title: AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping.
abstract: We describe methods for the assessment of amplified-fragment single nucleotide polymorphism and methylation (AFSM) sites using a quick and simple molecular marker-assisted breeding strategy based on the use of two restriction enzyme pairs (EcoRI-MspI and EcoRI-HpaII) and a next-generation sequencing platform. Two sets of 85 adapter pairs were developed to concurrently identify SNPs, indels and methylation sites for 85 lines of cassava population in this study. In addition to SNPs and indels, the simplicity of the AFSM protocol makes it particularly suitable for high-throughput full methylation and hemi-methylation analyses. To further demonstrate the ease of this approach, a cassava genetic linkage map was constructed. This approach should be widely applicable for genetic mapping in a variety of organisms and will improve the application of crop genomics in assisted breeding.
authors.affiliation: The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Xia
authors.affiliation: The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
authors.forename: Meiling
authors.initials: M
authors.lastname: Zou
authors.affiliation: The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
authors.forename: Shengkui
authors.initials: S
authors.lastname: Zhang
authors.affiliation: The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
authors.forename: Binxiao
authors.initials: B
authors.lastname: Feng
authors.affiliation: The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
authors.forename: Wenquan
authors.initials: W
authors.lastname: Wang
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008745:Methylation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods