Genetic regulation of homeostasis, uptake, bio-fortification and efficiency enhancement of iron in rice

Highlights

• Fe-deficiency and toxicity stress tolerance mechanisms in rice.

• Genes/QTLs for Fe-deficiency, toxicity and biofortification.

• Screening and breeding efforts for both the stresses.

Abstract

Soils of large areas of the globe are affected by deficiency or toxicity of iron (Fe), making it one of the major limitations to higher productivity of rice. Deficiency of Fe, an essential micronutrient for growth and development of rice, produces grain with low Fe-content. Consumption of low-Fe rice causes malnutrition affecting human health. Biofortification is an easy and low-cost way to enhance Fe content in rice, the staple food of more than half of the global population. Identification of relevant quantitative trait loci (QTLs) and genes controlling the stresses are needed for developing tolerant genotype(s). Fe deficiency is commonly observed in alkaline and aerobic soils, while toxicity is seen in low pH soils of lowland rice ecology. Rice plants cope up under deficiency or toxicity conditions through various morphological, physiological and differential gene expression strategies. Rice plant uses various transporter genes like OsNAS1, OsNAS2, OsIRT1, OsIRT2, OsNRAMP1, OsYSL15 and OsYSL16 under deficiency stress while OsIRT1, OsFRO2, OsVIT1, OsVIT2, OsNRAMP6, OsNAAT1, OsNAS3, OsNAC4, OsNAC5 and OsNAC6 under toxicity condition are involved for Fe homeostasis. Several QTLs including qFe3:1, qFe3:2, qFe7:1, qFe9:1, qFe9:2, qFe10:1, Fe11:1, qFe3.3 and qFe7.3 associated with grain-Fe content have been identified. Many Fe binding and transporters genes like OsZIP1, OsHMA4, OsACA2, OsZIP2, OsCNGC, OsZIP3, OsZIP5, OsZIP9, OsHma2, ABC transporter, OsNAS3, heavy metal transporter, Chy zinc finger and OsACA9 have been identified to improve grain-Fe content. Donor lines for grain-Fe content have been identified from rice germplasms showing even up to 147 μg g⁻¹ in brown rice. Fe content in rice grain has been enhanced to many folds using ferritin genes of soybean and common bean, NAS gene and mugineic acid synthase genes (HvNAS1 and HvNAAT-A,-B or IDS3) of barley, nicotianamine transporter gene (OsYSL2) and nicotinamine synthase genes (OsNAS1, OsNAS2 and OsNAS3) through transgenic approach. The paper analyses the mechanisms of tolerance to Fe-deficiency and toxicity, identification of genes/QTLs responsible for tolerance under the stresses and helping for biofortification, assesses the stress affected symptoms, reviews the screening and summarizes the efforts for breeding programs for improving tolerance to Fe-deficiency and toxicity in rice.

Introduction

Iron (Fe) is an essential micronutrient for growth, development and higher grain yield of rice (Wu et al., 2014; Aung et al., 2019; Zhang et al., 2018; Pradhan et al., 2020). It plays an important role in chloroplast development, chlorophyll synthesis, photosynthesis, nitrogen metabolism, respiration, enzymatic redox reactions and acts as an important electron donor (Taiz and Zeiger, 1991; Marschner, 1995; Sahrawat, 2005; Kobayashi and Nishizawa, 2012; Rout and Sahoo, 2015; Zhang et al., 2017). Abiotic stresses due to deficiency or excess of available Fe in soil cause nutritional disorder in rice plants. Fe-related soil stresses are commonly seen in many rice growing countries of the world. Deficiency of this nutrient in human also results serious health issues. More than two billion people suffer from Fe deficiency annually, which results in mortality of about 0.8 million people in the world (Stoltzfus and Dreyfuss, 1998; Wessells and Brown, 2012; Arcanjo et al., 2013; Simbauranga et al., 2015; Freitas et al., 2016: Trijatmiko et al., 2016; WHO, 2016; Dos Santos et al., 2017; Swamy et al., 2018). More than half of the world population, mostly from developing countries, is suffering from bioavailable micronutrient deficiencies (Seshadri, 2001; Shahzad et al., 2014; Mahender et al., 2016; Sarma et al., 2018). Micronutrient supplementation, food fortification and biofortification are the common ways to overcome this deficiency related problems. Fe-biofortification in rice will be a useful strategy to solve the problem of Fe-deficiency for the poor people in developing countries, for whom rice is the staple food (Nakandalage et al., 2016; Swamy et al., 2016; Trijatmiko et al., 2016).

