Natural rubber content GWAS
GLM and MLM associations, model diagnostics and audited downloads.
Trait and sample checks
126 F1 offspring were initially included; both parents and R09 were excluded. These records passed QC and entered both models.
Genomic relationship matrix
| Resequencing sample | Paper ID | Content (%) | Missing genotype rate | Run |
|---|---|---|---|---|
| F1-1 | R03 | 5.896 | 4.52% | CRR618485 |
| F1-2 | R04 | 1.859 | 4.29% | CRR618486 |
| F1-5 | R05 | 7.018 | 1.48% | CRR618487 |
| F1-6 | R06 | 4.037 | 1.95% | CRR618488 |
| F1-7 | R117 | 5.72 | 5.52% | CRR618599 |
| F1-8 | R07 | 0.297 | 5.61% | CRR618489 |
| F1-9 | R08 | 5.5 | 6.36% | CRR618490 |
| F1-11 | R10 | 7.337 | 4.95% | CRR618492 |
| F1-12 | R11 | 3.06 | 3.12% | CRR618493 |
| F1-13 | R12 | 4.554 | 4.02% | CRR618494 |
| F1-15 | R118 | 3.575 | 2.59% | CRR618600 |
| F1-16 | R13 | 2.134 | 4.63% | CRR618495 |
| F1-18 | R119 | 2.442 | 3.67% | CRR618601 |
| F1-19 | R14 | 2.244 | 4.80% | CRR618496 |
| F1-20 | R120 | 8.844 | 5.08% | CRR618602 |
| F1-21 | R121 | 1.639 | 1.54% | CRR618603 |
| F1-26 | R15 | 5.115 | 4.58% | CRR618497 |
| F1-29 | R16 | 9.515 | 5.08% | CRR618498 |
| F1-30 | R122 | 7.601 | 4.14% | CRR618604 |
| F1-31 | R17 | 6.061 | 4.29% | CRR618499 |
| F1-32 | R18 | 3.685 | 2.65% | CRR618500 |
| F1-33 | R123 | 4.587 | 3.59% | CRR618605 |
| F1-34 | R124 | 3.113 | 3.26% | CRR618606 |
| F1-36 | R125 | 4.11 | 3.90% | CRR618607 |
| F1-37 | R126 | 6.325 | 3.74% | CRR618608 |
Methods, sources and scope
This is one F1 family. Phenotypes are published mean natural rubber contents; the VCF was generated by this project from CRA009020 reads. Sample correspondence is supported by unique exact read-count matches; consistency with the author’s original bin coding remains unresolved. Results support exploratory within-family association; candidates require independent validation.
Biallelic SNPs on8 chromosomes; nonvarying offspring GT dosage excluded; GT depth ≥5; variant missingness ≤10%; MAF ≥0.05; sample missingness ≤15%; no HWE filtering in the F1 family. GLM uses nonmissing genotypes per variant; MLM handles residual missing calls by its software defaults. Nearest genes indicate proximity; published marker intervals are not full QTL confidence intervals.
Yang et al., 2023Published QTLsMethods & versionsNumerical validationWorkflow & provenanceFurther analysis plan