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Table 5 SNP markers significantly associated (−log10(p) ≥ 3) with yellow index identified by GWAS (model MLM + K + PCs) in the whole tetraploid wheat collection and in the durum sub-population evaluated in six environments (F09, V10, V12, F12, V13, V14)

From: The carotenoid biosynthetic and catabolic genes in wheat and their association with yellow pigments

SNP marker SNP allele Chrom Position cM Whole collection Durum sub-population
     F09 V10 V12 F12 V13 V14 Mean R2 (%) Effect F09 V10 V12 F12 V13 V14 Mean R2 (%) Effect
IWB73278 C/T 1B 12.8 - - 3 - - - -    - - - - - - -   
IWB4839 C/T 1B 150.9 3.4 - - - - - -    - - - - - - -   
IWB70428 A/C 2A 101.5 3.4 3 - - - - -    - - - - - - -   
IWB42586 C/T 2A 176.5 - - - - 4.2 - -    - - - - - - -   
IWB55230 C/T 2A 196.5 - - - - - - -    - - 3.2 - - - -   
IWB45885 C/T 2B 14.5 - 3.2 - - - 3.1 -    - - - - - - -   
IWB1756 A/G 3B 33.2 3.2 - - - - - -    - - - - - - -   
IWB58482 C/T 3B 160.1 - - - 3.2 - - -    - - - - - - -   
IWB43375 A/G 4A 80.5 - 3.4 3.3 - - - 3.0 4.8 −0.98 - - - - - - -   
IWB58319 A/G 4B 17.7 - 3.1 3.3 - - - 3.0 4.9 −0.58 - 3.6 - - - 3.1 3.3 10.1 −0.8
IWB72011 C/T 4B 43.9 - 3.4 - - 3.1 - 3.4 5.5 0.72 - 3 - - 3 3.7 3.3 11.1 1.33
IWB72977 A/G 5A 113.7 - - - - - 3.1 -     - - - - - -   
IWB71274 A/C 5B 44 - - - - - 3.4 -     - - - - - -   
IWB43483 A/G 5B 120.1 - 3.5 3 - - - 3.1 5.1 −0.72   - - - - - -   
IWB62049 G/T 5B 167.5 - - - - 3.2 - -     - - - - - -   
IWB14365 A/G 6A 93.4 - - - 3.2 - - -     - - 3.1 - - -   
IWB73296 A/G 6A 115.3 - - - 3.2 - - -     - - - - - -   
IWB68640 G/T 7A 14.1 3.2 - - - 3.2 4.6 3.5 5.7 0.81   - - - - - -   
IWB8374 A/G 7A 61.6 3.5 3.1 - 3.4 - - -    3.9 - 3.2 3.2 - 3.5 3.7 12.6 1.08
IWB72567 C/T 7A 102.3 4.1 5.5   4.1 3.6 - 3.5 6.2 −0.74 3.4 4.9 4 4 4.5 3.5 5 18.4 −1.25
IWB20381 C/T 7A 168.8 3.1 - - - - - -    - - - - - - -   
IWB59875 C/T 7A 180.3 - 5.4 3.1 4.2 3.2 3.1 3.7 6.1 0.83 - 4.3 3.1 4 - - 3.8 12.2 0.92
IWB49295 A/G 7A 203.4 - 4.2 - - 3.1 3.9 3.5 5.8 −0.78 - - - - - - -   
IWB72335 A/C 7B 58.3 - - - - 3.1 - -    - - - - - - -   
IWB9496 A/G 7B 185.2 - - - - - 4 3.5 5.8 −0.72 - - - - - - -   
  1. - = not significant
  2. R2 = Phenotypic variation explained by the QTL (%)
  3. Chromosome and map position from Maccaferri [29] and -log10(p) values are reported for each marker in each environment and in the mean of the environments. Phenotypic variation (R2) and additive effect are reported only for markers significant in the mean of all six environments