Table 1.
Quantitative trait loci (QTL) affecting grain mineral concentrations (GMCs) detected by a genome-wide association study (GWAS) in a panel of 698 germplasms.
| Trait | Clsta | Loci | Ch | Range | −log10 | FAEb | QTL reportedc | Refd |
|---|---|---|---|---|---|---|---|---|
| Fe | qFe1 | 1 | 841,961~959,278 | 4.8 | 0.300 | |||
| qFe3 | 3 | 4,145,494~4,182,173 | 3.8 | −0.263 | ||||
| qFe6-1 | 6 | 10,055,520~10,274,263 | 4.2 | −0.158 | ||||
| qFe6-2 | 6 | 16,404,065~21,506,253 | 3.6 | 0.320 | qFe6 | |||
| qFe7 | 7 | 27,770,508~27,788,464 | 3.1 | 0.148 | qFe7 | |||
| qFe10 | 10 | 10,945,859~11,075,230 | 4.3 | 0.337 | ||||
| Zn | qZn1 | 1 | 6,179,574~6,204,400 | 3.5 | −0.890 | id1005056-58 (Norton et al., 2014) | ||
| qZn7 | 7 | 22,891,126~26,101,517 | 3.6 | −0.680 | qZn7 | qZn7 (Huang et al., 2015; Hu et al., 2016);qZN-7 (Lu et al., 2008); id7003641 (Norton et al., 2014) | ||
| qZn9 | 9 | 5,174,170~7,387,104 | 3.4 | 1.795 | ||||
| qZn12 | 12 | 21,887,797~21,913,241 | 3.6 | −0.398 | qZn12 | |||
| Cd | Clst1a | qCd1-1 | 1 | 212,589~434,398 | 5.2 | −0.002 | qCd1 | |
| qCd1-2 | 1 | 1,603,456~1,905,348 | 4.5 | 0.003 | qCd1 | |||
| Clst1b | qCd1-3 | 1 | 8,542,202~18,485,590 | 6.1 | −0.002 | |||
| Clst2a | qCd2-1 | 2 | 10,199,643~18,518,546 | 5.8 | −0.002 | |||
| Clst2b | qCd2-2 | 2 | 25,207,241~33,640,277 | 5.4 | −0.002 | qCd2b (Zhang et al., 2014) | ||
| Clst3a | qCd3-1 | 3 | 1,652,156~2,158,456 | 4.7 | 0.002 | qCd3 (Zhang et al., 2014) | ||
| qCd3-2 | 3 | 3,337,100~3,355,424 | 4.5 | −0.002 | ||||
| Clst3b | qCd3-3 | 3 | 15,185,771~29,212,237 | 5.2 | 0.003 | |||
| qCd3-4 | 3 | 29,214,304~32,538,230 | 4.7 | 0.003 | ||||
| qCd3-5 | 3 | 32,638,170~35,155,759 | 5.9 | −0.002 | qCd3 (Huang et al., 2015) | |||
| Clst4a | qCd4-1 | 4 | 1,112,387~2,047,665 | 4.4 | −0.001 | |||
| qCd4-2 | 4 | 4,734,877~5,034,318 | 4.2 | 0.003 | ||||
| qCd4-3 | 4 | 5,302,854~5,801,556 | 4.8 | −0.002 | ||||
| qCd4-4 | 4 | 6,224,157~6,246,104 | 4.6 | 0.002 | ||||
| Clst4b | qCd4-5 | 4 | 16,868,613~16,869,822 | 4.4 | −0.001 | |||
| qCd4-6 | 4 | 18,424,682~18,529,758 | 4.8 | 0.002 | ||||
| Clst4c | qCd4-7 | 4 | 26,418,529~30,460,722 | 5.2 | 0.003 | qCd4 | qCd4-2 (Kashiwagi et al., 2009) | |
| Clst5a | qCd5-1 | 5 | 1,142,167~3,242,916 | 6.2 | −0.002 | qCd5 (Zhang et al., 2014) | ||
| qCd5-2 | 5 | 4,859,767~4,870,282 | 4.6 | 0.002 | ||||
| Clst5b | qCd5-3 | 5 | 8,264,080~8,297,556 | 4.7 | −0.002 | |||
| Clst5c | qCd5-4 | 5 | 13,797,802~14,052,508 | 9.9 | −0.002 | |||
| qCd5-5 | 5 | 14,065,017~14,071,607 | 4.5 | 0.002 | ||||
| qCd5-6 | 5 | 14,075,029~16,119,884 | 7.4 | −0.002 | ||||
| qCd5-7 | 5 | 16,818,124~19,141,063 | 6.7 | −0.002 | qCd5.1 (Huang et al., 2015) | |||
| Clst5d | qCd5-8 | 5 | 21,486,695~23,456,509 | 8.3 | −0.002 | |||
| Clst6a | qCd6-1 | 6 | 4,365,001~4,400,366 | 4.5 | 0.004 | |||
| Clst6b | qCd6-2 | 6 | 10,411,282~11,457,254 | 4.4 | −0.002 | qCd6 | Segment_on_Chr6 (Ishikawa et al., 2005) | |
| Clst6c | qCd6-3 | 6 | 22,117,058~22,123,339 | 4.3 | 0.002 | OsLCT1 (Uraguchi et al., 2011) | ||
| Clst6d | qCd6-4 | 6 | 27,586,307~27,591,921 | 4.9 | −0.002 | |||
| qCd6-5 | 6 | 27,919,935~27,938,490 | 6.3 | 0.003 | ||||
