Natural rubber content GWAS
GLM and MLM associations, model diagnostics and audited downloads.
GLM: PC1–PC3; MLM: PC1–PC3 and a standardized genomic relationship matrix. Interpretation is limited to this F1 family.
Genome-wide results for the selected model
Red dashed line: fixed exploratory screening at −log10(P)=4 (P≤1×10⁻⁴); gray dotted line: suggestive 1/M. Variants and candidate genes use the fixed cutoff; no empirical permutation calibration was performed.
View P≤1e-4 variants · View original Bonferroni reference plot
QQ plot and model statistics
λ = 0.978；Genome-wide threshold P ≤ 4.5e-08。
Filter association statistics
| Variant | Position (bp) | Effect allele | n | β | P | FDR q | Nearest gene |
|---|---|---|---|---|---|---|---|
| TK1151:1:112651177:T:C | Chr01:112,651,177 | C | 122 | -10.53 | 1.51e-06 | 0.0865 | TkA01G449580 |
| TK1151:1:20765774:G:A | Chr01:20,765,774 | A | 122 | -3.867 | 2.78e-06 | 0.0865 | TkA01G081350 |
| TK1151:1:99932398:G:A | Chr01:99,932,398 | A | 124 | -10.43 | 2.87e-06 | 0.0865 | TkA01G400290 |
| TK1151:1:30661804:C:T | Chr01:30,661,804 | T | 126 | -10.4 | 2.92e-06 | 0.0865 | TkA01G121250 |
| TK1151:1:64093009:A:C | Chr01:64,093,009 | C | 126 | -10.4 | 2.92e-06 | 0.0865 | TkA01G254100 |
| TK1151:1:158505141:C:T | Chr01:158,505,141 | T | 125 | 10.42 | 3e-06 | 0.0865 | TkA01G627810 |
| TK1151:1:18040053:C:T | Chr01:18,040,053 | T | 124 | -10.45 | 3.06e-06 | 0.0865 | TkA01G070550 |
| TK1151:1:18040068:C:A | Chr01:18,040,068 | A | 123 | -10.46 | 3.1e-06 | 0.0865 | TkA01G070550 |
| TK1151:1:118957315:A:C | Chr01:118,957,315 | C | 115 | -9.947 | 3.51e-06 | 0.0865 | TkA01G475170 |
| TK1151:1:85773526:T:G | Chr01:85,773,526 | G | 126 | 4.117 | 5.05e-06 | 0.114 | TkA01G345340 |
| TK1151:1:19575244:A:G | Chr01:19,575,244 | G | 119 | -3.887 | 8.85e-06 | 0.179 | TkA01G076640 |
| TK1151:1:8052540:G:T | Chr01:8,052,540 | T | 114 | -2.825 | 1.42e-05 | 0.24 | TkA01G031300 |
| TK1151:1:55016454:T:C | Chr01:55,016,454 | C | 119 | 1.941 | 1.78e-05 | 0.279 | TkA01G215880 |
| TK1151:1:132381525:A:C | Chr01:132,381,525 | C | 124 | -5.415 | 1.8e-05 | 0.279 | TkA01G527130 |
| TK1151:1:14007897:G:A | Chr01:14,007,897 | A | 125 | 2.994 | 1.81e-05 | 0.279 | TkA01G054230 |
| TK1151:1:126126144:T:C | Chr01:126,126,144 | C | 125 | -5.395 | 1.87e-05 | 0.285 | TkA01G503690 |
| TK1151:1:113553025:G:A | Chr01:113,553,025 | A | 125 | 2.766 | 2.06e-05 | 0.292 | TkA01G453990 |
| TK1151:1:30245177:C:A | Chr01:30,245,177 | A | 125 | 1.913 | 2.55e-05 | 0.33 | TkA01G119390 |
| TK1151:1:10487966:A:G | Chr01:10,487,966 | G | 121 | -2.384 | 4.83e-05 | 0.483 | TkA01G040630 |
| TK1151:1:41201569:T:A | Chr01:41,201,569 | A | 115 | 2.705 | 7.14e-05 | 0.596 | TkA01G161130 |
| TK1151:1:29460003:A:T | Chr01:29,460,003 | T | 119 | -2.427 | 7.73e-05 | 0.617 | TkA01G116340 |
| TK1151:1:66099415:A:G | Chr01:66,099,415 | G | 115 | 2.077 | 8.37e-05 | 0.628 | TkA01G262840 |
| TK1151:1:34824375:G:A | Chr01:34,824,375 | A | 120 | 5.073 | 0.000115 | 0.686 | TkA01G137210 |
| TK1151:1:112808204:T:C | Chr01:112,808,204 | C | 126 | 4.966 | 0.000117 | 0.686 | TkA01G449580 |
| TK1151:1:4774135:G:A | Chr01:4,774,135 | A | 116 | 2.988 | 0.000128 | 0.712 | TkA01G018570 |
Beta is the change in content percentage points per effect allele. Table filters do not alter the genome-wide plot above.
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