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Method Article
Sample preparation for 2b-RAD genotyping
Shi Wang
College of Marine Life Sciences, Ocean University of China
Corresponding Author
Eli Meyer
Department of Zoology, Oregon State
Corresponding Author
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This work is licensed under a CC BY-NC 3.0 License. Read Full License
High-throughput sequencing of restriction site-associated genomic DNA (RAD) is now a widely used approach for simultaneously discovering and profiling genetic polymorphisms. We describe an alternative approach for RAD genotyping with several useful features, called 2b-RAD for the use of type IIB restriction endonucleases (AlfI, BsaXI). The fragments excised by type IIB enzymes are uniform in length, streamlining library preparation and producing even sequencing coverage across the genome. The cohesive ends present on both 5’ and 3’ ends of each fragment make it possible to target a defined subset of restriction sites using modified adaptors. Marker density can be adjusted as needed in this way, greatly reducing sequencing coverage requirements and costs. 2b-RAD offers a cost-effective strategy for high-throughput genotyping that is widely suitable for linkage mapping and profiling genetic variation in natural populations.
Keywords
Genotyping, SNP discovery, Restriction-associated DNA, type IIB restriction endonuclease,
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Associated Publications
2b-RAD: a simple and flexible method for genome-wide genotyping
by Shi Wang, Eli Meyer, John K McKay, +1
Nature Methods (11 April, 2012)
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This is a preprint. It has not completed peer review.
Method Article
Sample preparation for 2b-RAD genotyping
Shi Wang
College of Marine Life Sciences, Ocean University of China
Corresponding Author
Eli Meyer
Department of Zoology, Oregon State
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 06 Jun, 2012
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
High-throughput sequencing of restriction site-associated genomic DNA (RAD) is now a widely used approach for simultaneously discovering and profiling genetic polymorphisms. We describe an alternative approach for RAD genotyping with several useful features, called 2b-RAD for the use of type IIB restriction endonucleases (AlfI, BsaXI). The fragments excised by type IIB enzymes are uniform in length, streamlining library preparation and producing even sequencing coverage across the genome. The cohesive ends present on both 5’ and 3’ ends of each fragment make it possible to target a defined subset of restriction sites using modified adaptors. Marker density can be adjusted as needed in this way, greatly reducing sequencing coverage requirements and costs. 2b-RAD offers a cost-effective strategy for high-throughput genotyping that is widely suitable for linkage mapping and profiling genetic variation in natural populations.
Figure 1
Figure 2
Associated Publications
2b-RAD: a simple and flexible method for genome-wide genotyping
by Shi Wang, Eli Meyer, John K McKay, +1
Nature Methods (11 April, 2012)