, 2021
Summary
M2-seq is an efficient whole-genome sequencing-based bulked segregant analysis (WGS-BSA) method for mapping mutant loci in the M2 generation. This rapid tool expedites gene cloning in plants, even those with long generation times.
Area of Science:
- Plant genetics
- Molecular biology
- Genomics
Background:
- Whole-genome sequencing-based bulked segregant analysis (WGS-BSA) is crucial for mapping plant genes.
- Existing methods like Mutmap require later generations (M3 or advanced), delaying gene cloning.
Purpose of the Study:
- To introduce M2-seq, an improved WGS-BSA method for expedited mapping of mutant loci.
- To demonstrate M2-seq's efficiency in identifying causal mutations in the M2 generation.
Main Methods:
- Developed M2-seq, a WGS-BSA approach utilizing only the M2 generation.
- Implemented a novel method to remove background variations without progenitor data.
- Utilized absolute delta single-nucleotide polymorphism (SNP) index values to eliminate linkage-based background noise.
Main Results:
- Successfully mapped causal mutations in 10 independent soybean M2 populations.
- M2-seq efficiently removed background variations and linkage biases.
- Identified candidate causal variations in the M2 generation, comparable to existing methods.
Conclusions:
- M2-seq significantly expedites mutant gene mapping and cloning, especially in species with long generation times.
- The method is efficient, rapid, and removes background variations effectively.
- M2-seq facilitates precise identification of causal mutations in the M2 generation.
