BMKCloud Log in


Genome-wide Association Analysis

The aim of Genome-Wide Association Studies (GWAS) is to identify genetic variants (genotypes) linked to specific traits (phenotypes). By scrutinizing genetic markers across the entire genome in a large number of individuals, GWAS extrapolates genotype-phenotype associations through population-level statistical analyses. This methodology finds extensive applications in researching human diseases and exploring functional genes related to complex traits in animals or plants.

At BMKGene, we offer two avenues for conducting GWAS on large populations: employing Whole-Genome Sequencing (WGS) or opting for a reduced representation genome sequencing method, the in-house-developed Specific-Locus Amplified Fragment (SLAF). While WGS suits smaller genomes, SLAF emerges as a cost-effective alternative for studying larger populations with longer genomes, effectively minimizing sequencing costs, while guaranteeing a high genetic marker discovery efficiency.

Service Details


Demo Result

Featured Publications



Service Advantages

● Extensive Expertise and publication records: with accumulated experience in GWAS, BMKGene has completed hundreds of species projects in population GWAS research, assisted researchers to publish more than 100 articles, and the cumulative impact factor reached 500.

● Comprehensive bioinformatics analysis: workflow includes SNP-trait association analysis, delivering a set of candidate genes and their corresponding functional annotation.

● Highly skilled bioinformatics team and short analysis cycle: with great experience in advanced genomics analysis, BMKGene’s team delivers comprehensive analyses with a swift turnaround time.

● Post-Sales Support: Our commitment extends beyond project completion with a 3-month after-sale service period. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results.

Service specifications and requirements

Type of sequencing

Recommended population scale

Sequencing strategy

Nucleotide requirements

Whole Genome Sequencing

200 samples


Concentration: ≥1 ng/ µL

Total amount≥ 30ng

Limited or no degradation or contamination

Specific-Locus Amplified Fragment (SLAF)

Tag depth: 10x

Number of tags:

<400 Mb: WGS is recommended

<1Gb: 100K tags

1Gb<genome<2Gb: 200K tags

>2Gb: 300K tags

Max 500k tags

Concentration ≥ 5 ng/µL

Total amount ≥80 ng

Nanodrop OD260/280=1.6-2.5

Agarose gel: no or limited degradation or contamination


Material Selection


Different varieties, subspecies, landraces/genebanks/mixed families/wild resources

Different varieties, subspecies, landraces

Half-sib family/full-sib family/wild resources

Service Work Flow

Sample QC

Experiment design

sample delivery

Sample delivery

Pilot experiment

RNA extraction

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

  • Previous:
  • Next:

  • 图片119

    Includes the following analysis:

    • Genome-wide association analysis: LM, LMM, EMMAX, FASTLMM model
    • Functional annotation of candidate genes

    SNP-trait association analysis – Manhattan plot



    SNP-trait association analysis – QQ plot




    Explore the advancements facilitated by BMKGene’s de GWAS services through a curated collection of publications:

    Lv, L. et al. (2023) ‘Insight into the genetic basis of ammonia tolerance in razor clam Sinonovacula constricta by genome-wide association study’, Aquaculture, 569, p. 739351. doi: 10.1016/J.AQUACULTURE.2023.739351.

    Li, X. et al. (2022) ‘Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects’, Molecular Plant, 15(8), pp. 1367–1383. doi: 10.1016/j.molp.2022.07.003.

    Li, J. et al. (2022) ‘Genome-Wide Association Mapping of Hulless Barely Phenotypes in Drought Environment’, Frontiers in Plant Science, 13, p. 924892. doi: 10.3389/FPLS.2022.924892/BIBTEX.

    Zhao, X. et al. (2021) ‘GmST1, which encodes a sulfotransferase, confers resistance to soybean mosaic virus strains G2 and G3’, Plant, Cell & Environment, 44(8), pp. 2777–2792. doi: 10.1111/PCE.14066.

    get a quote

    Write your message here and send it to us

    Send your message to us: