Breeding rice for salinity tolerance and salt-affected soils in Africa: a review

Figures & data

Table 1. Classification of salt-affected soils based on chemical properties (Daba & Qureshi, 2021).

Salt affected soil type	Soil electrical conductivity of saturation extracts (ECe) at 25 °C (dSm^−1)	Saturation (%) of Cation Exchange Capacity with Sodium (ESP)	Soil reaction (pH value)
Saline soil	>4	<15	<8.5
Saline sodic soil	>4	>15	<8.5
Sodic (alkaline) soil	<4	>15	8.5 – 10
None saline non sodic	<4	<15	Neutral

Table 2. Extent of salt affected soils in some African countries.

Country	Extent of salt affected soils in (Million hectares)	Reference
Senegal	1.7	(Thiam et al. (2021)
Egypt	7.36	(Daba & Qureshi, 2021)
Ethiopia	11.03	(Adhanom, 2019)
Chad	8.27	(Daba & Qureshi, 2021)
Nigeria	6.502	(Daba & Qureshi, 2021)
Sudan	4.8	(Salih & Elsheik, 2014)
Tanzania	3.6	(Meliyo et al., 2016)
Kenya	13.49	(Kathuli et al., 2014)
Cameroon	0.47	(FAO, 2022)
Ghana	0.79	(Asamoah et al., 2013)

Table 3. Salinity threshold levels for rice compared with other field crops.

Crop	Threshold level (dSm^−1))	Reference
Barley	8	(Kumar et al., 2020)
Cotton	7.7	(Sharif et al., 2019)
Sorghum	6.8	(Calone et al., 2020)
Wheat	6	(Sahoo & Baranda, 2018)
Soybean	5	(Phang et al.,2008)
Sunflower	4.8	(Kumar et al., 2020)
Groundnut	3.2	(Pratiwi et al., 2021)
Rice	3	(Hoang et al., 2016)
Maize	1.7	(EL Sabagh et al., 2021)
Sugarcane	1.7	(Kumar et al., 2023)

Figure 1. The common mechanisms involved in rice salt tolerance stress response (Liu et al., 2023).

Figure 2. Salinity response adaptations in plants, extracted from Hussain et al. (2019).

Table 4. Rice genotypes tolerant to salinity identified in different Africa countries.

Improved rice genotype	Country	Reference
WAR 73-1-M2-1 and WAR 77-3-2-2	Sierra Leon	(Gregorio et al., 2013)
IR63275-B-1-1-1-3-3-2	Gambia	(Gregorio et al., 2013)
FARO 44, NERICA 2, NERICA 8 and NERICA 5	Nigeria	(Umego et al., 2020)
HK11-NDIOL-11-LON-1 (V13), D20- ART20-ARS-1 (V18), D56-ARS-NCRIB-1-1 (V24) and HK72-NIONO-5-1-1 (V26).	Senegal	(Maïga et al., 2020)
CK73, ITA212 (FARO 35), ITA222 (FARO 36), OG0315, OG250315, OW0315, and TOG 5681	Nigeria	(Kargbo et al., 2019)
SATO 1 and SATO 9	Tanzania	(Sitta et al., 2022)
SR-1, GH1580, GH1599, Anyofula and GH1571	Ghana	(Anyomi et al., 2018)

Figure 3. Chromosome wise reported quantitative trait loci (QTL) for salt tolerance (Singh et al., 2021).

Table 5. The CRISPR/Cas9 system for enhancing salinity tolerance in rice.

Edited gene/s	Cas9 promotor	sgRNA promotor	Improved trait in mutants	Reference
OsRR22	PUB-H	U6	Salinity tolerance	(Zafar et al., 2020)
OsRR22	2 × 35Spro	OsU6a	Salinity tolerance, shoot length, shoot fresh and dry weight	(Zhang et al., 2019)
	Pubi-H
DST	OsUBQ	OsU3	Salinity tolerance, osmotic tolerance	(Kumar et al., 2020)
OsmiR535	UBI	OsU3	Salinity tolerance, osmotic tolerance, shoot length (86.8%), number of lateral roots (514% as compared with line overexpressing MIR535), primary root length (35.8%)
	35S pro	OsU6		(Yue et al., 2020)

Table 6. Improving salinity stress tolerance in rice using a genetic engineering approach.

