Table 4.
Summary of candidate genes identified from MQTLs for salinity tolerance in rice.
| MQTL | Gene stable ID | Symbol | Chr | Function | References |
|---|---|---|---|---|---|
| MQTL1.1 | Os01g0303600 | OsRFP | 1 | During plant responses to environmental stress, it helps in the post-translational alteration of target proteins | Lim et al. 201315 |
| MQTL1.1 | Os01g0304100 | OsCCC2 | 1 | The prevalence of cation-chloride cotransporters and their significance in major developmental processes and Cl- homeostasis in plants | Flores et al. 200749 |
| MQTL1.1 | Os01g0307500 | OsHKT1;5, SKC1, OsHKT8, OsHK1;5 | 1 | Salinity tolerance is determined by the HKT1;5 loci/alleles. HKT1;5 s are plasmalemma-localized Na + transporters that transfer xylem Na + into xylem parenchyma cells, lowering shoot Na + buildup | Somasundaram et al. 202044 |
| MQTL1.1 | Os01g0309800 | OsHypB | 1 | ABA, ethylene, jasmonic acid, salt and drought stress have all been proven to increase H2 generation | Zeng et al. 201341 |
| MQTL1.2 | Os01g0582400 | OsCYP | 1 | OsCyp2-P is a promising candidate gene for improving various abiotic stress tolerance as it works by scavenging reactive oxygen species (ROS) and maintaining ion homeostasis | Kumari et al. 201589 |
| MQTL1.4 | Os01g0566100 | OsEF3, OsELF3-2, OsELF3.2 | 1 | Important function in root development, grain weight and days to heading | Wang et al. 2021a90 |
| MQTL1.4 | Os01g0570800 | OsIQM | 1 | PEG, NaCl, jasmonic acid (JA) and abscisic acid (ABA) administration elicited responses in most IQM genes, implying that they play important roles in biotic and abiotic stress responses | Fan et al. 202191 |
| MQTL1.4 | Os01g0571300 | OsHsfA7 | 1 | Over-expressing OsHsfA7 rice demonstrated reduced damage symptoms and higher survival rates, leaf electrical conductivity and malondialdehyde levels when exposed to salt | Liu et al. 201392 |
| MQTL1.5 | Os01g0711600 | OsRTH1 | 1 | OsRTH1 modifies ethylene responses, revealing the biological importance of ethylene in rice seedling growth and development | Zhang et al. 201262 |
| MQTL1.6 | Os01g0350900 | OsIPI1 | 1 | Plant architecture was significantly altered in the ipi1 loss-of-function mutants, with more tillers, enlarged panicles and higher yield per plant | Wang et al. 201793 |
| MQTL1.6 | Os01g0353400 | OsGST4 | 1 | The ROS-scavenging activity of OsGST4 protein was identified and its mutant exhibited delayed growth and a high vulnerability to salt and oxidative stress | Xu et al. 201834 |
| MQTL2.3 | Os02g0558100 | OsCLC-2 | 2 | OsCLC-1 aids avoidance of chloride ions by accumulating them in vacuoles | Nakamura et al. 200650 |
| MQTL3.1 | Os03g0244600 | OSLAX | 3 | OsRAU1 is involved in the increased phloem auxin translocation in lateral roots and their primordia, which speeds up lateral root development | Chhun et al. 200794 |
| MQTL3.2 | Os03g0366200 | OsCBK | 3 | OsCBK is prevalent in sporogenous cells of the anther during meiosis and is significantly expressed in cell division zones | Li et al. 200695 |
| MQTL3.2 | Os03g0367000 | OsCYP | 3 | OsCYPs were shown to up-regulate a large number of genes in response to salt and desiccation stress | Ahn et al. 201031 |
| MQTL3.3 | Os03g0593200 | CBSDUF | 3 | CDCPs are important in stress response/tolerance as well as development | Kushwaha et al. 200996 |
| MQTL3.4 | Os03g0318600 | OsbZIP28, OsbZIP1 | 3 | In response to salicylic acid, jasmonic acid and abscisic acid, OsbZIP1 is constitutively produced in the roots and highly stimulated in rice leaves | Hasegawa et al. 202137 |
| MQTL3.4 | Os03g0319300 | OsCam1-1 | 3 | Calmodulin has been found to have a part in the signal transduction cascade in proline accumulation during salt stress and ABA has been shown to upregulate OsCam1-1 (the salt-stress-responsive calmodulin) gene expression | Yuenyong et al. 201840 |
| MQTL3.4 | Os03g0320600 | OSVQ | 3 | In plants treated with abscisic acid, OsVQ genes operate as essential co-regulators during the plant defense response to biotic and abiotic stresses | Kim et al. 201339 |
