Genetic Linkage Map

Platform Overview

A genetic linkage map represents “genetic distance” and order of genes or genetic markers in a species or experimental population. It is mainly based on recombination and crossover of homologous chromosomes, using diverse genetic markers as guides and recombinant frequency as “distance”.


QTL mapping

Genetic marker guided breeding

Genome assembly

Comparative genomics

Service Workflow

Material selection
Library construction and sequencing
Marker identification
Linkage map construction

Bioinformatic Analysis

SLAF-Linkage map

SLAF is a self-developed simplified genome sequencing strategy, which discovers genome-wide distributed markers, SNPs. SLAF based linkage map construction is remarkable for its number of markers, high-quality map, short turnaround time and high data usage, etc.

Resequencing-Linkage map

SNPs can be identified by whole genomes resequencing on species with a reference genome. The genetic linkage distance of these markers can be calculated to construct high-density linkage map. In OTL mapping, resequencing based linkage map enables extraction of targeted region sequences directly, which largely accelerate the process in functional gene identification and validation.

Linkage map with Biomarker Technologies

Self-developed simplified genome sequencing technique: SLAF-seq
HighMap software
Massive experience in linkage map construction covering hundreds of species, over 1,000 maps constructed.
Contributed to over 150+ high-impact publications, accumulated IF>650.
50+ skilled experts in analysis
Diverse successful cases
Highly-experienced technical team
3 distributed computer cluster servers
In-depth data interpretation
Optimized reports delivery
Professional after-sale support
Rapid analysis

Results Demo

Raw Data QC

It is crucial to ensure the quality of sequencing data is adequate for a reliable downstream analysis. Assessments on data production, base quality score, nuceotide distribution, etc. are processed to estimate reliability of sequencing

#Chr Pos Ref R01 R02
Chr1 113342 A G A
Chr1 163871 A G A
Chr1 232230 A A G
Chr1 232330 C C A
Chr1 232546 T T C

Genetic Variation Identification

Single Nucleotide Polymorphism (SNP) and Insertion-Deletion (InDel) are typical genetic markers, which are of great frequency and diveristy. Identification of SNP and InDels is processed by GATK and samtools. variation site is annotated by SnpEff.

Polymorphic Marker Identification

Based on variations identified from previous step, polymorphic markers can be identified between parenting samples to process genotyping in offspring markers.

Genetic Linkage Map Construction

In order to ensure the quality of linkage map, markers in offspring samples has to pass filtration based on sequencing depth in parenting samples, marker integrity, abnormal markers, separation markers. The markers of high-quality obtained will be subjected to self-developed Highmap-map software to construct high density linkage map.

Genetic Linkage Map Evaluation

To ensure the quality of linkage map, assessments are processed on marker integrity, haplotype source evaluation, linkage relation evaluation and collinearity analysis on linkage map.


1How to choose population for linkage map of a known species?
Depending on heterozygosity of parents 1)For heterozygous parents: Use F1 2)For homozygous parents: Use: F2, BC, RIL, DH, etc.
2What's the recommended sequencing depth of parenting and offspring samples in resequencing based linkage map?
We recommend 10-20 X for parenting samples. For species with high-quality reference genome (chromosome-level with N50> 1 Mb), 1 X for offspring samples is enough. For species with relatively poor reference genome, 3 X for offspring samples is recommended.
3What are the softwares used for map construction?
R-qtl, MapQTL, WinQTLcart and ICiMapping