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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

MLM 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 236；Bonferroni 0；FDR≤0.05 46Download all plotted results TSV.gz

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

QQ plot and model statisticsMLM QQ plot

λ = 1.031；Genome-wide threshold P ≤ 4.5e-08。

MLM converged with the GRM variance component near its lower boundary. This conditional fit does not establish zero trait heritability; interpret it with the family design and robustness checks. V(G)=1e-05；V(e)=4.3028。

Filter association statistics

Examples: Chr01Lowest-P variantFixed 4 screeningAll results
Current filter 236 recordsDownload current filter TSV
VariantPosition (bp)Effect allelenβPFDR qNearest gene
TK1151:6:91279448:T:CChr06:91,279,448C1262.9665.15e-080.0463TkA06G368510
TK1151:2:115973518:A:TChr02:115,973,518T126-4.1822.18e-070.0463TkA02G455250
TK1151:8:70383246:A:CChr08:70,383,246C1263.1452.32e-070.0463TkA08G270160
TK1151:4:4042389:T:AChr04:4,042,389A1261.7026.78e-070.0463TkA04G016310
TK1151:7:74767437:C:TChr07:74,767,437T1267.3327.1e-070.0463TkA07G297620
TK1151:2:41556449:A:GChr02:41,556,449G1261.9887.11e-070.0463TkA02G162070
TK1151:7:74767452:G:AChr07:74,767,452A1267.3127.61e-070.0463TkA07G297620
TK1151:2:130028214:A:CChr02:130,028,214C126-10.041.43e-060.0463TkA02G506880
TK1151:2:41555288:C:TChr02:41,555,288T1261.9681.53e-060.0463TkA02G162070
TK1151:5:45231414:C:TChr05:45,231,414T126-3.8751.56e-060.0463TkA05G177450
TK1151:1:99932398:G:AChr01:99,932,398A126-9.9961.59e-060.0463TkA01G400290
TK1151:1:18040053:C:TChr01:18,040,053T126-9.9881.62e-060.0463TkA01G070550
TK1151:3:75945291:A:GChr03:75,945,291G126-9.9821.65e-060.0463TkA03G308830
TK1151:3:75945301:A:TChr03:75,945,301T126-9.9821.65e-060.0463TkA03G308830
TK1151:5:62735099:C:GChr05:62,735,099G126-9.9791.66e-060.0463TkA05G252240
TK1151:7:24731449:C:TChr07:24,731,449T126-9.9771.66e-060.0463TkA07G094780
TK1151:1:18040068:C:AChr01:18,040,068A126-9.9771.67e-060.0463TkA01G070550
TK1151:1:112651177:T:CChr01:112,651,177C126-9.9761.67e-060.0463TkA01G449580
TK1151:4:56548315:C:TChr04:56,548,315T126-9.9771.67e-060.0463TkA04G222210
TK1151:1:30661804:C:TChr01:30,661,804T126-9.9691.69e-060.0463TkA01G121250
TK1151:1:64093009:A:CChr01:64,093,009C126-9.9691.69e-060.0463TkA01G254100
TK1151:2:19562145:G:CChr02:19,562,145C1269.9691.69e-060.0463TkA02G075560
TK1151:2:30564354:A:CChr02:30,564,354C126-9.9691.69e-060.0463TkA02G117290
TK1151:2:53377534:G:AChr02:53,377,534A1269.9691.69e-060.0463TkA02G209120
TK1151:3:110564088:A:GChr03:110,564,088G1269.9691.69e-060.0463TkA03G443530

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

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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