Rice Science ›› 2022, Vol. 29 ›› Issue (5): 412-434.DOI: 10.1016/j.rsci.2022.05.002
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Ratan Kumar Ganapati1, Shahzad Amir Naveed1, Sundus Zafar2, Wang Wensheng1, Xu Jianlong1,2()
Received:
2021-12-24
Accepted:
2022-05-02
Online:
2022-09-28
Published:
2022-07-04
Contact:
Xu Jianlong
Ratan Kumar Ganapati, Shahzad Amir Naveed, Sundus Zafar, Wang Wensheng, Xu Jianlong. Saline-Alkali Tolerance in Rice: Physiological Response, Molecular Mechanism, and QTL Identification and Application to Breeding[J]. Rice Science, 2022, 29(5): 412-434.
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Fig. 2. Ion homeostasis pathways and nitrogen metabolism of rice under saline-alkali stress. AKT, Low-affinity K+ transporter; GDH, Glutamate dehydrogenase; GOGAT, Glutamate synthase; GS, Glutamine synthetase; HAK, K+ transporter; HKT, High-affinity K+ transporter; NHX, Na+/H+ exchanger; NiR, Nitrite reductase; NR, Nitrate reductase; SOS, Salt overly sensitive; ABI1, Abscisic acid insensitive 1; NADH, Nicotinamide adenine dinucleotide; NADPH, Nicotinamide adenine dinucleotide phosphate; ROS, Reactive oxygen species; Pi, Phosphoric acid; PPi, Pyrophosphoric acid. Modified from Martínez-Atienza et al (2007), Pérez-Tienda et al (2014), Liang et al (2015), Hanin et al (2016) and El Mahi et al (2019).
Fig. 3. Saline-alkali stress signaling pathway and adaptation mechanisms [modified from Shi and Zhu (2002) and Chen et al (2021)]. ABA, Abscisic acid; ABA8ox, ABA-8′- hydroxylase; ABI1, Abscisic acid insensitive 1; ABI2, Abscisic acid insensitive 2; ADP, Adenosine diphosphate; AKT1, Arabidopsis K+ transporter 1; AP2, APETALA2; ATP, Adenosine triphosphate; BOR1-4, Boron transporter 1-4; bZIP, Basic- domain leucine zipper; CAX1a, Ca2+/H+ exchanger; CBL4, Calcineurin B-like protein; CIPK24, CBL- interacting protein kinase 24; DMI3, Doesn’t make infections 3; GORK, Guard-cell outward rectifying K+ channel; ATPase, ATP enzyme; HKT1, High affinity K+ transporter; MYB, v-Myb avian myeloblastosis viral oncogene homolog; NAC, NAM, ATAF1/2 and CUC2; NHX, Na+/H+ exchanger; PL kinase, Pyridoxal kinase; PLP, Pyridoxal-5-phosphate; RBOHs, Respiratory burst oxidase homologs; SKOR, Stelar K+ outward rectifier; SOS1, Salt overly sensitive 1; SOS4, Salt overly sensitive 4; V-ATPase, Vacuolar-ATPase; V-PPase, Vacuolar H+-pyrophosphatase; ROS, Reactive oxygen species; PPi, Pyrophosphoric acid; Pi, Phosphoric acid.
