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. 2022 Mar 16;13:840614. doi: 10.3389/fpls.2022.840614

TABLE 2.

Significant loci associated with GZnC and GFeC in at least three environments in 166 wheat accessions using three models in GAPIT.

Traita Environmentb Chrc Physical interval (Mb)d Representative SNPe Allelef,g MAFf,h P-value (× 10–4)f R2 (%)f,i Effectf P-value for PHj P-value for TKWk Reported QTLl
GZnC E1, E2, BLUE 1A 515.79–516.03 AX_108845138 C/T 0.11 1.11 11.88 2.58 0.439 0.765 QGZn.cimmyt-1A
E2, E3, BLUE 1A 580.42–586.13 AX_109976007 C/G 0.44 2.36 9.62 2.25 0.935 0.461 QGZn.cau-1A
E2, E3, BLUE 2A 246.51 AX_109885783 C/G 0.13 5.87 8.55 2.87 0.883 0.867
E2, E3, BLUE 3A 10.22 AX_111534768 G/A 0.18 1.91 9.91 3.19 0.964 0.164
E1, E2, E3, BLUE 3A 19.89–22.61 AX_111528452 T/G 0.31 0.15 13.57 3.06 0.377 0.001
E2, E3, BLUE 3A 696.23 AX_108843516 C/A 0.44 4.82 8.62 2.19 0.489 0.585 QGZn.cimmyt-3A.1
E2, E3, BLUE 3A 721.64–724.58 AX_109875082 T/A 0.46 0.20 13.53 2.63 0.061 0.850 QGZn.cimmyt-3A.2
E2, E3, BLUE 3B 202.41 AX_110479767 A/G 0.19 5.69 8.39 5.73 0.482 0.698
E2, E3, BLUE 3B 242.66 AX_109384871 G/A 0.17 7.35 8.04 6.80 0.177 0.527
E2, E3, BLUE 5A 591.28–592.63 AX_94729189 G/C 0.24 1.96 10.11 2.46 0.075 0.063
E2, E3, BLUE 5D 319.22 AX_94388289 C/G 0.20 4.21 8.81 2.82 0.284 0.599
E2, E3, BLUE 6A 17.77 AX_110365398 A/G 0.36 6.80 8.20 1.76 0.831 0.872
E1, E2, E3, BLUE 6A 28.31–31.37 AX_111556928 A/G 0.16 0.18 10.03 2.67 0.813 0.397
E2, E3, BLUE 6B 142.73 AX_110935664 A/G 0.39 0.79 11.44 2.41 0.391 0.830 QGZn.uh-6B
E1, E2, BLUE 6D 16.8–16.81 AX_108846745 T/C 0.49 4.32 8.83 1.75 0.602 0.507
E2, E3, BLUE 6D 27.52 AX_95220141 G/A 0.20 1.45 10.55 3.19 0.554 0.422
E2, E3, BLUE 6D 357.01 AX_110431664 T/C 0.25 2.78 9.38 2.81 0.008 0.706
E1, E2, BLUE 7A 706.91 AX_94741862 T/G 0.35 9.57 7.73 1.64 0.205 0.343 QGZn.ua-7A
E1, E2, E3, BLUE 7B 533.78–540.78 Tdurum_contig65979_ 289 A/G 0.39 1.34 10.48 1.97 0.920 0.974
E1, E2, E3, BLUE 7B 626.06–626.07 BS00022045_51 A/G 0.48 0.52 13.09 1.66 0.091 0.524 QGZn.cimmyt-7B.5
E1, E2, E3, BLUE 7B 687.32–689.92 AX_110464521 G/A 0.26 0.76 12.48 1.75 0.708 0.491
E1, E2, BLUE 7B 708.11 AX_95000860 T/C 0.49 1.97 10.98 1.51 0.716 0.918 GZn-IWA4150
E2, E3, BLUE 7D 203.16 AX_110717434 C/T 0.14 0.19 13.24 3.83 0.231 0.891
E1, E3, BLUE 7D 506.11 GENE_3452_1116 G/A 0.38 2.74 9.47 1.86 0.485 0.399
E1, E2, E3, BLUE 7D 605.17 AX_108866365 C/G 0.19 1.24 10.60 2.16 0.697 0.812
GFeC E2, E3, BLUE 1A 15.43 AX_95081354 C/T 0.20 5.43 8.37 2.07 0.047 0.102
E1, E2, BLUE 1B 15.65–15.74 AX_86185361 C/G 0.30 2.03 9.12 1.72 0.222 0.182
E2, E4, BLUE 1B 26.17–26.37 AX_111633663 A/C 0.45 0.11 13.03 2.01 0.007 0.246
E1, E4, BLUE 1B 38.63–38.83 AX_109837760 T/G 0.48 0.45 11.13 1.71 0.002 0.742 QGFe.cimmyt-1B
E2, E3, BLUE 1B 660.01 Tdurum_contig68980_ 448 A/G 0.29 4.96 7.97 1.43 0.202 0.018
E1, E4, BLUE 1B 688.28–689.27 AX_110457631 C/T 0.36 1.37 9.64 1.42 0.087 0.618
E1, E4, BLUE 5A 495.92 AX_109311262 G/A 0.09 6.82 7.56 2.01 0.000 0.331 QGFe.sau-5A.1
E2, E3, BLUE 5B 531.58 AX_94967094 C/T 0.39 5.82 7.76 1.39 0.668 0.480 QGFe.cimmyt-5B.2
E2, E3, BLUE 5B 548.33 AX_111484713 G/A 0.20 1.89 9.22 1.68 0.404 0.002
E2, E3, BLUE 5B 622.54 AX_111033847 C/T 0.32 2.38 8.92 1.50 0.097 0.176 QGFe.cimmyt-5B.3
E3, E4, BLUE 5B 679.03 AX_109412899 G/A 0.18 3.13 8.56 1.69 0.696 0.163 QGFe.cimmyt-5B.4
E3, E4, BLUE 7A 706.91 AX_94741862 T/G 0.35 1.19 9.82 1.38 0.196 0.165 QGFe.iari-7A
E3, E4, BLUE 7B 706.37–706.86 Tdurum_contig61856_ 900 A/C 0.36 0.52 10.93 1.42 0.001 0.035 QGFe.cimmyt-7B
E2, E3, BLUE 7D 54.99 AX_108920250 C/T 0.44 0.14 14.49 2.27 0.989 0.005
E2, E3, BLUE 7D 69.31 AX_111359934 G/A 0.40 4.67 8.58 1.65 0.937 0.142
E1, E2, E3, E4, BLUE 7D 614.51–614.92 AX_95151824 T/G 0.32 0.96 10.12 1.43 0.122 0.101 QGFe.sau-7D

aGZnC, grain zinc concentration; GFeC, grain iron concentration.

bE1, E2, E3, E4: Beijing, Gaoyi, Shijiazhuang, and Xinjiang locations, respectively, 2019–2020; BLUE, best linear unbiased estimation; BLUE-value was also used to conduct GWAS and was regarded as one environment.

cChr, chromosome.

dPhysical positions of single nucleotide polymorphism (SNP) markers were based on IWGSC RefSeq v.1.0 (http://www.wheatgenome.org/).

eThe most significant SNP with the lowest p across environments for the corresponding locus was regarded as a representative.

fThe information in corresponding columns are based on the representative SNP.

g“_” indicates the favorable allele with the increasing effect on GZnC or GFeC.

hMAF: minor allele frequency.

iR2 indicates the percentage of phenotypic variance explained by the SNP marker.

jPH, plant height. The values of p for association between the representative markers of GZnC/GFeC QTL and plant height were calculated by GAPIT using the MLM model.

kTKW, thousand kernel weight. The p for association between the representative markers of GZnC/GFeC QTL and thousand kernel weight were calculated by GAPIT using the MLM model.

lThe closest linked markers or mid-points of previous reported QTL intervals are present in Tong et al. (2020). Those loci with physical distances smaller than or approximate to one LD block away from reported QTL were considered as the same with the previous QTL.