Specific Locus Amplified Fragment Sequencing

SLAF-seq is an optimized version of ddRADseq, specifically intended for large-scale genotyping experiments (Sun et al., 2013). The enzymes and the sizes of the restriction fragments are optimized with training data to ensure even distribution and avoid repeats. The fragments are also selected over a tight range, to optimize PCR amplification. The protocol is similar to ddRAD, with a first digestion with MseI, heat inactivation, and a second digestion with AluI. The resulting fragments are PCR-amplified, adapters are added, and the fragments are purified to produce the sequencing library.


  • Deep sequencing for genotyping accuracy
  • Reduced-representation strategy to reduce sequencing costs
  • Predesigned reduced-representation scheme to optimize marker efficiency
  • Double barcode system for large populations


  • Does not cover the whole genome


Illumina Library prep and Array Kit Selector


Andrews K. R., Good J. M., Miller M. R., Luikart G. and Hohenlohe P. A. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016;


Zhao X., Huang L., Zhang X., et al. Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq. Sci Rep. 2016;6:29345

Geng X., Jiang C., Yang J., Wang L., Wu X. and Wei W. Rapid Identification of Candidate Genes for Seed Weight Using the SLAF-Seq Method in Brassica napus. PLoS One. 2016;11:e0147580

Zhang J., Yuan H., Li M., et al. A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq). PLoS One. 2016;11:e0157777

Wei Q. Z., Fu W. Y., Wang Y. Z., et al. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis. Sci Rep. 2016;6:27496

Xu X., Chao J., Cheng X., et al. Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy. PLoS One. 2016;11:e0151401

Ye Y., Cai M., Ju Y., et al. Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia. PLoS One. 2016;11:e0158970

Zhang H., Yi H., Wu M., et al. Mapping the Flavor Contributing Traits on “Fengwei Melon” (Cucumis melo L.) Chromosomes Using Parent Resequencing and Super Bulked-Segregant Analysis. PLoS One. 2016;11:e0148150

Cai C., Cheng F. Y., Wu J., Zhong Y. and Liu G. The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing. PLoS One. 2015;10:e0128584

Ma J. Q., Huang L., Ma C. L., et al. Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). PLoS One. 2015;10:e0128798

Qin D., Dong J., Xu F., et al. Characterization and fine mapping of a novel barley Stage Green-Revertible Albino Gene (HvSGRA) by Bulked Segregant Analysis based on SSR assay and Specific Length Amplified Fragment Sequencing. BMC Genomics. 2015;16:838

Shan T., Pang S., Li J., Li X. and Su L. Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Genomics. 2015;16:902

Wang J., Zhang K., Zhang X., et al. Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter. PLoS One. 2015;10:e0141261

Wang W., Zhang T., Zhang G., et al. Genome-wide association study of antibody level response to NDV and IBV in Jinghai yellow chicken based on SLAF-seq technology. J Appl Genet. 2015;56:365-373

Xu F., Sun X., Chen Y., Huang Y., Tong C. and Bao J. Rapid identification of major QTLs associated with rice grain weight and their utilization. PLoS One. 2015;10:e0122206

Xu X., Lu L., Zhu B., Xu Q., Qi X. and Chen X. QTL mapping of cucumber fruit flesh thickness by SLAF-seq. Sci Rep. 2015;5:15829

Xu Y., Huang L., Ji D., Chen C., Zheng H. and Xie C. Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta). BMC Plant Biol. 2015;15:228

Zhang J., Zhang Q., Cheng T., et al. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc). DNA Res. 2015;22:183-191

Zhang Y., Zhang J., Huang L., et al. A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq). Planta. 2015;242:1335-1347