Gene | MSU locus | Function/Protein | Reference |
---|---|---|---|
OsGSK1 | LOC_Os01g10840 | CGMC_GSK.2-CGMC includes CDA, MAPK, GSK3, and CLKC kinases | Koh et al, |
OsMYB6 | LOC_Os01g16810 | MYB family transcription factor | Tang et al, |
OsSKC1 | LOC_Os01g20160 | Na+-selective transporter | Lin et al, |
OsGATA8 | LOC_Os01g24070 | GATA zinc finger domain containing protein | Nutan et al, |
OsKAT1 | LOC_Os01g55200 | Potassium channel KAT1 | Obata et al, |
OsVTC1-1 | LOC_Os01g62840 | Mannose-1-phosphate guanyltransferase | Kumar et al, |
OsABF1 | LOC_Os01g64730 | bZIP transcription factor domain containing protein | Zou et al, |
OsABI5 | LOC_Os01g64730 | bZIP transcription factor domain containing protein | Zou et al, |
OsEREBP2 | LOC_Os01g64790 | AP2 domain containing protein | Zhang X et al, |
OsHAK6 | LOC_Os01g70660 | K+ transporter | Quan et al, |
OsGMST1 | LOC_Os02g17500 | Transporter family protein | Cao et al, |
RSS1 | LOC_Os02g39390 | Expressed protein | Toda et al, |
Osa-MIR396c | Osa-Chr2 34287861 | miR396-mediated salt stress tolerance | Gao et al, |
OsITPK2 | LOC_Os03g12840 | Inositol 1,3,4-trisphosphate 5/6-kinase | Du et al, |
OsMAPK5 | LOC_Os03g17700 | CGMC_MAPKCGMC_2_ERK.2-CGMC includes CDA, MAPK, GSK3, and CLKC kinases | Diédhiou et al, |
OsMYB2 | LOC_Os03g20090 | MYB family transcription factor | Yang et al, |
OsbZIP3 | LOC_Os03g20310 | TGA transcription factor, bZIP transcription factor, defense response | Liu et al, |
OsCam1-1 | LOC_Os03g20370 | OsCam1-1-calmodulin | Boonburapong and Buaboocha, |
OsTZF1 | LOC_Os05g10670 | Zinc finger CCCH type family protein | Jan et al, |
OsTPS1 | LOC_Os05g44210 | Trehalose-6-phosphate synthase | Li H W et al, |
OsNHX1 | LOC_Os07g47100.3 | Sodium/hydrogen exchanger | Liu et al, |
OsRNS4 | LOC_Os09g36680 | Ribonuclease T2 family domain containing protein | Zheng et al, |
OsGSTU4 | LOC_Os10g38489 | Glutathione S-transferase GSTU6 | Sharma et al, |
OsNRT1 | LOC_Os10g40600.1 | Peptide transporter PTR2 | Lin et al, |
OsNAC5 | LOC_Os11g08210 | NAC1 transcription factor | Takasaki et al, |
OsATG10b | LOC_Os12g32210 | Autophagy-related protein 10 | Shin et al, |
OsSOS1 | LOC_Os12g44360 | Sodium/hydrogen exchanger 7 | El Mahi et al, |
OsNHA1 | LOC_Os12g44360 | Na+/H+ antiporter | Zhou et al, |
Table 1. Some candidate genes/transcription factors/proteins are responsive to saline-alkali stress and their functions.