Gene	Protein	Function	Reference
OsNHX1	Vacuolar (Na^+, K^+) /H^+ antiporter	Improved salt tolerance	(Hoang et al., 2016)
OsKAT1	Shaker K^+ channel	K^+ content	(Obata et al., 2007)
OsCDPK7	CDPK	Enhanced salt tolerance	(Saijo et al., 2000)
OsMAPK5	MAPK	Enhanced salt tolerance	(Xiong & Yang, 2003)
GS2	Chloroplastic glutamine synthetase	Salt tolerance	(Hoshida et al., 2000)
GlyII	Glyoxalase II	Salt tolerance	(Singla-Pareek et al., 2008)

Daba, A. W., & Qureshi, A. S. (2021). Review of soil salinity and sodicity challenges to crop production in the lowland irrigated areas of Ethiopia and its management stategies. Land, 10(12), 1377. https://doi.org/10.3390/land10121377

 Web of Science ®Google Scholar

Thiam, S., Villamor, G. B., Faye, L. C., Henri, J., Sène, B., Diwediga, B., & Kyei, N. (2021). Monitoring land use and soil salinity changes in coastal landscape: A case study from Senegal. Environmental Monitoring and Assessment, 193(5), 259. https://doi.org/10.1007/s10661-021-08958-7

 PubMed Web of Science ®Google Scholar

Adhanom, O. M. (2019). Salinity and sodicity hazard characterization in major irrigated areas and irrigation water sources, Northern Ethiopia. Cogent Food and Agriculture, 5(1), 1673110. https://doi.org/10.1080/23311932.2019.1673110

 Web of Science ®Google Scholar

Salih, S. A., & Elsheik, M. A. (2014, March 17–18). The nature and properties of salt affected soil in South Khartoum [Paper presentation]. International Conference on Biological, Civil and Environmental Engineering (BCEE-2014)]. https://doi.org/10.15242/IICBE.C0314140

 Google Scholar

Meliyo, J. L., Kashenge-Killenga, S., Victor, K. M., Mfupe, B., Hiza, S., Kihupi, L., Boman, B., & Dick, W. (2016). Evaluation of salt affected soils for rice (Oryza Sativa) production in Ndungu irrigation scheme same district, Tanzania. Sustainable Agriculture Research, 6(1), 24–38. https://doi.org/10.5539/sar.v6n1p24

 Google Scholar

Kathuli, P., Itabari, J. K., Sijali, I. V., Gatuthu, J., & Kiaura, S. (2014). Diagnosis of sources of soil salinisation in selected irrigation schemes in semi-arid lands of Taita-Taveta County in Kenya. Joint proceedings of the 27th Soil Science Society of East Africa and the 6th African Soil Science Society, October 2013 (pp. 1–9).

 Google Scholar

FAO. (2022). Halt soil salinization, boost soil productivity. Proceeding of the Global Symposium on Salt -Affected Soils, 20–22 October 2021, Rome. https://doi.org/10.4060/cb9565en

 Google Scholar

Asamoah, A., Antwi-Boaasiako, C., Frimpong-Mensah, K., & Soma Dohan, M. (2013). Adoptable technique(s) for managing Ghanaian saline soils. Octa Journal of Environmental Research, 1(1), 48–51.

 Google Scholar

Kumar, V. V. S., Verma, R. K., Yadav, S. K., Yadav, P., Watts, A., Rao, M. V., & Chinnusamy, V. (2020). CRISPR-Cas9 mediated genome editing of drought and salt tolerance (OsDST) gene in Indica mega rice cultivar MTU1010. Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology, 26(6), 1099–1110. https://doi.org/10.1007/s12298-020-00819-w

 PubMed Web of Science ®Google Scholar

Sharif, I., Aleem, S., Farooq, J., Rizwan, M., Younas, A., Sarwar, G., & Chohan, S. M. (2019). Salinity stress in cotton: Effects, mechanism of tolerance and its management strategies. Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology, 25(4), 807–820. https://doi.org/10.1007/s12298-019-00676-2

