Table 1 Overview of significant associations detected with EMMAX and MLMM
RankB. oleraceaA. thalianaVariance explained
TraitChrPosMethodRRBayesBGene IDOrthologDescriptionPhenotypicGeneticMAF
Apical Length226,787,029MLMMI30,55929,378Bol035969AtSec6Cell growth4.137.30.05
Apical Length320,986,662MLMMI23971712Bol035507AT1G53730Protein coding11.6105.30.03
Apical Length64,914,166MLMMI49021785Bol032997Protein kinase10.696.00.08
Apical Length634,494,415MLMMU21111194Bol040102AT1G71780Biological processes2.220.30.13
Cluster Width25,063,181EMMAXU84Bol007138AT1G03220Proteolysis19.134.10.22
Curd Width23,528,844EMMAXU11Bol021232AT5G19110Heat stress14.432.60.44
Curd Width25,063,181EMMAXU64Bol007138AT1G03220Proteolysis12.127.40.22
Length of Nearest Branch925,012,587MLMMU22Bol012235unknown7.9158.70.06
Number of Branches62,323,306EMMAXU22Bol035509AT1G75310Protein binding6.223.70.06
Number of Branches62,323,306MLMMU22Bol035509AT1G75310Protein binding6.223.70.06
Number of Branches741.524,584EMMAXU11Bol024369AT2G17050NBS gene family8.532.60.21
Number of Branches741,524,584MLMMU11Bol024369AT2G17050NBS gene family8.532.60.21
Number of Days to Budding137,688,065EMMAXU11Bol023068AT3G09240Signaling pathway13.514.40.2
Number of Days to Budding137,688,065MLMMU11Bol023068AT3G09240Signaling pathway13.514.40.2
Number of Days to Budding22,708,156MLMMU56Bol024638AT5G10090Flowering related16.417.40.57
Number of Days to Budding22,708,163MLMMU65Bol024638AT5G65160Flowering related16.417.40.57
Number of Days to Budding22,708,182MLMMU74Bol024638AT5G65180Flowering related16.417.40.57
Number of Days to Budding62,949,314EMMAXI1861572Bol026132AT1G75010Flowering25.226.80.05
Number of Days to Budding62,949,314MLMMI1861572Bol026132AT1G75010Flowering25.226.80.05
Number of Days to Budding7936,738EMMAXI25Bol027177unknown4.24.50.36
Number of Days to Budding7936,738MLMMI25Bol027177unknown4.24.50.36
Number of Days to Budding7936,770EMMAXI11Bol027177unknown6.46.80.23
Number of Days to Budding7936,770MLMMI11Bol027177unknown6.46.80.23
Number of Days to Budding741,524,584MLMMU23Bol024369AT2G17050NBS gene family4.14.40.21
  • The Rank column indicates which rank the significant association had among marker effects in the genomic prediction with ridge regression (RR) or BayesB methods. The last letter in the Method column indicates in which data set the QTL was discovered (U, unimputed, I, imputed). Phenotypic and genotypic variance indicate the percentage of variance explained by the respective SNP. Chr, chromosome; MAF, minor allele frequency; Pos, position.