Gene | MSU locus | Function/Protein | Reference |
---|---|---|---|
OsGSK1 | LOC_Os01g10840 | CGMC_GSK.2-CGMC includes CDA, MAPK, GSK3, and CLKC kinases | Koh et al, |
OsMYB6 | LOC_Os01g16810 | MYB family transcription factor | Tang et al, |
OsSKC1 | LOC_Os01g20160 | Na+-selective transporter | Lin et al, |
OsGATA8 | LOC_Os01g24070 | GATA zinc finger domain containing protein | Nutan et al, |
OsKAT1 | LOC_Os01g55200 | Potassium channel KAT1 | Obata et al, |
OsVTC1-1 | LOC_Os01g62840 | Mannose-1-phosphate guanyltransferase | Kumar et al, |
OsABF1 | LOC_Os01g64730 | bZIP transcription factor domain containing protein | Zou et al, |
OsABI5 | LOC_Os01g64730 | bZIP transcription factor domain containing protein | Zou et al, |
OsEREBP2 | LOC_Os01g64790 | AP2 domain containing protein | Zhang X et al, |
OsHAK6 | LOC_Os01g70660 | K+ transporter | Quan et al, |
OsGMST1 | LOC_Os02g17500 | Transporter family protein | Cao et al, |
RSS1 | LOC_Os02g39390 | Expressed protein | Toda et al, |
Osa-MIR396c | Osa-Chr2 34287861 | miR396-mediated salt stress tolerance | Gao et al, |
OsITPK2 | LOC_Os03g12840 | Inositol 1,3,4-trisphosphate 5/6-kinase | Du et al, |
OsMAPK5 | LOC_Os03g17700 | CGMC_MAPKCGMC_2_ERK.2-CGMC includes CDA, MAPK, GSK3, and CLKC kinases | Diédhiou et al, |
OsMYB2 | LOC_Os03g20090 | MYB family transcription factor | Yang et al, |
OsbZIP3 | LOC_Os03g20310 | TGA transcription factor, bZIP transcription factor, defense response | Liu et al, |
OsCam1-1 | LOC_Os03g20370 | OsCam1-1-calmodulin | Boonburapong and Buaboocha, |
OsTZF1 | LOC_Os05g10670 | Zinc finger CCCH type family protein | Jan et al, |
OsTPS1 | LOC_Os05g44210 | Trehalose-6-phosphate synthase | Li H W et al, |
OsNHX1 | LOC_Os07g47100.3 | Sodium/hydrogen exchanger | Liu et al, |
OsRNS4 | LOC_Os09g36680 | Ribonuclease T2 family domain containing protein | Zheng et al, |
OsGSTU4 | LOC_Os10g38489 | Glutathione S-transferase GSTU6 | Sharma et al, |
OsNRT1 | LOC_Os10g40600.1 | Peptide transporter PTR2 | Lin et al, |
OsNAC5 | LOC_Os11g08210 | NAC1 transcription factor | Takasaki et al, |
OsATG10b | LOC_Os12g32210 | Autophagy-related protein 10 | Shin et al, |
OsSOS1 | LOC_Os12g44360 | Sodium/hydrogen exchanger 7 | El Mahi et al, |
OsNHA1 | LOC_Os12g44360 | Na+/H+ antiporter | Zhou et al, |
Trait | QTL | Chr | Marker interval/ Position (Mb) | LOD/ P-value | PVE (%) | Allele/ Cross combination | Reference |
---|---|---|---|---|---|---|---|
