Rice is a great source of energy and protein for the human population, and it is beneficial to human health. Also, rice is the staple food for more than half of the world’s population. Micronutrients play an important role in increasing agricultural productivity, and various factors, including toxic levels of elements such as aluminum, iron, heavy metals and salts as well as deficiency of nutrients such as zinc and phosphorus, have negative effects on rice productivity. Deficiency of nutrients is becoming more serious due to increased nutrient demand from intensive agriculture. Different methods of applying nutrients have been suggested, but the application of fertilizers is unaffordable for many poor farmers in developing regions. There is considerable diversity in rice germplasm, and this variation can be exploited to develop tolerant rice varieties that can withstand unfavorable conditions through breeding programs. Regarding our review of problem soils, beside field nutrition management, many quantitative trait loci (QTLs) and gene specific markers have been determined and could be used in marker-aided breeding program. Moreover, a combination of genetic and agronomic strategies, such as the use of tolerant varieties, nutrient, soil and cultural management, may be more effective in attaining sustainable agriculture.