F1 family · genome-wide association
Natural rubber content GWAS
GLM and MLM associations, model diagnostics and audited downloads.
126 F11,109,918 SNPTK1151Content (%)
Candidate genes at the fixed cutoff of 4
Variants with P≤1×10⁻⁴ are grouped by the existing overlapping/nearest gene annotation, with one row per gene in this model. Proximity is not causal validation; no new LD candidate intervals were constructed.
GLM：172 screening variants · 142 mapped genes；unique gene union 206；supported by both 131。
Current filter 142 genesDownload filtered candidate genes TSVDownload candidate genes from both models TSVDownload variant–gene evidence TSV
| Gene | Minimum P | Variants | In-gene variants | Models | Lead variant | Distance (bp) |
|---|---|---|---|---|---|---|
| TkA06G368510 Chr06:91,264,968–91,265,541 AnnotationProtein of unknown function | 4.49e-08 | 2 | 0 | GLM;MLM | TK1151:6:91279448:T:C | 13,907 |
| TkA02G455250 Chr02:115,927,162–115,930,306 AnnotationSimilar to MSL8: Mechanosensitive ion channel protein 8 (Arabidopsis thaliana OX%3D3702) | 3.68e-07 | 1 | 0 | GLM;MLM | TK1151:2:115973518:A:T | 43,212 |
| TkA08G270160 Chr08:70,385,487–70,387,068 AnnotationSimilar to ALPHAC-AD: AP-2 complex subunit alpha-2 (Arabidopsis thaliana OX%3D3702) | 7.37e-07 | 1 | 0 | GLM;MLM | TK1151:8:70383246:A:C | 2,241 |
| TkA04G016310 Chr04:4,063,659–4,065,092 AnnotationSimilar to CAM4: Calmodulin-4 (Arabidopsis thaliana OX%3D3702) | 8.07e-07 | 2 | 0 | GLM;MLM | TK1151:4:4042389:T:A | 21,270 |
| TkA07G297620 Chr07:74,741,888–74,748,752 AnnotationSimilar to RE1: Retrovirus-related Pol polyprotein from transposon RE1 (Arabidopsis thaliana OX%3D3702) | 1.19e-06 | 5 | 0 | GLM;MLM | TK1151:7:74767452:G:A | 18,700 |
| TkA01G449580 Chr01:112,636,565–112,638,210 AnnotationSimilar to UBA1C: UBP1-associated proteins 1C (Arabidopsis thaliana OX%3D3702) | 1.51e-06 | 1 | 0 | GLM;MLM | TK1151:1:112651177:T:C | 12,967 |
| TkA03G581390 Chr03:147,539,668–147,540,164 AnnotationProtein of unknown function | 1.65e-06 | 1 | 0 | GLM;MLM | TK1151:3:147542479:C:T | 2,315 |
| TkA02G162070 Chr02:41,555,961–41,560,350 AnnotationSimilar to N: TMV resistance protein N (Nicotiana glutinosa OX%3D35889) | 1.83e-06 | 9 | 6 | GLM;MLM | TK1151:2:41556449:A:G | 0 |
| TkA03G308830 Chr03:75,934,076–75,938,711 AnnotationSimilar to YPQ1: Probable vacuolar amino acid transporter YPQ1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX%3D559292) | 1.9e-06 | 2 | 0 | GLM;MLM | TK1151:3:75945291:A:G | 6,580 |
| TkA02G506880 Chr02:130,026,761–130,029,711 AnnotationSimilar to ALDH2B4: Aldehyde dehydrogenase family 2 member B4%2C mitochondrial (Arabidopsis thaliana OX%3D3702) | 1.92e-06 | 1 | 1 | GLM;MLM | TK1151:2:130028214:A:C | 0 |
| TkA07G341770 Chr07:85,311,258–85,314,594 AnnotationSimilar to SKU5: Monocopper oxidase-like protein SKU5 (Arabidopsis thaliana OX%3D3702) | 2.02e-06 | 1 | 0 | GLM;MLM | TK1151:7:85280297:A:T | 30,961 |