Dry weight of root | qDWRO-9a | 9 | RM1553-RM7424 | 14.12 | 27.4 | Tarommahali | Sabouri and Sabouri, |
qDWRO-9b | 9 | RM7424-RM5702 | 12.88 | 25.5 | Tarommahali | ||
qDRW11 | 11 | RM6091-RM229 | 2.90 | 18.3 | Jiucaiqing/IR26 | Wang Z F et al, | |
Dry weight of shoot | qDWS9 | 9 | RM278-RM215 | 2.31 | 11.5 | Jiucaiqing/IR36 | Yao et al, |
qDSW12.1 | 12 | RM5609-RM7376 | 4.70 | 38.0 | Jiucaiqing/IR26 | Wang Z F et al, | |
Dry mass of shoot | qDM3 | 3 | RM1022-RM6283 | 20.50 | 20.9 | Khazar | Sabouri et al, |
qDM8 | 8 | RM4955-RM152 | 20.24 | 17.7 | Khazar | ||
K+/Na+ homeostasis | qST1.1 | 1 | 40.3 | 4.90 | 22.1 | Dongxiang/Ningjing 15 | Quan et al, |
qST1.2 | 1 | 10.6 | 3.30 | 10.0 | Dongxiang/Ningjing 15 | ||
qNa | 1 | RM8068-RM8231 | 24.40 | 22.2 | Khazar | Sabouri and Sabouri, | |
qNa:K | 6 | RM3827-RM340 | 16.68 | 12.4 | Khazar | ||
Saltol | 1 | RM1287-RM10825 | - | - | Pokkali | Thomson et al, | |
Saltol | 1 | RM493 | 12.47 | 18.4 | Pokkali | Alam et al, | |
Root Na+/K+ ratio | qNAK-2 | 2 | RM318-RM262 | 2.73 | 19.3 | Jiucaiqing/IR36 | Yao et al, |
qNAK-6 | 6 | RM3827-RM340 | 16.86 | 12.4 | Khazar | Sabouri et al, | |
Leaf chlorophyll content | qCHL2 | 2 | RM12713-RM6318 | 11.30 | 14.0 | Pokkali/IR29 | Thomson et al, |
qCHL4 | 4 | RM3843-RM127 | 3.90 | 13.0 | Pokkali/IR29 | ||
Salt tolerant rating | qSTR5 | 5 | RM413-RM161 | 2.72 | 14.3 | Jiucaiqing/IR36 | Yao et al, |
qSTR-6 | 6 | RM3727-RM340 | 17.51 | 17.3 | Khazar | Sabouri et al, | |
K+ in root | qKr1.2 | 1 | RM473A-RM128 | 7.80 | 30.0 | Tarome-Molae/Tiqing | Fotokian and Ahamadi, |
K+ in shoot | qK2 | 2 | 19.80-20.15 | 8.00 | 26.1 | IRGC96717/Zhenshan 97 | Nakhla et al, |
qSKC-1 | 1 | C1211-S2139 | 11.74 | 40.1 | Nona Bokra/Koshihikari | Lin et al, | |
Shoot Na+ concentration | qSNC2 | 2 | RM1313-RM12938 | 4.49 | 17.6 | Caidao/WD20342 | Li N et al, |
qSNC3 | 3 | RM1221-RM130 | 4.79 | 21.2 | Caidao/WD20342 | ||
qSNC6 | 6 | RM20517-RM412 | 4.49 | 14.2 | Caidao/WD20342 | ||
qSNC8 | 8 | RM502-RM210 | 4.76 | 15.5 | Caidao/WD20342 | ||
qSNC3 | 3 | 14.98 | 0.00 | 13.6 | - | Li et al, | |
qSNC-7 | 7 | C1057-R2401 | 7.66 | 48.5 | Nona Bokra/Koshihikari | Lin et al, | |
Root Na+ concentration | qRNC12 | 12 | RM270-RM1300 | 3.50 | 15.0 | Caidao/WD20342 | Li N et al, |
Root number | qRN6-2 | 6 | RM7555-RM527 | 2.60 | 29.9 | Gaochan 106/Changbai 9 | Qi et al, |
qRN11 | 11 | RM2596-RM286 | 2.31 | 13.4 | Gaochan 106/Changbai 9 | ||
Relative root number | qRRN6-2 | 6 | RM7555-RM527 | 2.23 | 10.8 | Gaochan 106/Changbai 9 | Qi et al, |
