Table 5 Summary of candidate genes for yield, agronomic traits, and Fe and Zn concentrations in QTLs identified.
QTL | Chr | LOC names | Location | Gene names | GO/TO | Reference |
|---|---|---|---|---|---|---|
qDF2.3 | 2 | Os02g0820500 | 36114364–36115470 | dh1 | floral organ development | Li et al.73 |
qPH1.2 | 1 | Os01g0927000 | 42449035–42459242 | SDG714 | Culm; leaf; zinc ion binding | Ding et al.96 |
1 | Os01g0919900 | 41902665–41906463 | OsSSI2 | Culm; leaf; transition metal ion binding | Jiang et al.97 | |
1 | Os01g0926700 | 42427937–42430956 | OsIRX10 | Culm; leaf | Chen et al.74 | |
1 | Os06g0583400 | 41,344,121–41,347,086 | HDT702 | Narrowed leaf; stem thickness | Hu et al.98 | |
1 | Os01g0907900 | 41,279,485–41,283,041 | lhd2/ pla2 | Tiller bud outgrowth; stem anatomy and morphology trait | ||
1 | Os01g0940000 | 43095050–43097830 | OsCKX4 | plant height; plant growth hormone sensitivity; | Gao et al.75 | |
1 | Os01g0883800 | 40138232–40141316 | sd1 | Semi-dwarf; Gibberellin biosynthesis; iron ion binding | Sasaki et al.76 | |
qNT11.1 | 11 | Os11g0523800 | 20763199–20769515 | OsARF1 | Shoot length; plant growth hormone sensitivity | Song et al.101 |
qNP11.1 | 11 | Os11g0587000 | 24064168–24073582 | OsD27 | Auxin transport; tiller number | Lin et al.77 |
qPL1.1 | 1 | Os01g0866400 | 39275432–39278261 | OsFBP1 | Photosynthetic sucrose biosynthesis; Growth retardation; metal ion binding | Lee et al.102 |
1 | Os01g0878700 | 39893617–39889322 | OsAAP6 | starch and storage protein biosynthesis in developing rice grain; seed quality | Peng et al.103 | |
qPL8.2 | 8 | Os08g0509600 | 25362546–25366701 | WFP | Panicle branching; zinc ion binding; panicle number | Miura et al.78 |
8 | Os01g0350900 | 25,362,546–25,366,701 | OsIPI1 | Panicle branching; zinc ion binding; panicle size | Jiao et al.79 | |
qYLD4.4 | 4 | Os04g0469800 | 23,867,864–23,865,707 | CL4 (= dwarf11)/ OsD11 | panicle architecture; short main rachis; yield and productivity | |
4 | Os04g0473800 | 24091114–24096437 | OsFCP1 | Maintenance of shoot apical meristem; | Ohmori et al.105 | |
4 | Os07g0572100 | 24194135–24196073 | DAO | Pollen development; Anther dehiscence; Seed development; | Zhao et al.106 | |
4 | Os04g0473900 | 24097480–24107361 | DWA1 | heme binding; Drought tolerance; | Zhu and Xiong.107 | |
4 | Os04g0475900 | 24217103–24217955 | Rf17 | Sterility; multicellular organismal development | Fujii and Toriyama.108 | |
4 | Os04g0479000 | 24354013–24358518 | OsCRC1 | Sterility; Pollination, fertilization, fertility—Meiosis | Miao et al.109 | |
qYLD6.2 | 6 | Os06g0570100 | 22897875–22905149 | dwarf35/ D35 | Dwarfism; Gibberellin biosynthesis; | Itoh et al.81 |
6 | Os06g0561000 | 22355411–22359638 | OsMIOX | Drought tolerance | Duan et al.110 | |
qTGW5.1 | 5 | Os05g0121600 | 1134012–1138301 | OsRSR1 | Seed amylose content; grain size; 1000-seed weight | Fu and Xue86 |
