title: Construction of the first high-density genetic linkage map of Salvia miltiorrhiza using specific length amplified fragment (SLAF) sequencing.
abstract: Salvia miltiorrhiza is an important medicinal crop in traditional Chinese medicine (TCM). Knowledge of its genetic foundation is limited because sufficient molecular markers have not been developed, and therefore a high-density genetic linkage map is incomplete. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-throughput strategy for large-scale SNP (Single Nucleotide Polymorphisms) discovery and genotyping based on next generation sequencing (NGS). In this study, genomic DNA extracted from two parents and their 96 F1 individuals was subjected to high-throughput sequencing and SLAF library construction. A total of 155.96 Mb of data containing 155,958,181 pair-end reads were obtained after preprocessing. The average coverage of each SLAF marker was 83.43-fold for the parents compared with 10.36-fold for the F1 offspring. The final linkage map consists of 5,164 SLAFs in 8 linkage groups (LGs) and spans 1,516.43 cM, with an average distance of 0.29 cM between adjacent markers. The results will not only provide a platform for mapping quantitative trait loci but also offer a critical new tool for S. miltiorrhiza biotechnology and comparative genomics as well as a valuable reference for TCM studies.
authors.affiliation: State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China.
authors.forename: Tian
authors.initials: T
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China.
authors.forename: Linlin
authors.initials: L
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China.
authors.forename: Yuling
authors.initials: Y
authors.lastname: Pan
authors.affiliation: State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China.|Agronomy College, Shandong Agricultural University, Taian, Shandong, China.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China.|Agronomy College, Shandong Agricultural University, Taian, Shandong, China.
authors.forename: Zhenqiao
authors.initials: Z
authors.lastname: Song
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D018744:DNA, Plant / Q000032:analysis; D008040:Genetic Linkage; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D027561:Salvia miltiorrhiza / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018744:DNA, Plant