| qCd6-6 | 6 | 28,441,362~29,887,070 | 5.3 | −0.002 | qCd6 (Zhang et al., 2014) | |||
| Clst7a | qCd7-1 | 7 | 9,491,735~10,356,836 | 6.2 | 0.004 | qGCd7/qSCd7 (Ishikawa et al., 2010) qCdp7 (Abe et al., 2011) | ||
| Clst7b | qCd7-2 | 7 | 17,677,268~24,927,574 | 4.7 | 0.002 | qCDCN-7 (Shen et al., 2008) | ||
| Clst8a | qCd8-1 | 8 | 098,858~736,546 | 5.6 | −0.002 | qCd8 | Segment_on_Chr8 (Ishikawa et al., 2005) | |
| Clst8b | qCd8-2 | 8 | 4,494,409~7,760,106 | 5.4 | −0.002 | |||
| Clst8c | qCd8-3 | 8 | 24,758,957~26,561,629 | 4.3 | −0.002 | qCd8 (Zhang et al., 2014) | ||
| qCd8-4 | 8 | 27,252,563~27,275,319 | 7.1 | 0.003 | ||||
| qCd8-5 | 8 | 27,313,865~27,323,824 | 5.0 | −0.002 | ||||
| qCd8-6 | 8 | 27,425,405~27,460,834 | 4.9 | 0.002 | ||||
| qCd8-7 | 8 | 27,501,982~27,582,900 | 6.9 | −0.002 | ||||
| Clst9a | qCd9-1 | 9 | 12,135,431~12,165,192 | 5.1 | −0.002 | |||
| qCd9-2 | 9 | 12,405,421~17,243,659 | 7.8 | 0.004 | ||||
| Clst10 | qCd10-1 | 10 | 8,425,690~14,527,032 | 5.3 | −0.002 | |||
| qCd10-2 | 10 | 16,043,069~18,482,561 | 5.5 | −0.002 | ||||
| Clst11a | qCd11-1 | 11 | 6,233,769~6,354,200 | 3.2 | 0.001 | qCd11 | ||
| qCd11-2 | 11 | 8,096,875~8,953,846 | 7.7 | −0.002 | ||||
| qCd11-3 | 11 | 9,162,686~9,204,553 | 5.3 | 0.002 | ||||
| qCd11-4 | 11 | 9,396,989~16,643,233 | 8.6 | −0.002 | ||||
| Clst11b | qCd11-5 | 11 | 16,648,036~16,691,008 | 6.3 | 0.002 | |||
| qCd11-6 | 11 | 16,774,292~16,850,863 | 6.9 | −0.002 | ||||
| qCd11-7 | 11 | 16,915,560~20,181,453 | 5.1 | 0.002 | qCd11 (Kashiwagi et al., 2009) | |||
| qCd11-8 | 11 | 23,757,657~23,977,853 | 4.4 | −0.002 | qCd11 (Tang, 2007) | |||
| qCd11-9 | 11 | 25,493,176~27,669,556 | 4.2 | 0.002 | qCd11 (Tang, 2007) | |||
| Clst12a | qCd12-1 | 12 | 1,615,274~1,630,986 | 4.7 | −0.002 | |||
| qCd12-2 | 12 | 2,275,959~2,471,184 | 5.3 | 0.004 | ||||
| qCd12-3 | 12 | 2,956,398~8,288,204 | 4.0 | −0.001 | ||||
| Clst12b | qCd12-4 | 12 | 11,270,271~11,777,847 | 5.9 | 0.004 | |||
| qCd12-5 | 12 | 12,194,972~14,140,041 | 5.1 | −0.001 | ||||
| qCd12-6 | 12 | 14,681,128~15,757,691 | 7.7 | 0.003 | ||||
| qCd12-7 | 12 | 15,804,848~15,872,325 | 5.2 | −0.002 | ||||
| qCd12-8 | 12 | 16,987,855~17,467,228 | 4.9 | 0.002 | ||||
| Clst12c | qCd12-9 | 12 | 24,218,754~25,662,740 | 4.1 | −0.001 | qSCd12 (Ishikawa et al., 2010) | ||
| Mn | qMn3 | 3 | 20,083,700~20,107,682 | 4.6 | 1.317 | |||
| qMn5 | 5 | 15,026,427~15,945,778 | 4.3 | −0.518 | ||||
| qMn8 | 8 | 27,194,754~27,212,235 | 4.0 | 0.943 | ||||
| Cu | qCu5 | 5 | 3,343,234~3,704,085 | 5.1 | −0.333 | qCu5 (Zhang et al., 2014) | ||
| qCu11 | 11 | 14,314,371~14,705,331 | 4.8 | 0.262 | ||||
| Se | qSe4-1 | 4 | 3,566,285~5,597,802 | 5.6 | 0.005 | |||
| qSe4-2 | 4 | 11,568,849~12,645,615 | 4.2 | 0.004 | ||||
| qSe11 | 11 | 27,190,782~27,196,075 | 3.8 | 0.003 |
a
QTL cluster.
b
Favorable allele effect (FAE) values of the peak markers.
c
A GMCs-related QTL detected by linkage mapping in our previous report (Xu et al., 2015), in which the three parents for the BC populations were also involved in our germplasms for the GWAS mapping.
d
The number in brackets are reference codes as listed in reference section.