 PubMed Web of Science ®Google Scholar

Calone, R., Sanoubar, R., Lambertini, C., Speranza, M., Vittori Antisari, L., Vianello, G., & Barbanti, L. (2020). Salt tolerance and Na allocation in sorghum bicolor under variable soil and water salinity. Plants (Basel, Switzerland), 9(5), 561. https://doi.org/10.3390/plants9050561

 PubMedGoogle Scholar

Sahoo, S., & Baranda, B. (2018). Salinity tolerance in wheat. Marumegh, 3(1), 61–65. https://doi.org/10.3390/plants12183330

 Google Scholar

Phang, T. H., Shao, G., & Lam, H. M. (2008). Salt tolerance in soybean. Journal of Integrative Plant Biology, 50(10), 1196–1212. https://doi.org/10.5772/intechopen.102835

 PubMed Web of Science ®Google Scholar

Pratiwi, H., Nugrahaeni, N., & Taufiq, A. (2021). Identification of peanut germplasm tolerance to salinity stress. Buletin Palawija, 19(1), 1. https://doi.org/10.21082/bulpa.v19n1.2021.p1-9

 Google Scholar

Hoang, T. M. L., Tran, T. N., Nguyen, T. K. T., Williams, B., Wurm, P., Bellairs, S., & Mundree, S. (2016). Improvement of salinity stress tolerance in rice: challenges and opportunities. Agronomy, 6(4), 54. https://doi.org/10.3390/agronomy6040054

 Google Scholar

EL Sabagh, A., Çiğ, F., Seydoşoğlu, S., Leonardo, Battaglia, M. L., Javed, T., Iqbal, M. A., Mubeen, M., Ali, M., Ali, M., Bengisu, G., Konuşkan, Ö., Barutcular, C., Erman, M., Açikbaş, S., Hossain, A., Islam, M. S., Wasaya, A., Ratnasekera, D., Arif, M., & Ahmad, Z. (2021). Salinity stress in maize: Effects of stress and recent developments of tolerance for improvement. Cereal Grains, 1–20. https://doi.org/10.5772/intechopen.98745

 Google Scholar

Kumar, R., Dhansu, P., Kulshreshtha, N., Meena, M. R., Kumaraswamy, M. H., Appunu, C., Chhabra, M. L., & Pandey, S. K. (2023). Identification of salinity tolerant stable sugarcane cultivars using AMMI, GGE and some other stability parameters under multi environments of salinity stress. Sustainability, 15(2), 1119. https://doi.org/10.3390/su15021119

 Web of Science ®Google Scholar

Liu, Y., Wang, F., Zhang, A., Chen, Z., Luo, X., Kong, D., Zhang, F., Yu, X., Liu, G., & Luo, L. (2023). Improvement of salinity tolerance in water-saving and drought-resistance rice (WDR). International Journal of Molecular Sciences, 24(6), 5444. https://doi.org/10.3390/ijms24065444

 PubMed Web of Science ®Google Scholar

Hussain, S., Shaukat, M., Ashraf, M., Zhu, C., Jin, Q., & Zhang, J. (2019). Salinity stress in arid and semi-arid climates: effects and management in field crops. Climate Change and Agriculture, 12, 123–145. https://doi.org/10.5772/intechopen.87982

 Google Scholar

Gregorio, G. B., Islam, R., Vergara, G. V., & Thirumeni, S. (2013). Recent advances in rice science to design salinity and other abiotic stress tolerant rice varieties. SABRAO Journal of Breeding and Genetics, 45(1), 31–41.

 Google Scholar

Umego, C., Ntui, V. O., Ita, E. E., Opara, C., & Uyoh, E. A. (2020). Screening of rice accessions for tolerance to drought and salt stress using morphological and physiological parameters. American Journal of Plant Sciences, 11(12), 2080–2102. https://doi.org/10.4236/ajps.2020.1112147

 Google Scholar

Maïga, Y., Mawussi, G., Faye, O. N., & Fall, A. (2020). Screening of rice lines (Oryza Spp L. 1753) for salinity tolerance at vegetative stage under Senegal River valley conditions. Journal of Experimental Agriculture International, 42(4), 71–81. https://doi.org/10.9734/jeai/2020/v42i430501

