Comprehensive Review on Grain Quality Enhancement and Development of Disease-Resistant Genotypes in Rice (Oryza sativa L.): Addressing Food Security Through Sustainable Agriculture

Rice is an important second most widely consumed cereal crop and is the staple food for over 90% of the Asian population due to its nutritional benefits, history, cultural factors and also medicinal properties. According to Food and Agriculture Organization (FAO) the major rice producing countries are China, India, Indonesia, Bangladesh and Vietnam, these countries are responsible for more than 75 per cent production of the total rice production across the world. White rice is widely consumed as compared to colored or pigmented rice, even though are found to be much more nutritious than white rice. Colored rice possess unique color, flavor therefore they are used as an ingredient in many dishes and pigmented rice is becoming popular among health-conscious food consumers for its antioxidants mainly because it is a good source of bioactive compounds (Veni, 2019). However, due to the rising awareness among the population (mostly urban) now the demand for pigmented rice is also increasing. The rice bran oil is a good source of essential fatty acids and antioxidants like tocopherols (Vitamin E), tocotrienols and ɤ-oryzanols which have antitumor/cancer and blood cholesterol reducing properties and thus help prevent heart problems (Veni, 2019). According to Ayurvedic treatises, rice can alleviate or subdue the tridoshas (humors) – vata, pitta, and kapha – whose imbalance in the human body causes various types of diseases (Ahuja et al., 2008). Because of dark colour black rice bran contains the same anthocyanin antioxidants found in blueberries or blackberries (Veni, 2019). It has come to light that the population is facing various health problems like stunting, low fertility, anorexia, etc due to Zn deficiency in their diet. These health and nutritional problems have to be addressed urgently in order to achieve sustainable development goals by reducing the mortality of children and women, and improving people’s general health by providing a nutritious diet (Descalsota-Empleo et al., 2019). Enhancing the Zn, Fe content in rice through biofortification has become important. Alongside the grain quality of rice, it is also important to manage the destructive pest and disease cycles in rice to avoid yield losses threatening food security of the nation. Bacterial leaf blight of rice remains one of the most destructive diseases affecting rice cultivation as a result of which drastic loss of production in terms of both quantity and quality can be observed. Therefore, developing rice varieties with improved grain nutritional quality along with strong resistance to BLB is equally important and should be prioritised in rice breeding programs.

Grain Nutritional Quality

Understanding the nutritional and chemical properties of rice grain is crucial for addressing nutritional deficiencies and improving human health. Rice grain contains carbohydrates (starch as the main component), proteins (glutelin being the major component), fiber and various micronutrients like vitamins (vitamin B6, niacin, thiamin) and minerals (iron, zinc, magnesium, potassium, manganese). Each of this composition are further discussed below briefly. 

Carbohydrates: Wide acceptance of rice in terms of its texture, cooking quality is all dependent upon rice starch. The basic attributes associated with rice starch that have given it merit over other cereal and non-cereal starches include hypo-allergenicity, digestibility, bland flavour, small granule (3-10 μm), white colour, greater acid resistance, greater freeze-thaw stability of pastes and a wide range of amylose/ amylopectin ratios (Fm, 2023).  There are mainly three types of starch on the basis of its rate of digestion, rapidly digestible starch, slowly digestible starch and resistant starch. Their properties are different from one another due to the difference in their amylose content. There are two main polymers in rice starch granules, i.e. amylose and amylopectin along with some minor constituents like the proteins (0.25%), the lipids (0.1-0.3%) and the compounds of phosphorus (Fm, 2023). CR Dhan 310 and CR Dhan 311 are two carbohydrate improved varieties of rice developed by the ICAR-NRRI, Cuttack by the help of backcrossing.

Proteins: The major protein component of rice is glutelin (80%). Research has proven that various factors like selection of cropping season, location, climate, drying, storage methods affect this protein content. Protein content ranged from 4.5 to 15.9 per cent in Oryza sativa varieties and 10.2 to 15.9 per cent in Oryza glaberrima varieties (Muttagi, 2020). The low expression alleles, OsAPP6 and the OsGluA2^LET, are promising target genes for low PC rice breeding through MAS. (Gong et al., 2006).
Micronutrients: Several micronutrients can also be found in rice grain depending upon the type of rice, soil, storage, drying, milling methods. The mineral content between both black and brown rice is very similar. A serving of either rice meets 8% of the daily value for zinc and 20% of the daily value for phosphorus. But the black rice is a slightly better source of iron meeting 6% of the daily value compared to 5% of the daily value in a serving of brown rice (Veni, 2019).

Fiber: The fiber content found in white rice (0.5-0.1%) is usually lower than that of brown rice (3-4%). Red rice is known to be rich in iron and zinc while black and purple rice are especially high in protein and crude fiber (Veni, 2019). Gene pyramiding, which involves combining multiple desirable genes to a single plant variety, is a strategical approach for improving the fiber quality in rice.

