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Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)

High-throughput genotyping, especially on large-scale population, is a fundamental step in genetic association studies, which provides genetic basis for functional gene discovery, evolutionary analysis, etc. Instead of deep whole genome re-sequencing, reduced representation genome sequencing (RRGS) is introduced to minimize sequencing cost per sample, while maintain reasonable efficiency on genetic marker discovery. This is commonly achieved by extracting restriction fragment within given size range, which is named reduced representation library (RRL). Specific-locus amplified fragment sequencing (SLAF-Seq) is a self-developed strategy for SNP genotyping with or without a reference genome. 
Platform: Illumina NovaSeq Platform


Service Details

Demo Results

Featured Publications

Service Details

Technical Scheme

111

Work flow

流程图

Service Advantages

High marker discovery efficiency - High-throughput sequencing technology assists SLAF-Seq in discovering hundreds of thousands of tags within the whole genome.

Low dependence on the genome - It can be applied to species either with or without a reference genome.

Flexible scheme design - Single-enzyme, dual-enzyme, multi-enzyme digestion and various types of enzymes, all can be selected to cater different research goal or species. Pre-evaluation in silico is used to assure an optimal enzyme design.

Efficient enzymatic digestion - Pre-experiment was carried out to optimize the conditions, which makes the formal experiment stable and reliable. Fragment collection efficiency can achieve over 95%.

Evenly distributed SLAF tags - SLAF tags are evenly distributed in all chromosomes to the greatest extent, achieving an average of 1 SLAF per 4 kb.

Effective avoidance of repeats - Repetitive sequence in SLAF-Seq data is reduced to lower than 5%, especially in species with high level of repeats, such as wheat, maize, etc.

Extensive experience -Over 2000 closed SLAF-Seq projects on hundreds of species covering plants, mammals, birds, insects, aqua-organisms, etc.

Self-developed bioinformatic workflow - An integrated bioinformatic workflow for SLAF-Seq was developed by BMKGENE to ensure reliability and accuracy of final output.

 

Service Specifications

 

Platform

Conc.(ng/gl)

Total (ug)

OD260/280

Illumina NovaSeq

>35

>1.6  (Volumn>15μl)

1.6-2.5

Note: Three samples, each with three enzyme schemes, will be performed for pre-experiment.

Recommended Sequencing Strategy

Sequencing depth: 10X/Tag

Genome Size

Recommended SLAF Tags

< 500 Mb

100K or WGS 

500 Mb- 1 Gb

100 K

1 Gb -2 Gb

200 K

Giant or complex genomes

300 - 400K

 

Applications

 

Recommended

Population Scale

 

Sequencing strategy and depth

 

Depth

 

Tag Number

 

GWAS

 

Sample number ≥ 200

 

10X

 

 

 

 

 

According to

genome size

 

Genetic Evolution

 

Individuals of each

subgroup ≥ 10;

total samples ≥ 30

 

10X

 

Recommended Sample Delivery

Container: 2 ml centrifuge tube

For most of samples, we recommend not to preserve in ethanol.

Sample labeling: Samples need to be clearly labeled and identical to submitted sample information form.

Shipment: Dry-ice: Samples need to be packed in bags first and buried in dry-ice.

Service Workflow

Sample QC
Pilot experiment
SLAF experiment
Library Preparation
Sequencing
Data analysis
After sale Services

Sample QC

Pilot experiment

SLAF-experiment

Library Preparation

Sequencing

Data Analysis

After-sale Services


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    3. Variation annotation

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    Year

    Journal

    IF

    Title

    Applications

    2022

    Nature communications

    17.694

    Genomic basis of the giga-chromosomes and giga-genome of tree peony

    Paeonia ostii

    SLAF-GWAS

    2015

    New Phytologist

    7.433

    Domestication footprints anchor genomic regions of agronomic importance in 

    soybeans

    SLAF-GWAS

    2022

    Journal of  Advanced Research

    12.822

    Genome-wide artificial introgressions of Gossypium barbadense into G. hirsutum

    reveal superior loci for simultaneous improvement of cotton fiber quality and yield

    traits

    SLAF-Evolutionary genetics

    2019

    Molecular Plant

    10.81

    Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy 

    Rice as  an Evolutionary Game

    SLAF-Evolutionary genetics

    2019

    Nature Genetics

    31.616

    Genome sequence and genetic diversity of the common carp, Cyprinus carpio

    SLAF-Linkage map

    2014

    Nature Genetics

    25.455

    The genome of cultivated peanut provides insight into legume karyotypes, polyploid 

    evolution and crop domestication.

    SLAF-Linkage map

    2022

    Plant Biotechnology Journal

    9.803

    Identification of ST1 reveals a selection involving hitchhiking of seed morphology 

    and oil content during soybean domestication

    SLAF-Marker development

    2022

    International Journal of Molecular Sciences

    6.208

    Identification and DNA Marker Development for a Wheat-Leymus mollis 2Ns (2D)

    Disomic Chromosome Substitution 

    SLAF-Marker development

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