This objective for this project is simulate and compare GWAS power in different crop speices under vairous situations including number of QTNs, effect values, and heritability.
All the files about this project are located at /work/schnablelab/cmiao/GWAS-in-Crop-Species in UNL HCC crane cluster.
We collected several crop spieceis genotype data from published papers
- Sorghum bicolor
- including 1,943 georeferenced landraces and 404,627 SNPs
- Genotyping-by-sequecing with 23% having MAF < 0.01 and 65% of SNPs having MAF < 0.1.
- Setaria italica
- including 916 diverse varieties and 726,080 SNPs
- low coverage genome resquecing with about 0.7X.
- Oryza sativa
- A total of 1,568 rice accessions and 700,000 SNPs.
- using micro-array technology.
- Zea mays Whole genome resquecning
- The paper wasn't published.
- This data also contains other close species, like teosinte and tripsacum.
- 916 maize lines and 60 million SNPs
- whole genome resquencing technology with 1X ~ 46X
- Zea mays GBS
- 2,815 maize inbred accessions and 681,257 SNPs
- Genotyping by sequencing technology was used
All the raw genotype data are loated at /work/schnablelab/cmiao/GWAS-in-Crop-Species/Genotypes with a readme file describing the data resource in each speices directory.