qRRN11-1 | 11 | RM21-RM202 | 3.67 | 10.6 | Gaochan 106/Changbai 9 | ||
qRRN11-2 | 11 | RM286-RM6894 | 2.10 | 23.9 | Gaochan 106/Changbai 9 | ||
Seedling height | qSH1 | 1 | RM499-RM2318 | 3.77 | 15.8 | Gaochan 106/Changbai 9 | Qi et al, |
qSH11-1 | 11 | RM144-RM7654 | 2.55 | 11.8 | Gaochan 106/Changbai 9 | ||
qSH11-2 | 11 | RM2596-RM286 | 2.47 | 16.5 | Gaochan 106/Changbai 9 | ||
qSH1 | 1 | 36.09-36.28 | 18.40 | 57.1 | IRGC96717/Zhenshan 97 | Nakhla et al, | |
qSH12.2 | 12 | RM7376-RM6953 | 4.60 | 30.6 | Jiucaiqing/IR26 | Wang Z F et al, | |
Relative seedling height | qRSH5 | 5 | RM3870-RM7452 | 2.22 | 29.9 | Gaochan 106/Changbai 9 | Qi et al, |
qRSH6-2 | 6 | RM7555-RM527 | 3.60 | 34.6 | Gaochan 106/Changbai 9 | ||
Root length | qRL8-1 | 8 | RM38-RM515 | 2.23 | 10.6 | Gaochan 106/Changbai 9 | |
qRL11-2 | 11 | RM2596-RM286 | 2.09 | 21.1 | Gaochan 106/Changbai 9 | ||
qRL7 | 7 | RM1048-RM11 | 18.49 | 16.2 | Tarommahali/Khazar | Sabouri and Sabouri, | |
Relative root length | qRRL11 | 11 | 21.69-22.56 | 7.55 | 18.8 | Xiaobaijingzi/Kongyu 131 | Li X W et al, |
Germination rate | qGR6.2 | 6 | Z604-RM276 | 10.58 | 23.5 | Wujiaozhan/Nipponbare | Zeng et al, |
Alkali stress root length | qARL11 | 11 | 21.69-22.56 | 6.03 | 11.4 | Xiaobaijingzi/Kongyu 131 | Li X W et al, |
Alkali damage rate | qADS3 | 3 | RM251-RM3280 | <0.0001 | 14.9 | TN1/CJ06 | Cheng et al, |
qADS7 | 7 | RM3826-RM1279 | <0.0001 | 11.3 | TN1/CJ06 | ||
Dead leaf rate | qDLRa5-2 | 5 | RM289-RM413 | 4.41 | 33.3 | Yiai 1/Lishuinu | Liang et al, |
qDLRs8-1 | 8 | RM22741-RM404 | 7.65 | 18.3 | Yiai 1/Lishuinu | ||
Dead seedling rate | qDSRs4-2 | 4 | RM307-RM471 | 4.46 | 27.2 | Yiai 1/Lishuinu | |
qDSRs8-1 | 8 | RM22741-RM404 | 6.54 | 16.0 | Yiai 1/Lishuinu | ||
Survival days of seedlings | qSDS1 | 1 | RM1329-RM1331 | 3.08 | 12.8 | Caidao/WD20342 | Li N et al, |
qSDS-1 | 1 | C813-C86 | 4.88 | 18.0 | Nona Bokra/Koshihikari | Lin et al, | |
Enhanced salt tolerance | qST1 | 1 | Est12-RZ569A | 11.58 | 27.8 | Gihobyeo | Lee et al, |
qST6 | 6 | 25.60 | 4.12 | 19.4 | Dongxiang/Ningjing 15 | Quan et al, | |
Alkali tolerance | qAT11 | 11 | 22.00 | - | - | Xiaobaijingzi/Kongyu 131 | Li X W et al, |
ALT1 | 1 | RM11740-RM3285 | - | - | alt1/Kasalath | Guo et al, | |
Score of alkalinity tolerance | qSAT3 | 3 | 14.98 | <0.0001 | 13.4 | - | Li et al, |
qSAT4 | 4 | 21.53 | <0.0001 | 14.0 | - |
Table 2. Main-effect QTLs for saline-alkaline tolerance detected in rice populations.