High yielding modern rice varieties are poor in grain-Fe content (Zimmermann and Hurrell, 2002; Brinch-Pedersen et al., 2007; Mahender et al., 2016). However, genetic variations exists for Fe content in grains of rice germplasms (Yang et al., 1998; Jiang et al., 2008; Jahan et al., 2013; Zeng et al., 2010; Mahender et al., 2016; Trijatmiko et al., 2016). Commonly grown rice varieties contain only 7–8 μg g⁻¹, however, few germplasm lines contain upto 147 μg g⁻¹ in brown rice (Zeng et al., 2010). Fe content in rice grain can be enhanced many folds using transgenic approach. Once stable transgenic donor line is obtained, the increased Fe-content can be transferred to high yielding varieties through molecular breeding approaches (Masuda et al., 2013).

The deficiency of Fe is a major constraint for achieving higher yield in rice under alkaline calcareous soil with higher pH (Marcher, 1995; Kim and Guerinot, 2007). About 30% of the global soils are alkaline in nature which suffer from Fe-deficiency. Rice grown in such soils produces low yield with poor quality (Abadia et al., 2011; Swamy et al., 2018). Low availability of Fe in soils often causes leaf chlorosis and less photosynthesis, leading to reduction in yield and quality of rice. However, tolerant rice plants cope up with the soil deficiency condition through various morphological, physiological and differential gene expression strategies. Under such insufficient soil Fe condition, two absorption strategies have been developed by rice plants. Rice root shows symptoms of cluster roots and swelling of apical root tips under deficiency of iron (Schmidt et al., 2000; Schikora and Schmidt, 2002). Again, the practice of consuming polished rice reduces Fe content in the grains.

Accumulation in higher concentration of Fe is toxic to rice plant (Howeler, 1973; Prade et al., 1993; Jugsujinda and Patrick, 1993; Genon et al., 1994; Audebert, 2006; Becker and Asch, 2005; Chérif et al., 2009; Audebert and Fofana, 2009; Stein et al., 2009; Sikirou et al., 2015, 2016; Zhang et al., 2018). Rice rhizosphere is considered as the first line of defence against excess Fe-uptake. Toxicity is commonly observed in lowland rice ecology showing abundance of soluble ferrous (Fe²⁺) in soil. It generates reactive oxygen species (ROS) and hydroxyl radicals (OH) under the toxic situation. These compounds damage the rice plants there by reduce grain yield. The problem is very severe in West and Central African countries (Sikirou et al., 2015; Oort, 2018). The toxicity is also observed in Burundi, Benin, Ivory Coast, Burkina Faso, Niger, Gambia, Guinea, Guinea-Bissau, Liberia, Nigeria, Senegal, Sierra Leone, Togo, India, China, Indonesia, Malaysia, Thailand, Philippines, Sri Lanka, Colombia, Vietnam and Brazil (Moorman and Van Breeman, 1978; Oort, 2018). The area coverage with Fe-rich soils in Africa is estimated to be about 427 million ha (Oort, 2018). Rice yield loss due to this problem in Africa varies from 12% to 100% (Audebert and Sahrawat, 2000). In India, around 2 million ha of rice area are affected by Fe-toxicity (Prasad et al., 2020). Parts of Odisha, Kerala, Tamil Nadu and north-eastern states of India face this problem (Pawar et al., 2017).

Biofortification usually refers to the process of enriching food grains for nutritive elements in crop plants through genetic approaches. This way of enriching food grains is an easy, effective and cheaper way to supplement micronutrient deficiencies in cereal crops and much cheaper to grains fortification. The popular high yielding varieties are poor in essential micronutrients and need to be biofortified to enhance the nutritive value. Adequate variability for Fe-content exists in natural rice population. By over-expressing ferritin gene, Fe-content was increased to many folds in transgenic rice lines compared to the control genotypes. Transgenic rice lines with higher Fe-content derived from other crops are already available for successful crop improvement programme (Goto et al., 1999; Lee et al., 2009; Ogo et al., 2011; Kobayashi and Nishizawa, 2012; Lee et al., 2012; Paul et al., 2012; Bashir et al., 2013; Masuda et al., 2013; Slamet-Loedin et al., 2015; Trijatmiko et al., 2016; Boonyaves et al., 2017). These transgenic lines may be useful as potential donors by the rice breeders for enhancing of grain-Fe content in popular rice varieties through molecular breeding approach. Micronutrients improvement may not be antagonistic to grain yield enhancement in rice as there is the presence of separate genomic regions controlling micronutrient traits in major crops (Welch and Graham, 2004; Pradhan et al., 2019, 2020).