Genome Wide Association Study

The home page of "Polygenic Basis Seedless Grapes" can be accessed by clicking here.

Data preparation

Input Data

WGS data: .R1.fastq.gz and .R2.fastq.gz
VCF File

Dependency The detials of all tools can be available in their offical website as followed and most of them can quickly install using Anaconda:

PLINK2.0, VCFtools, GEMMA

Data filtering

You could be checked the raw VCF file obtained from this repository (Population Genetics Analysis Pipeline).

If needed, you can separate the VCF file into SNPs and InDels.

vcf="all_miss0.8GQ20maf0.0001.id.vcf"

#vcftools --vcf ${vcf}.vcf --remove-indels --recode --out ${vcf}.rmindel
#vcftools --vcf ${vcf}.vcf --keep-only-indels --recode --out ${vcf}.rmsnp

Here, we only retain samples with phenotype values.

plink --vcf ./all_miss0.8GQ20maf0.0001.id.vcf \
--vcf-half-call m \
--geno 0.2 \
--maf 0.05 \
--hwe 1e-5 \
--keep keep444.txt \
--recode vcf-iid \
--allow-extra-chr \
--const-fid \
--threads 5 \
--make-bed \
--out 444_geno0.2gq20maf0.005hwe1e-5.id

-------------
./keep444.txt:
0  B1
0  B2
0  B3
...

Insert phenotype values manually

Please replace the sixth line of the 444_geno0.2gq20maf0.005hwe1e-5.id.fam file with their phenotype values. Using the Excel VLOOKUP function is recommended.

GEMMA and GWAS ploting

We selected the linear mixed model (LMM) and used all three tests: Wald test, likelihood ratio test, and score test with the -lmm 4 option. Detailed documentation for the GEMMA software is available here. The GEMMA offical GitHub: https://github.com/genetics-statistics.

name='444_geno0.2gq20maf0.005hwe1e-5.id'
gemma -bfile ${name} -gk 2 -miss 0.2 -maf 0.05 -hwe 1e-5 -o ${name}
gemma -bfile ${name} -n 1 -miss 0.2 -maf 0.05 -hwe 1e-5 -k ./output/${name}.sXX.txt -lmm 4 -o ${name}

name='444_geno0.2gq20maf0.005hwe1e-5.id'
# Please ensure your chromosome IDs contain only numbers. Alternatively, you can use the following code to revise your chromosome numbers:
# for i in {01..19}; do sed -i "s/Chr${i}/${i}/g" ${name}.assoc.txt ;done 

Rscript ./manhattan.R ${name}.assoc.txt p_wald

# sudo yum install poppler-utils
pdftoppm -png -singlefile ${name}.assoc.txtp_wald_manhattan.pdf ./manhattan.plot
pdftoppm -png -singlefile ${name}.assoc.txtp_wald_qq.pdf ./qq.plot

Others ploting

Please check the tool of LDBlockShow, and population analysis pipeline.

Code availability and Citation

All scripts could be found in this repository above. If you have any question, please do not hesitate contact us. Xu Wang: [email protected]

Wang, Xu, et al. "Integrative genomics reveals the polygenic basis of seedlessness in grapevine" Current Biology (2024). doi: https://doi.org/10.1016/j.cub.2024.07.022

immortal2333 / genome_wide_association_study Goto Github PK