Trait | QTL | Chr | Marker interval/ Position (Mb) | LOD/ P-value | PVE (%) | Allele/ Cross combination | Reference |
---|---|---|---|---|---|---|---|
Dry weight of root | qDWRO-9a | 9 | RM1553-RM7424 | 14.12 | 27.4 | Tarommahali | Sabouri and Sabouri, |
qDWRO-9b | 9 | RM7424-RM5702 | 12.88 | 25.5 | Tarommahali | ||
qDRW11 | 11 | RM6091-RM229 | 2.90 | 18.3 | Jiucaiqing/IR26 | Wang Z F et al, | |
Dry weight of shoot | qDWS9 | 9 | RM278-RM215 | 2.31 | 11.5 | Jiucaiqing/IR36 | Yao et al, |
qDSW12.1 | 12 | RM5609-RM7376 | 4.70 | 38.0 | Jiucaiqing/IR26 | Wang Z F et al, | |
Dry mass of shoot | qDM3 | 3 | RM1022-RM6283 | 20.50 | 20.9 | Khazar | Sabouri et al, |
qDM8 | 8 | RM4955-RM152 | 20.24 | 17.7 | Khazar | ||
K+/Na+ homeostasis | qST1.1 | 1 | 40.3 | 4.90 | 22.1 | Dongxiang/Ningjing 15 | Quan et al, |
qST1.2 | 1 | 10.6 | 3.30 | 10.0 | Dongxiang/Ningjing 15 | ||
qNa | 1 | RM8068-RM8231 | 24.40 | 22.2 | Khazar | Sabouri and Sabouri, | |
qNa:K | 6 | RM3827-RM340 | 16.68 | 12.4 | Khazar | ||
Saltol | 1 | RM1287-RM10825 | - | - | Pokkali | Thomson et al, | |
Saltol | 1 | RM493 | 12.47 | 18.4 | Pokkali | Alam et al, | |
Root Na+/K+ ratio | qNAK-2 | 2 | RM318-RM262 | 2.73 | 19.3 | Jiucaiqing/IR36 | Yao et al, |
qNAK-6 | 6 | RM3827-RM340 | 16.86 | 12.4 | Khazar | Sabouri et al, | |
Leaf chlorophyll content | qCHL2 | 2 | RM12713-RM6318 | 11.30 | 14.0 | Pokkali/IR29 | Thomson et al, |
qCHL4 | 4 | RM3843-RM127 | 3.90 | 13.0 | Pokkali/IR29 | ||
Salt tolerant rating | qSTR5 | 5 | RM413-RM161 | 2.72 | 14.3 | Jiucaiqing/IR36 | Yao et al, |
qSTR-6 | 6 | RM3727-RM340 | 17.51 | 17.3 | Khazar | Sabouri et al, | |
K+ in root | qKr1.2 | 1 | RM473A-RM128 | 7.80 | 30.0 | Tarome-Molae/Tiqing | Fotokian and Ahamadi, |
K+ in shoot | qK2 | 2 | 19.80-20.15 | 8.00 | 26.1 | IRGC96717/Zhenshan 97 | Nakhla et al, |
qSKC-1 | 1 | C1211-S2139 | 11.74 | 40.1 | Nona Bokra/Koshihikari | Lin et al, | |
Shoot Na+ concentration | qSNC2 | 2 | RM1313-RM12938 | 4.49 | 17.6 | Caidao/WD20342 | Li N et al, |
qSNC3 | 3 | RM1221-RM130 | 4.79 | 21.2 | Caidao/WD20342 | ||
qSNC6 | 6 | RM20517-RM412 | 4.49 | 14.2 | Caidao/WD20342 | ||
qSNC8 | 8 | RM502-RM210 | 4.76 | 15.5 | Caidao/WD20342 | ||
qSNC3 | 3 | 14.98 | 0.00 | 13.6 | - | Li et al, | |
qSNC-7 | 7 | C1057-R2401 | 7.66 | 48.5 | Nona Bokra/Koshihikari | Lin et al, | |
Root Na+ concentration | qRNC12 | 12 | RM270-RM1300 | 3.50 | 15.0 | Caidao/WD20342 | Li N et al, |
Root number | qRN6-2 | 6 | RM7555-RM527 | 2.60 | 29.9 | Gaochan 106/Changbai 9 | Qi et al, |
qRN11 | 11 | RM2596-RM286 | 2.31 | 13.4 | Gaochan 106/Changbai 9 | ||
