ArticlePloS one2013
SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 442 papers, 1 of them a synthesis that pooled it.
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442 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Allele frequency and gene expression differences under key winter stresses in temporal populations of two timothy cultivars.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- SLAF-seq efficiently identifies SNP markers for wheat (Triticum aestivum L.) improvement.BMC genomics · 2026Article
- Conspecific Scaffold-Level Genome Assembly Outperforms Heterospecific Chromosome-Level Assemblies for Assessing Genetic Indicators in a Threatened Marine Fish.Evolutionary applications · 2026Article
- Construction of the First Genetic Linkage Map and QTL Analysis for Morphological Traits inPlants (Basel, Switzerland) · 2026Article
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- Minor Allele Frequency Filtering Can Strongly Bias Uniqueness Estimates Within and Across Species.Ecology and evolution · 2026Article
- Genome-wide variation in and between two closely related underutilised horsegram species (AoB PLANTS · 2026Article
- Identification of Genes Associated with the Pan-Vibrios Resistance (PVR) Trait of Pacific White Shrimp (Biology · 2026Article
- Genome-wide detection of fine-scale population stratification and long-distance dispersal of the Chinese mitten crab (Animal cells and systems · 2026Article
- Integrative analysis of plastome, single-copy nuclear genePlant diversity · 2026Article
382 more citing papers are in PubMed but not listed here.
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20 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq). SLAF-seq technology has several distinguishing characteristics: i) deep sequencing to ensure genotyping accuracy; ii) reduced representation strategy to reduce sequencing costs; iii) pre-designed reduced representation scheme to optimize marker efficiency; and iv) double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations.
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