B73xPT_QTL

Phenotypic data: Evaluation 97 of B73 x Palomero Toluqueño
BC1S5 families (B73 as recurrent parent), their parentals and other genotypes
used as checks in lowland (Valle de Balderas, PV, 165 m.a.s.l.) and highland
(Metepec, MT, 2600 m.a.s.l.) environments, collected from 2015 to 2019. Linear
mixed-effects models were fitted using the ‘lme4’ package in R for each
phenotypic trait. Location was included in the model as a fixed effect, and the
effect of year, genotype, genotype by location interaction, and block nested
within location were included as random. BLUP (Best Linear Unbiased Prediction)
values for the genotypic effect (G) and genotype by location interactions (GxE)
were extracted using the ranef() function in the ‘lme4’ package. BLUP values
for each genotype and location combination (G+GxE) were calculated by adding
genotypic BLUPs and GxE BLUPs. The fitted values for genotypic effect were
calculated by adding genotypic BLUPs to the grand mean, and the fitted values
for each genotype and location combination were estimated by adding BLUPs of
the G+GxE to the estimated location mean.

Genetic
map: Genetic
Map of the B73 x PT BC1S5 population for 98 families and 918 total markers. The
map was estimated using ASMAP and qtl packages for R.

Altitude eGWAS results: Raw results of the eGWAS analysis to measure the association between genetic loci and the elevation of native environment for landrace accessions across Mexico.

LOD profile: LOD profile of the
multi-qtl models for different traits for each set of phenotypic data.
The red shape describes the Bayes credible interval for each QTL.

Effect Plots: Effect plots
estimated with effectplot function of r-qtl for each QTL detected for a set of
phenotypic data using fitted values.

Reaction norms: Reaction norms drawn for all the QTLs detected in the analysis by estimating the QTL effect with R/qtl effectplot function in VB and MT phenotypic sets using fitted values.

Supplemental figure: Supplemental figures.