Relative root number | qRRN6-2 | 6 | RM7555-RM527 | 2.23 | 10.8 | Gaochan 106/Changbai 9 | Qi et al, |
qRRN11-1 | 11 | RM21-RM202 | 3.67 | 10.6 | Gaochan 106/Changbai 9 | ||
qRRN11-2 | 11 | RM286-RM6894 | 2.10 | 23.9 | Gaochan 106/Changbai 9 | ||
Seedling height | qSH1 | 1 | RM499-RM2318 | 3.77 | 15.8 | Gaochan 106/Changbai 9 | Qi et al, |
qSH11-1 | 11 | RM144-RM7654 | 2.55 | 11.8 | Gaochan 106/Changbai 9 | ||
qSH11-2 | 11 | RM2596-RM286 | 2.47 | 16.5 | Gaochan 106/Changbai 9 | ||
qSH1 | 1 | 36.09-36.28 | 18.40 | 57.1 | IRGC96717/Zhenshan 97 | Nakhla et al, | |
qSH12.2 | 12 | RM7376-RM6953 | 4.60 | 30.6 | Jiucaiqing/IR26 | Wang Z F et al, | |
Relative seedling height | qRSH5 | 5 | RM3870-RM7452 | 2.22 | 29.9 | Gaochan 106/Changbai 9 | Qi et al, |
qRSH6-2 | 6 | RM7555-RM527 | 3.60 | 34.6 | Gaochan 106/Changbai 9 | ||
Root length | qRL8-1 | 8 | RM38-RM515 | 2.23 | 10.6 | Gaochan 106/Changbai 9 | |
qRL11-2 | 11 | RM2596-RM286 | 2.09 | 21.1 | Gaochan 106/Changbai 9 | ||
qRL7 | 7 | RM1048-RM11 | 18.49 | 16.2 | Tarommahali/Khazar | Sabouri and Sabouri, | |
Relative root length | qRRL11 | 11 | 21.69-22.56 | 7.55 | 18.8 | Xiaobaijingzi/Kongyu 131 | Li X W et al, |
Germination rate | qGR6.2 | 6 | Z604-RM276 | 10.58 | 23.5 | Wujiaozhan/Nipponbare | Zeng et al, |
Alkali stress root length | qARL11 | 11 | 21.69-22.56 | 6.03 | 11.4 | Xiaobaijingzi/Kongyu 131 | Li X W et al, |
Alkali damage rate | qADS3 | 3 | RM251-RM3280 | <0.0001 | 14.9 | TN1/CJ06 | Cheng et al, |
qADS7 | 7 | RM3826-RM1279 | <0.0001 | 11.3 | TN1/CJ06 | ||
Dead leaf rate | qDLRa5-2 | 5 | RM289-RM413 | 4.41 | 33.3 | Yiai 1/Lishuinu | Liang et al, |
qDLRs8-1 | 8 | RM22741-RM404 | 7.65 | 18.3 | Yiai 1/Lishuinu | ||
Dead seedling rate | qDSRs4-2 | 4 | RM307-RM471 | 4.46 | 27.2 | Yiai 1/Lishuinu | |
qDSRs8-1 | 8 | RM22741-RM404 | 6.54 | 16.0 | Yiai 1/Lishuinu | ||
Survival days of seedlings | qSDS1 | 1 | RM1329-RM1331 | 3.08 | 12.8 | Caidao/WD20342 | Li N et al, |
qSDS-1 | 1 | C813-C86 | 4.88 | 18.0 | Nona Bokra/Koshihikari | Lin et al, | |
Enhanced salt tolerance | qST1 | 1 | Est12-RZ569A | 11.58 | 27.8 | Gihobyeo | Lee et al, |
qST6 | 6 | 25.60 | 4.12 | 19.4 | Dongxiang/Ningjing 15 | Quan et al, | |
Alkali tolerance | qAT11 | 11 | 22.00 | - | - | Xiaobaijingzi/Kongyu 131 | Li X W et al, |
ALT1 | 1 | RM11740-RM3285 | - | - | alt1/Kasalath | Guo et al, | |
Score of alkalinity tolerance | qSAT3 | 3 | 14.98 | <0.0001 | 13.4 | - | Li et al, |
qSAT4 | 4 | 21.53 | <0.0001 | 14.0 | - |
QTL | Gene | Locus | Function | QTL donor | Reference |
---|---|---|---|---|---|
qAT11 | OsFBDUF54 | LOC_Os11g37390 | OsFBDUF54-F-box and DUF domain containing protein-regulate alkaline stress | Xiaobaijingzi | Li X W et al, |