| MQTL3.4 | Os03g0321700 | OsWRKY55 | 3 | OsWRKY55 was found to be expressed in osmotic and abscisic acid (ABA) treatments and to play a vital role in rice plant height regulation | Huang et al. 202138 |
| MQTL3.4 | Os03g0332400 | OsGLYII2 | 3 | Increased photosynthesis and lower oxidative damage under stress circumstances appear to be the mechanism allowing for increased stress tolerance | Ghosh et al. 201497 |
| MQTL3.4 | Os03g0337500 | OsHAK8 | 3 | OsHAK8, a rice potassium transporter, is involved in K + uptake and translocation. Widely expressed in roots and the protein was directed to the plasma membrane | Wang et al. 2021b98 |
| MQTL4.1 | Os04g0169100 | Os-ERL1, OsETR2 | 4 | Abiotic stresses and phytohormones govern OsARD expression, which is expressed in roots under flood circumstances and inhibited by abiotic stresses such as water deficit, excessive salt and low temperature | Lin et al. 200563 |
| MQTL4.1 | Os04g0176400 | OsSCP | 4 | Several pollen-specific elements were discovered during the search for promoter regions and these promoters were active in mature pollen grains and pollen tubes. OsSCPs play a key part in the maturation of mature pollen and the creation of pollen tubes | Park et al. 200651 |
| MQTL4.2 | Os04g0304400 | OsMADS25 | 4 | In the presence of nitrate, MADS-box Transcription Factors greatly increases primary root length, lateral root number, lateral root length and shoot fresh weight | Xu et al. 201199 |
| MQTL5.2 | Os05g0312600 | CML | 5 | Increased tolerance to excessive salt and drought was associated with altered expression of stress/ABA-responsive genes when OsMSR2 was expressed | Ahmadi et al. 201146 |
| MQTL6.2 | Os06g0504100 | MADS | 6 | In rice, MADS-box genes are expressed during reproductive development and stress | Ahmadi et al. 201146 |
| MQTL6.2 | Os06g0504900 | OsWRKY | 6 | The OsWRKY31 gene was discovered to promote lateral root development and elongation when it was overexpressed | Zhang et al. 2008100 |
| MQTL6.3 | Os06g0603000 | PE-1 | 6 | PE-1 was found mostly in roots, stems, leaves, leaf sheaths and juvenile panicles and was associated with lower chlorophyll concentration, increased photosynthesis and lower pollen fertility | Rao et al. 201954 |
| MQTL6.3 | Os06g0603600 | OsSPX1 | 6 | Rice seedlings with high OsSPX1 levels are resistant to cold and oxidative stress. Rice normal anther and pollen development was hampered by OsSPX1 downregulation, which disrupted glucose metabolism and sugar transport, resulting in semi-male sterility and reduced seed-setting rate and grain yield | Zhang et al. 201635 |
| MQTL6.3 | Os06g0606000 | OsSOS2 | 6 | SOS2 overexpressing plants were found to have better ion and redox homeostasis in the presence of salinity and it plays a function at both the seedling and reproductive stages | Kumar et al. 202245 |
| MQTL6.4 | Os06g0506600 | OsUBC | 6 | Drought, salt stress and ABA dramatically up-regulated UBC genes involved in hormone-mediated stress responses, which were preferentially expressed in leaves, panicles and/or seeds | EZ et al. 2015101 |
| MQTL6.6 | Os06g0335500 | IAA | 6 | Many genes were responsive to diverse abiotic stimuli, demonstrating that plant development and abiotic stress interact, as evidenced by the root growth of transgenic rice | Song et al. 2009102 |
| MQTL6.6 | Os06g0348800 | OsGLK1 | 6 | OsGLK1 is a crucial regulator of chloroplast development, since it governs chloroplast development under the control of light and phytohormones | Nakamura et al. 2009103 |
| MQTL6.7 | Os06g0610350 | MOC1 | 6 | The MONOCULM 1 (MOC1) gene was discovered to be the first important regulator of rice tiller number | Lin et al. 201253 |
| MQTL7.1 | Os07g0448100 | OsPIP2 | 7 | OsPIP2;2 performed a role in cell membrane integrity and efficiently protected rice cells from osmotic stress-induced electrolyte leakage | Bai et al. 2021104 |