Breeding Strategies to Enhance Nutritional Quality

To effectively enhance grain nutritional quality in rice, breeding strategies such as Marker-Assisted Selection (MAS), Genomic Selection (GS), and CRISPR/Cas9-based genome editing are being widely utilized:

• Marker-Assisted Selection (MAS): It enables the precise selection of key genes associated with high zinc, iron and glutelin content, making it particularly useful for traits governed by known QTLs or single genes. For instance, OsNAS1–3 (nicotianamine synthase genes) and low-expression alleles like OsAPP6 have been successfully targeted in MAS programs (Gregorio et al., 2000; Wang et al., 2013).
• Genomic Selection (GS): It captures both major and minor gene effects controlling nutritional traits like amylose content, starch structure, and micronutrient levels, and is efficient for improving multiple traits simultaneously (Zafar et al., 2023).
• CRISPR/Cas9 gene editing allows for highly specific improvements in genes involved in protein biosynthesis, phytic acid reduction, and antioxidant production, such as enhancing lysine content or knocking out anti-nutritional factors (Li et al., 2020; Fiaz et al., 2019).

These advanced breeding tools, when integrated with traditional selection, offer an effective, rapid, and sustainable way to develop nutritionally superior rice varieties.

Factors Affecting the Nutritional Quality of Rice Grain- Tolerance to Abiotic Stress

Maintaining the grain quality in rice is important for improving the overall yield both qualitatively and quantitatively. The grain quality of rice depends upon a number of factors like genetic, environmental, agronomic, etc. The physical and chemical properties of rice grain can be affected by various abiotic factors as stated below.

Soil: This is an important factor that can affect the health quality of rice grain. Adequate amount of nutrient availability (like nitrogen, phosphorous, potassium) within the soil can interfere with the micronutrient content (essential vitamins, minerals) of the grain. Usage of compost and green manure can be beneficial to enhance the soil health. Even though having the potential for rice cultivation, presence of salinity in coastal areas of Asia makes it unsuitable for rice cultivation. Some varieties tolerant to saline soils include CSR10, CSR13, CSR23 developed by Central Soil Salinity Research Institute (CSSRI).

Climatic factors: Several climatic factors like rainfall, humidity, pressure, temperature fluctuations can influence the starch quality and nutrient content. With most of the high- yielding varieties being susceptible to drought, it serves as one of the major abiotic stress for farmers. Sahbhagi Dhan (IR74371-70-1-1) is a promising drought- tolerant variety developed through conventional breeding.

Irrigation: Water availability and its management practices help to maintain the nutrient uptake and can also directly affect the nutritional composition of rice grain. Water stagnation conditions can lead to iron deficiency.
Processing methods: Extreme milling processes can lead to the removal of outer bran layer of rice leading to loss of nutrients. Other processing factors like harvesting (like delaying the harvest), drying and storage can also affect the grain quality in rice. Appropriate storage of harvested rice grains can help to prevent nutrient loss and degradation.

Among the biotic factors, diseases (26%), insects (20%) and weeds (23%) are affecting large amount of yield loss, both in terms of quality and quantity (Shekhar et al., 2020). Pest infestation and disease outbreak are major issues faced by farmers in rice cultivation that results in yield loss. Severity of disease cycles are mainly observed at the booting and flowering stages. One such severe disease of rice, bacterial leaf blight, is further discussed below.

Bacterial Leaf Blight in Rice

The major reason reported for yield loss (up to 26%) is due to diseases caused by widespread of pathogens. There are many different diseases of rice like brown leaf spot (Helminthosporium oryzae), leaf scald (Rhynchosoprium oryzae), false smut (Ustilaginoidea virens), bacterial leaf blight (Xanthomonas oryzae pv. oryzae), etc. Among these, bacterial leaf blight (BLB) is the most destructive disease. Bacterial Blight is one of the oldest recorded rice diseases, which was first found by a farmer in the Fukuoka area of southern Japan in 1884 (Nino-Liu et al., 2006). In 1990, BLB was named as Xanthomonas oryzae pv. oryzae. In Japan, this disease has been referred to as “white withering disease” since 1881, where it was previously recorded in various localities of southern Japan (Shekhar et al., 2020). Most important rice growing states viz. Andhra Pradesh, Punjab, Haryana and western Uttar Pradesh states of India, major epidemic of this disease occurred during 1979 -1980 (Shekhar et al., 2020). Damage caused by this disease was significantly increased due to the widespread cultivation of semi-dwarf and hybrid rice varieties, as well as massive input of nitrogen fertilizer (Jiang et al., 2020). Bacterial leaf blight disease can certainly reduce the grain nutritional quality of rice by directly affecting the starch and nutrient content. The Xanthomonas oryzae pv. oryzae survive on different hosts viz. Brachiaria mutica, Cenchus ciliaris, Cyperus difformis, C. rotundus, Cynodon dactylon, Echinochloa crusgalli, Leersia spp (Leersia hexandra, Leersia oryzoides), Leptochloa chinensis, Panicum maximum, Zizania aquatica, Z. palustris, Leersia. Oryzoides and Zizania latifolia in temperate region and Laptochloa spp. and Cyperus spp. in tropical region (Shekhar et al., 2020). