Table 2.
Significances of phenotypic variations among different haplotypes of 192 candidate genes within important quantitative trait locus (QTL) regions for three major grain mineral concentrations (GMCs) in milled grains in two subsets of a panel of 698 germplasms.
| X-setd | G-set | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Linkage_QTLa | GWAS_Locib | Regions | Candidatesc | Fe | Zn | Cd | Fe | Zn | Cd |
| qCd1 | qCd1-1 | Chr1:320874-353617 | Os01g0106700 | * | **** | *** | * | ||
| qCd1-2 | Chr1:1806093-1905348 | Os01g0133100 | **** | **** | **** | * | |||
| qCd4 | qCd4-7 | Chr4 : 30064612-30164612 | Os04g0594800 | *** | *** | ** | **** | ||
| Os04g0596200 | * | ** | **** | ||||||
| Os04g0597300 | * | **** | |||||||
| qCd6 | qCd6-2 | Chr6:10602046-10912129 | Os06g0293000 | ** | * | * | **** | ||
| Os06g0293100 | ** | **** | *** | * | *** | **** | |||
| Os06g0294100 | * | **** | *** | ** | **** | ** | |||
| qFe6 | qFe6-2 | Chr6:16404065-17615233 | Os06g0483301 | **** | **** | *** | * | ||
| Os06g0483500 | **** | *** | *** | ** | |||||
| Os06g0483900 | **** | **** | *** | ** | * | ||||
| Os06g0484400 | **** | **** | *** | * | *** | ||||
| Os06g0485100 | **** | **** | *** | ** | **** | ** | |||
| Os06g0486900 | ** | ** | ** | ** | ** | ||||
| Os06g0487300 | ** | **** | *** | ** | ** | ** | |||
| Os06g0488200 | **** | **** | *** | ** | **** | ||||
| Os06g0489500 | * | **** | *** | ** | **** | ||||
| Os06g0489900 | *** | *** | *** | *** | **** | ||||
| Os06g0490400 | *** | **** | *** | * | *** | *** | |||
| Os06g0491566 | *** | **** | *** | **** | **** | **** | |||
| Os06g0492300 | **** | **** | *** | * | *** | ||||
| Os06g0494100 | **** | *** | **** | **** | *** | ||||
| Os06g0496000 | *** | **** | *** | ** | **** | ||||
| Os06g0496601 | **** | ** | * | ** | **** | **** | |||
| Os06g0498500 | **** | **** | *** | ** | **** | ** | |||
| Os06g0499100 | ** | ** | **** | **** | * | ||||
| Os06g0499500 | **** | **** | *** | ** | **** | ||||
| Os06g0499550 | **** | ** | |||||||
| qZn7 | qZn7 | Chr7:22841126-22941126 | Os07g0568300 | ** | **** | *** | *** | * | |
| Os07g0568400 | **** | *** | |||||||
| Os07g0568500 | **** | *** | ** | **** | * | ||||
| Os07g0569000 | * | **** | *** | **** | ** | ||||
| Os07g0569500 | ** | * | ** | **** | |||||
| Os07g0569550 | ** | ** | **** | ||||||
| Os07g0569800 | **** | *** | ** | **** | **** | ||||
| qCd8 | qCd8-1 | Chr8:496639-582447 | Os08g0110000 | **** | |||||
| Os08g0110600 | * | ** | ** | ** | *** | *** | |||
a
QTL detected by linkage mapping in our previous report (Xu et al., 2015).
b
Loci detected by a genome-wide association study (GWAS) in this work.
c
The gene highlighted as sample cases in the latter part of haplotype analysis were shown in bold.
d
X-set = indica/Xian set, G-set = japonica / Geng set,
*, **, ***, and ****
represents significant level of 0.05, 0.01, 0.001, and 0.0001, respectively, in the pair-wise comparison using Duncan's t-test for the different haplotypes of each gene.