qST1.1 | OsSKC1 | LOC_Os01g20160 | Na+ transporter regulation of K+/Na+ homeostasis | Sea Rice 86 | Wu et al, |
qSKC1 | OsSKC1 | LOC_Os01g20160 | Na+ transporter regulation of K+/Na+ homeostasis | Nona Bokra | Ren et al, |
qST1.2 | OsSKC1 | LOC_Os01g0307500 | Cation transporter family protein, SKC1 | Ningjing 16 | Quan et al, |
qSE3 | OsHAK21 | LOC_Os03g37930 | K+ transport, enhances tolerance at germination and establishment of seedling | Jiucaiqing | He et al, |
HST1 | OsRR22 | LOC_Os06g08440 | Upregulated genes included OsHKT1 | hst1 mutant | Takagi et al, |
Saltol | OsGATA8 / OsSKC1 | LOC_Os01g24070 | GATA zinc finger domain containing protein | Pokkali | Nutan et al, |
ALT1 | ALT1 | LOC_Os07g57110 | A putative core subunit ATPase of chromatin remodeling complex | alt1 mutant | Guo et al, |
qRSL7 | OsSAP16 | LOC_Os07g38240 | ZOS7-05-C2H2 zinc finger protein | Weiguo | Lei et al, |
Table 3. Some cloned and fine-mapped genes/QTLs for saline-alkali tolerance in rice.
QTL | Gene | Locus | Function | QTL donor | Reference |
---|---|---|---|---|---|
qAT11 | OsFBDUF54 | LOC_Os11g37390 | OsFBDUF54-F-box and DUF domain containing protein-regulate alkaline stress | Xiaobaijingzi | Li X W et al, |
qST1.1 | OsSKC1 | LOC_Os01g20160 | Na+ transporter regulation of K+/Na+ homeostasis | Sea Rice 86 | Wu et al, |
qSKC1 | OsSKC1 | LOC_Os01g20160 | Na+ transporter regulation of K+/Na+ homeostasis | Nona Bokra | Ren et al, |
qST1.2 | OsSKC1 | LOC_Os01g0307500 | Cation transporter family protein, SKC1 | Ningjing 16 | Quan et al, |
qSE3 | OsHAK21 | LOC_Os03g37930 | K+ transport, enhances tolerance at germination and establishment of seedling | Jiucaiqing | He et al, |
HST1 | OsRR22 | LOC_Os06g08440 | Upregulated genes included OsHKT1 | hst1 mutant | Takagi et al, |
Saltol | OsGATA8 / OsSKC1 | LOC_Os01g24070 | GATA zinc finger domain containing protein | Pokkali | Nutan et al, |
ALT1 | ALT1 | LOC_Os07g57110 | A putative core subunit ATPase of chromatin remodeling complex | alt1 mutant | Guo et al, |
qRSL7 | OsSAP16 | LOC_Os07g38240 | ZOS7-05-C2H2 zinc finger protein | Weiguo | Lei et al, |
Fig. 4. Schematic diagram of saline-alkali stress tolerance mechanism and development of stress-tolerant varieties. Modified from Fang et al (2021). GWAS, Genome-wide association study.
Fig. 5. Molecular recurrent selection system for improving saline-alkali tolerance using dominant male sterility (DMS) gene-based genomic selection (GS) and high- yielding and saline-alkali tolerant donors.
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