| TkA01G081350 Chr01:20,768,007–20,769,870 AnnotationSimilar to GIP: Copia protein (Drosophila melanogaster OX%3D7227) | 2.78e-06 | 1 | 0 | GLM;MLM | TK1151:1:20765774:G:A | 2,233 |
| TkA01G400290 Chr01:99,924,504–99,927,315 AnnotationSimilar to FLZ14: FCS-Like Zinc finger 14 (Arabidopsis thaliana OX%3D3702) | 2.87e-06 | 1 | 0 | GLM;MLM | TK1151:1:99932398:G:A | 5,083 |
| TkA01G121250 Chr01:30,688,434–30,689,671 AnnotationSimilar to PER60: Peroxidase 60 (Arabidopsis thaliana OX%3D3702) | 2.92e-06 | 1 | 0 | GLM;MLM | TK1151:1:30661804:C:T | 26,630 |
| TkA01G254100 Chr01:64,096,862–64,098,212 AnnotationSimilar to CDKD-3: Cyclin-dependent kinase D-3 (Arabidopsis thaliana OX%3D3702) | 2.92e-06 | 1 | 0 | GLM;MLM | TK1151:1:64093009:A:C | 3,853 |
| TkA02G075560 Chr02:19,559,124–19,562,988 AnnotationSimilar to SPO11-1: Meiotic recombination protein SPO11-1 (Arabidopsis thaliana OX%3D3702) | 2.92e-06 | 1 | 1 | GLM;MLM | TK1151:2:19562145:G:C | 0 |
| TkA02G117290 Chr02:30,591,557–30,595,002 AnnotationSimilar to LSH10: Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 10 (Arabidopsis thaliana OX%3D3702) | 2.92e-06 | 1 | 0 | GLM;MLM | TK1151:2:30564354:A:C | 27,203 |
| TkA02G209120 Chr02:53,367,176–53,376,434 AnnotationSimilar to TIC236: Protein TIC236%2C chloroplastic (Arabidopsis thaliana OX%3D3702) | 2.92e-06 | 2 | 0 | GLM;MLM | TK1151:2:53377534:G:A | 1,100 |
| TkA03G443530 Chr03:110,578,608–110,581,624 AnnotationProtein of unknown function | 2.92e-06 | 2 | 0 | GLM;MLM | TK1151:3:110564088:A:G | 14,520 |
| TkA03G462970 Chr03:115,550,179–115,552,808 AnnotationSimilar to ROPGEF1: Rop guanine nucleotide exchange factor 1 (Arabidopsis thaliana OX%3D3702) | 2.92e-06 | 1 | 0 | GLM;MLM | TK1151:3:115558834:A:T | 6,026 |
| TkA03G479000 Chr03:119,758,547–119,762,102 Annotationgene model | 2.92e-06 | 2 | 1 | GLM;MLM | TK1151:3:119778197:T:A | 16,095 |
| TkA05G318300 Chr05:78,570,666–78,571,982 AnnotationSimilar to VHA-B3: V-type proton ATPase subunit B3 (Arabidopsis thaliana OX%3D3702) | 2.92e-06 | 1 | 0 | GLM;MLM | TK1151:5:78561366:G:A | 9,300 |
| TkA07G297570 Chr07:74,728,265–74,728,615 AnnotationProtein of unknown function | 2.92e-06 | 1 | 0 | GLM;MLM | TK1151:7:74707404:T:G | 20,861 |
| TkA08G033790 Chr08:8,609,624–8,623,084 AnnotationSimilar to At2g15630: Pentatricopeptide repeat-containing protein At2g15630%2C mitochondrial (Arabidopsis thaliana OX%3D3702) | 2.92e-06 | 2 | 2 | GLM;MLM | TK1151:8:8610082:A:G | 0 |
| TkA08G109840 Chr08:28,562,356–28,565,627 AnnotationProtein of unknown function | 2.92e-06 | 1 | 1 | GLM;MLM | TK1151:8:28563882:T:C | 0 |
Distance 0 means the lead variant overlaps the gene interval. Supporting models each meet P≤1×10⁻⁴; this is not independent replication.
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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