| Crop Database
| Crop Database
germplasm phenotype genotype jbrowse gwas tools
| 16/2/2024 | v2.10.0 | Major release - Support more software: rTASSEL - User is able to run PCA analysis before submitting GWAS job Minor release - Support more method: SUPER, BLINK - New genotype version (wgsV2.9.0) in pre-filtered sets - Remove BMS phenotype import - User is able to set PCA parameter for GAPIT - User is able to delete submitted job - UI improvement |
| 27/9/2022 | v2.9.0 | Minor release - New genotype panel wgsV2.7.1 (389 Taxa and 11,619,690 Variants) |
| Bug fix - Add Random.model=FALSE to avoid error on GAPIT.RandomModel |
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| 13/10/2021 | v2.8.1 | Bug Fix - Fix error on creating job - Fix error on converting Plink format - UI improve |
| 28/09/2021 | v2.8.0 | Minor release - Support multi-locus analysis (MLMM and FarmCPU) for GAPIT |
| 14/09/2021 | v2.7.0 | Minor release - Support maize and blast isolate - Link to Blast DB http://sinin.kps.ku.ac.th/blastdb/ |
| 3/08/2021 | v2.6.0 | Minor release - New genotype panel wgsV2.6.0.0 (421 Taxa and 11,546,486 Variants) |
| 21/04/2021 | v2.5.0 | Minor release - Sharing result via link |
| Bug fix - Bonferroni cut-off in TASSEL result - Hide PDF button for TASSEL result - Limit top-30k SNPs to plot in interactive manhattan plot for TASSEL result - UI improve | ||
| 13/01/2021 | v2.4.0 | Minor release - Split 'Run a new job' to 2 pages; run with rice database and run with user's genotype data (No login require) |
| Bug fix - Multiple-trait result fix | ||
| 17/12/2020 | v2.3.0 | Minor release - New filtering option with TASSEL - New prunning and thinning filtering - Include GLM method for GAPIT - Require login to access 'Run a new job' page |
| 3/12/2020 | v2.2.0 | Minor release - New analysis option using TASSEL |
| 24/9/2020 | v2.1.0 | Minor release - New result-importing function - Update R packages regarding R 4.0.2 |
| 22/6/2020 | v2.0.1 | Bug fix - Import from BMS now supporting v15.0 |
| 29/4/2020 | v2.0.0 | Major release - Import phenotype from BMS study - Support multi-trait in one phenotype file - Cross-domain cookie: Link to user in RGD internal system |
| - | v1.0.0 | Limitations - File uploaded has to be < 2 MB - Sessions are memorized on computer that submits the job |
From wgsV2.7.1 SNP set ( 11,619,690 SNPs / 389 varieties ), filtering is done by PLINK or TASSEL with these following steps
| 1) Filtering taxa | Remove all other varieties, keep only exist in your phenotype file ** Missing and MAF is calculated from this subset, not from the whole set |
| 2) Filtering missing | Remove SNPs having missing value more than specified (default > 10%) For TASSEL, since decimal number cannot be input as minimum count, the number is rounded for missing filtering. For example, if you have 389 varieties of phenotype, missing 0.1 will be set for minimum count as round(389 * (1 - 0.1)) = round(350.1) = 350 If you have 352 varieties of phenotype and set missing for 0.2, the minimum count will be round(352 * (1 - 0.2)) = round(281.6) = 282 |
| 3) Filtering MAF | Remove SNPs having Minor Allele Frequency less than specified (default < 5%) |
| 4) Prunning by LD | Remove SNPs residing in the same linkage, determined by pairwise correlation (r2) (default > 0.1) |
| 5) Thinning by distance | Remove SNPs having distance less than specified (default < 1k bases) |
You can save time of filtering by using pre-filtered genotypes. However, missing and MAF of these genotypes are filtered from 421 varieties (not from varieties you have in your phenotypes).
From the initial SNP set wgsV2.9.0 ( SNPs 13,047,160 / 706 varieties ), the detail of each genotype set is listed as follow
| Genotype set | No. of Varieties | No. of SNPs |
| Miss 0.1, MAF 0.05 | 706 | 3,191,307 |
| Miss 0.2, MAF 0.05 | 706 | 3,623,616 |
| Miss 0.3, MAF 0.05 | 706 | 3,900,663 |
| Miss 0.1, MAF 0.05, Prune 0.1 | 706 | 85,115 |
| Miss 0.1, MAF 0.05, Prune 0.1, Thin 1k | 706 | 61,319 |
Phenotype file to be uploaded must be in this following format
| <Trait> | Trait_1 | Trait_2 | ... |
| W00XXX | value | value | ... |
| W00XXX | value | value | ... |
| ... |
For BMS import, GIDs will be converted to WCode, and then, put in this format.
If any GID is unable to map to WCode, it will be filtered out in genotype filtering.
 | Wang, J. and Zhang, Z., 2021. GAPIT Version 3: boosting power and accuracy for genomic association and prediction. Genomics, Proteomics & Bioinformatics. |
 | Monier, B., Casstevens, T.M., Bradbury, P.J. and Buckler, E.S., 2022. rTASSEL: An R interface to TASSEL for analyzing genomic diversity. Journal of Open Source Software, 7(76), p.4530. |
 | Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y. and Buckler, E.S., 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 23(19), pp.2633-2635. |