SLAF-Seq

SLAF-Seq

Specific locus amplified fragment sequencing (SLAF-seq) is an optimized version of ddRADseq, specifically intended for large-scale genotyping experiments.

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 the PCR reaction. The protocol is similar to ddRAD, for example with a first digestion with MseI, heat inactivation and a second digestion with AluI. The resulting fragments are PCR amplified, adaptors added and the fragments purified.

Pros:

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

Cons:

• Does not cover whole genome

• CLASH-Seq: Sun X., Liu D., Li W., Liu H., Hong W., et al. (2016) SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One 8:e58700

1. Zhao X., Huang L., Zhang X., Wang J., Yan D., et al. (2016) Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq. Sci Rep 6: 29345
2. Geng X., Jiang C., Yang J., Wang L., Wu X., et al. (2016) Rapid Identification of Candidate Genes for Seed Weight Using the SLAF-Seq Method in Brassica napus. PLoS One 11: e0147580
3. Zhang J., Yuan H., Li M., Li Y., Wang Y., et al. (2016) A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq). PLoS One 11: e0157777
4. Wei Q. Z., Fu W. Y., Wang Y. Z., Qin X. D., Wang J., et al. (2016) Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis. Sci Rep 6: 27496
5. Xu X., Chao J., Cheng X., Wang R., Sun B., et al. (2016) 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 11: e0151401
6. Ye Y., Cai M., Ju Y., Jiao Y., Feng L., et al. (2016) Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia. PLoS One 11: e0158970
7. Zhang H., Yi H., Wu M., Zhang Y., Zhang X., et al. (2016) Mapping the Flavor Contributing Traits on "Fengwei Melon" (Cucumis melo L.) Chromosomes Using Parent Resequencing and Super Bulked-Segregant Analysis. PLoS One 11: e0148150
8. Cai C., Cheng F. Y., Wu J., Zhong Y. and Liu G. (2015) The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing. PLoS One 10: e0128584
9. Ma J. Q., Huang L., Ma C. L., Jin J. Q., Li C. F., et al. (2015) 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 10: e0128798
10. Qin D., Dong J., Xu F., Guo G., Ge S., et al. (2015) 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 16: 838
11. Shan T., Pang S., Li J., Li X. and Su L. (2015) 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 16: 902
12. Wang J., Zhang K., Zhang X., Yan G., Zhou Y., et al. (2015) Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter. PLoS One 10: e0141261
13. Wang W., Zhang T., Zhang G., Wang J., Han K., et al. (2015) Genome-wide association study of antibody level response to NDV and IBV in Jinghai yellow chicken based on SLAF-seq technology. J Appl Genet 56: 365-373
14. Xu F., Sun X., Chen Y., Huang Y., Tong C., et al. (2015) Rapid identification of major QTLs associated with rice grain weight and their utilization. PLoS One 10: e0122206
15. Xu X., Lu L., Zhu B., Xu Q., Qi X., et al. (2015) QTL mapping of cucumber fruit flesh thickness by SLAF-seq. Sci Rep 5: 15829
16. Xu Y., Huang L., Ji D., Chen C., Zheng H., et al. (2015) 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 15: 228
17. Zhang J., Zhang Q., Cheng T., Yang W., Pan H., et al. (2015) 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
18. Zhang Y., Zhang J., Huang L., Gao A., Zhang J., et al. (2015) A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq). Planta