 Google Scholar

Kargbo, S. S., Showemimo, F. A., Porbeni, J. B. O., & Akintokun, P. O. (2019). Response of rice genotypes to salinity under hydroponic conditions. Agro-Science, 18(3), 11. https://doi.org/10.4314/as.v18i3.3

 Google Scholar

Sitta, B., Kashenge, S., Lee, S.-B., Kyung-Ho, K., Bulegeya, V., Batare, M., & Mwakapala, R. (2022). Morphogenetic response of assorted rice genotypes to salinity in Tanzania. European Journal of Agriculture and Food Sciences, 4(5), 19–27. https://doi.org/10.24018/ejfood.2022.4.5.504

 Google Scholar

Anyomi, W. E., Ashalley, R., Amoah, N. A., Blay, E. T., & K, O. (2018). Hydroponic screening of rice seedlings for salinity tolerance. Researchjournali’s Journal of Agriculture, 5(6), 1–15.

 Google Scholar

Singh, R. K., Kota, S., & Flowers, T. J. (2021). Salt tolerance in rice: Seedling and reproductive stage QTL mapping come of age. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 134(11), 3495–3533. https://doi.org/10.1007/s00122-021-03890-3

 PubMed Web of Science ®Google Scholar

Zafar, K., Sedeek, K. E. M., Rao, G. S., Khan, M. Z., Amin, I., Kamel, R., Mukhtar, Z., Zafar, M., Mansoor, S., & Mahfouz, M. M. (2020). Genome editing technologies for rice improvement: Progress, prospects, and safety concerns. Frontiers in Genome Editing, 2, 5. https://doi.org/10.3389/fgeed.2020.00005

 PubMedGoogle Scholar

Zhang, A., Liu, Y., Wang, F., Li, T., Chen, Z., Kong, D., Bi, J., Zhang, F., Luo, X., Wang, J., Tang, J., Yu, X., Liu, G., & Luo, L. (2019). Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene. Molecular Breeding, 39(3), 47. https://doi.org/10.1007/s11032-019-0954-y

 PubMed Web of Science ®Google Scholar

Yue, E., Cao, H., & Liu, B. (2020). OsmiR535, a potential genetic editing target for drought and salinity stress tolerance in Oryza Sativa. Plants (Basel, Switzerland), 9(10), 1337. https://doi.org/10.3390/plants9101337

 PubMedGoogle Scholar

Obata, T., Kitamoto, H. K., Nakamura, A., Fukuda, A., & Tanaka, Y. (2007). Rice shaker potassium channel OsKAT1 confers tolerance to salinity stress on yeast and rice cells. Plant Physiology, 144(4), 1978–1985. https://doi.org/10.1104/pp.107.101154

 PubMed Web of Science ®Google Scholar

Saijo, Y., Hata, S., Kyozuka, J., Shimamoto, K., & Izui, K. (2000). Over-expression of a single Ca 2 + -dependent protein kinase confers both cold and salt/drought tolerance on rice plants. The Plant Journal: For Cell and Molecular Biology, 23(3), 319–327. https://doi.org/10.3389/fpls.2022.1043757

 PubMed Web of Science ®Google Scholar

Xiong, L., & Yang, Y. (2003). Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid – inducible mitogen-activated protein kinase. The Plant Cell, 15(3), 745–759. https://doi.org/10.1105/tpc.008714

 PubMed Web of Science ®Google Scholar

Hoshida, H., Tanaka, Y., Hibino, T., Hayashi, Y., Tanaka, A., Takabe, T., & Takabe, T. (2000). Enhanced tolerance to salt stress in transgenic rice that overexpresses chloroplast glutamine synthetase. Plant Molecular Biology, 43(1), 103–111. https://doi.org/10.1023/A:1006408712416

 PubMed Web of Science ®Google Scholar

Singla-Pareek, S. L., Yadav, K., Pareek, A., Sopory, ÆM. K., & Reddy, S. K. (2008). Enhancing salt tolerance in a crop plant by overexpression of glyoxalase II. Transgenic Research, 17(2), 171–180. https://doi.org/10.1007/s11248-007-9082-2

 PubMed Web of Science ®Google Scholar