| MQTL7.1 | Os07g0451300 | OsNAC45 | 7 | OsNAC45 played an important role during ABA signal responses by reducing ROS accumulation in roots and increased salinity tolerance in rice | Zhang et al. 2020a105 |
| MQTL7.2 | Os07g0150100 | OsDDP | 7 | Under salinity stress, OsDDPs were differently regulated, with OsDDP6 being increased at all developmental stages in the salt tolerant rice genotype FL478 | Ganie et al. 201759 |
| MQTL8.1 | Os08g0445700 | OsTPS | 8 | Through ABA signaling, OsTPS8 may modulate suberin deposition in rice and Salinity tolerance is also aided by SAPK9-mediated regulation of altered ABA-responsive genes | Vishal et al. 2019106 |
| MQTL8.2 | Os08g0409100 | OsTPP | 8 | Drought, salt and cold resistance have been demonstrated in trehalose producing genes | Iordachescu and Imani, 2008107 |
| MQTL9.1 | Os09g0286400 | OsNHX | 9 | In lateral roots, the vascular bundle, the water pore and the basal section of seedling shoots, OsNHX1 or OsNHX5 promoter activity was seen. Salt stress, hyperosmotic stress and ABA increase the expression of OsNHX1, OsNHX2, OsNHX3 and OsNHX5 in rice tissues in distinct ways | Fukuda et al. 201148 |
| MQTL9.3 | Os09g0439200 | OsJAZ8, OsTIFY10c | 9 | OsJAZ8 is associated with enhanced salt tolerance, demonstrating the importance of jasmonate signaling during stress tolerance | Peethambaran et al. 2018108 |
| MQTL9.3 | Os09g0448200 | OsHAK | 9 | McHAK1 and McHAK4 have a role in maintaining potassium levels in leaves and roots during salt stress and their expression is enhanced in leaves and roots in response to excessive salinity | Ahmadi et al. 201146 |
| MQTL9.3 | Os09g0455200 | OsHsf | 9 | By increasing ABA sensitivity and temporal modulation of salt responsive genes involved in signaling and ion homeostasis, OsHsfC1b improves salt and osmotic stress tolerance | Schmidt et al. 2012109 |
| MQTL9.3 | Os09g0457100 | OsABA | 9 | In rice, the OsABA8ox3 gene is critical for modulating ABA levels and osmotic stress tolerance | Cai et al. 201536 |
| MQTL9.4 | Os09g0393200 | OsJMJ | 9 | Under salt treatment, JMJ-C members were highly expressed in the flag leaf stage of FL478 | Chowrasia et al. 201852 |
| MQTL9.4 | Os09g0416200 | OsGMST | 9 | Under salt stress, OsGMST1 was upregulated and knocking it out in rice resulted in hypersensitivity to salt stress | Deng et al. 2019110 |
| MQTL10.1 | Os10g0544900 | OsPP2Cs | 10 | The majority of PP2C genes are involved in stress tolerance, particularly the ABA response | Xue et al. 2008111 |
| MQTL10.1 | Os10g0553300 | OsTPS1 | 10 | Rice seedlings with higher trehalose and proline concentrations when OsTPS1 was overexpressed showed more resistance to cold, high salinity and drought | Li et al. 2011112 |
| MQTL10.1 | Os10g0560400 | OsCCT | 10 | CCT family genes regulated the heading date under both long day and short-day conditions | Zhang et al. 2015113 |
| MQTL10.1 | Os10g0563600 | OsMSRA | 10 | The key involvement of OsMSRA4.1 is in the fight against oxidative stress and salt tolerance | Guo et al. 200933 |
| MQTL10.1 | Os10g0564800 | OsCBL1 | 10 | OsCBL1 regulates rice seedling growth and regulates lateral root elongation by modulating auxin production | Yang et al. 2019114 |
| MQTL11.3 | Os11g0284900 | OsWRKY | 11 | WRKY genes play a role in regulating ABA responses in plants | Xie et al. 2005115 |
| MQTL11.3 | Os11g0490900 | OsApx | 11 | Abiotic stress, such as salt, heat, strong light and methyl viologe, induces APXs (APx1/2 s) to change redox homeostasis (increased levels of H2O2 and ascorbate) | Bonifacio et al. 201132 |
| MQTL12.1 | Os12g0478200 | OsABA | 12 | Drought and salt were found to induce the expression of the OsABF1 gene, which encodes a bZIP transcription factor, in seedling shoots and roots | Hossain et al. 20109 |
| MQTL12.2 | Os12g0489100 | OsMB | 12 | OsM4 and OsMB11 are substantially expressed in drought and salinity stress, they could be used to develop stress-resistant crops | Kushwaha et al. 201696 |