5 | Os05g0128400 | 1,653,536–1,657,100 | OsMTP1 | Zn; Cd and Ni translocation; zinc ion transport; seed development | Yuan et al.87 | |
qGL9.1 | 9 | Os09g0529700 | 21576480–21580155 | OsVPS22 | Chalky kernel; seedling lethality; seed-physiological traits | Zhang et al.111 |
qGW3.3 | 3 | Os03g0738600 | 31080803–31082117 | OsLOX2 (L-2) | Promoting early seed germination; seed longevity; iron ion binding | Huang et al.112 |
3 | Os03g0733800 | 30825494–30829356 | OsERO1 | Seed storage protein; disulfide bond formation in endosperm | Onda et al.113 | |
qZn1.1 | 1 | Os01g0717601 | 29,880,280–29,878,435 | OsSAP13 | Zinc ion binding | |
1 | Os01g0719100 | 29970767—29965064 | OsRZFP34/OsRFP1/OsUCIP18/OsRING160 | Zinc ion binding | ||
1 | Os01g0719600 | 30003532–30005946 | OsHMP5 | Metal ion binding; heavy metal transport | ||
qZn3.1 | 3 | Os03g0307300 | 10,930,895–10,929,483 | OsNAS1 | Iron ion transport; cellular response to zinc ion starvation | |
3 | Os03g0320400 | 11560162–11562564 | OsSET16 | Zinc ion binding | ||
qZn4.1 | 4 | Os04g0289800 | 12597819–12602415 | OsDLN109 | Metal ion binding | |
4 | Os04g0298200 | 13,183,064–13,176,740 | OsMTP7 | Response to zinc ion | ||
qZn5.1 | 5 | Os05g0128200 | 1662021–1664438 | OsC3H33/OsTZF5 | Zinc ion binding | |
qZn5.2 | 5 | Os05g0490700 | 24162788–24168825 | OsSET22 | Zinc ion binding; histone-lysine N-methyltransferase activity | |
5 | Os05g0488800 | 24026206–24023536 | OsSIRP1 | Zinc ion binding | ||
5 | Os05g0497600 | 24469517–24464254 | OsAIR1 | Zinc ion binding | ||
5 | Os05g0520300 | 25,832,469–25,834,622 | OsGATA1 | Zinc ion binding | ||
5 | Os05g0525900 | 26172349–26171092 | OsC3H37 | Zinc ion binding; DNA binding | ||
5 | Os05g0534500 | 26541970–26538000 | OsHMP31 | Metal ion transport | ||
5 | Os05g0550000 | 27,317,413-27,320,555 | OsRFPH2-20 | Zinc finger, C3HC4 type domain containing protein | ||
qZn6.1 | 6 | Os06g0542300 | 20405495–20404296 | OsHMP32 | Metal ion binding | |
6 | Os06g0560000 | 21396824–21399402 | OsFerroportin | Iron ion transmembrane transporter activity | ||
qZn6.2 | 6 | Os06g0690700 | 28797545–28789015 | OsHMA1 | Zinc ion homeostasis | |
6 | Os06g0695600 | 29063780–29059687 | OsRFP | Zinc ion binding | ||
qZn7.2 | 7 | Os07g0623200 | 25790391–25792723 | OsHMA7 | Heavy metal ion transporter; regulation of yield and grain Fe–Zn content | Kappara et al.114 |
7 | Os07g0626600 | 25963652–25958769 | OsHAM701 | Zinc ion binding | ||
7 | Os07g0626900 | 25977110–25979990 | OsRFPHC-6 | Zinc ion binding | ||
qZn7.3 | 7 | Os07g0682400 | 28932966–28928654 | OsC3H53 | Zinc ion binding | |
qZn10.1 | 10 | Os10g0502600 | 19174055–19171741 | OsMSBP2 | Heme binding | |
qFe1.1 | 1 | Os01g0826000 | 35332705–35333504 | OsHMP7 | Metal ion transport | |
1 | Os01g0830200 | 35,517,546–35513518 | OsRFP/OsDLN24/ OsRING179 | Zinc ion binding |
