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F1 family · genome-wide association

Natural rubber content GWAS

GLM and MLM associations, model diagnostics and audited downloads.

126 F11,109,918 SNPTK1151Content (%)
AssociationsCandidate genesSamples & quality
GLMMLM

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

GLM Manhattan plot

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.

1,109,918 valid tests; P≤1e-4 variants 172；Bonferroni 1；FDR≤0.05 1Download all plotted results TSV.gz

View P≤1e-4 variants · View original Bonferroni reference plot

QQ plot and model statisticsGLM QQ plot

λ = 0.978；Genome-wide threshold P ≤ 4.5e-08。

Filter association statistics

Examples: Chr01Lowest-P variantFixed 4 screeningAll results
Current filter 172 recordsDownload current filter TSV
VariantPosition (bp)Effect allelenβPFDR qNearest gene
TK1151:6:91279448:T:CChr06:91,279,448C1162.9524.49e-080.0498TkA06G368510
TK1151:2:115973518:A:TChr02:115,973,518T126-4.333.68e-070.0865TkA02G455250
TK1151:8:70383246:A:CChr08:70,383,246C1243.1597.37e-070.0865TkA08G270160
TK1151:4:4042389:T:AChr04:4,042,389A1151.7538.07e-070.0865TkA04G016310
TK1151:7:74767452:G:AChr07:74,767,452A1257.5861.19e-060.0865TkA07G297620
TK1151:7:74767437:C:TChr07:74,767,437T1267.5631.36e-060.0865TkA07G297620
TK1151:1:112651177:T:CChr01:112,651,177C122-10.531.51e-060.0865TkA01G449580
TK1151:3:147542479:C:TChr03:147,542,479T1162.2011.65e-060.0865TkA03G581390
TK1151:2:41556449:A:GChr02:41,556,449G1182.0431.83e-060.0865TkA02G162070
TK1151:3:75945291:A:GChr03:75,945,291G122-10.511.9e-060.0865TkA03G308830
TK1151:3:75945301:A:TChr03:75,945,301T122-10.511.9e-060.0865TkA03G308830
TK1151:2:130028214:A:CChr02:130,028,214C121-10.531.92e-060.0865TkA02G506880
TK1151:7:85280297:A:TChr07:85,280,297T124-10.522.02e-060.0865TkA07G341770
TK1151:1:20765774:G:AChr01:20,765,774A122-3.8672.78e-060.0865TkA01G081350
TK1151:1:99932398:G:AChr01:99,932,398A124-10.432.87e-060.0865TkA01G400290
TK1151:1:30661804:C:TChr01:30,661,804T126-10.42.92e-060.0865TkA01G121250
TK1151:1:64093009:A:CChr01:64,093,009C126-10.42.92e-060.0865TkA01G254100
TK1151:2:19562145:G:CChr02:19,562,145C12610.42.92e-060.0865TkA02G075560
TK1151:2:30564354:A:CChr02:30,564,354C126-10.42.92e-060.0865TkA02G117290
TK1151:2:53377534:G:AChr02:53,377,534A12610.42.92e-060.0865TkA02G209120
TK1151:3:110564088:A:GChr03:110,564,088G12610.42.92e-060.0865TkA03G443530
TK1151:3:115558834:A:TChr03:115,558,834T126-10.42.92e-060.0865TkA03G462970
TK1151:3:119778197:T:AChr03:119,778,197A12610.42.92e-060.0865TkA03G479000
TK1151:5:78561366:G:AChr05:78,561,366A12610.42.92e-060.0865TkA05G318300
TK1151:7:74707404:T:GChr07:74,707,404G12610.42.92e-060.0865TkA07G297570

Beta is the change in content percentage points per effect allele. Table filters do not alter the genome-wide plot above.

1/7Next
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