RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

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 188,143 recordsDownload current filter TSV
VariantPosition (bp)Effect allelenβPFDR qNearest gene
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
TK1151:1:18040068:C:AChr01:18,040,068A126-9.9771.67e-060.0463TkA01G070550
TK1151:1:112651177:T:CChr01:112,651,177C126-9.9761.67e-060.0463TkA01G449580
TK1151:1:30661804:C:TChr01:30,661,804T126-9.9691.69e-060.0463TkA01G121250
TK1151:1:64093009:A:CChr01:64,093,009C126-9.9691.69e-060.0463TkA01G254100
TK1151:1:158505141:C:TChr01:158,505,141T1269.9591.74e-060.0463TkA01G627810
TK1151:1:118957315:A:CChr01:118,957,315C126-9.9491.8e-060.0463TkA01G475170
TK1151:1:20765774:G:AChr01:20,765,774A126-3.6191.85e-060.0463TkA01G081350
TK1151:1:85773526:T:GChr01:85,773,526G1264.0682.01e-060.0485TkA01G345340
TK1151:1:19575244:A:GChr01:19,575,244G126-3.8052.49e-060.0577TkA01G076640
TK1151:1:8052540:G:TChr01:8,052,540T126-2.7394.77e-060.093TkA01G031300
TK1151:1:132381525:A:CChr01:132,381,525C126-5.3996.74e-060.121TkA01G527130
TK1151:1:30245177:C:AChr01:30,245,177A1261.8931.05e-050.167TkA01G119390
TK1151:1:126126144:T:CChr01:126,126,144C126-5.2571.17e-050.173TkA01G503690
TK1151:1:113553025:G:AChr01:113,553,025A1262.5161.89e-050.226TkA01G453990
TK1151:1:10487966:A:GChr01:10,487,966G126-2.3132.03e-050.232TkA01G040630
TK1151:1:55016454:T:CChr01:55,016,454C1261.7622.08e-050.235TkA01G215880
TK1151:1:14007897:G:AChr01:14,007,897A1262.6282.23e-050.247TkA01G054230
TK1151:1:66099415:A:GChr01:66,099,415G1262.0423.29e-050.312TkA01G262840
TK1151:1:41201569:T:AChr01:41,201,569A1262.6253.34e-050.314TkA01G161130
TK1151:1:112808204:T:CChr01:112,808,204C1264.9364.65e-050.356TkA01G449580
TK1151:1:52059913:C:TChr01:52,059,913T1262.4784.71e-050.358TkA01G204460
TK1151:1:52626396:T:CChr01:52,626,396C126-2.0815.12e-050.373TkA01G206730
TK1151:1:29460003:A:TChr01:29,460,003T126-2.1475.2e-050.373TkA01G116340

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

1/7526Next
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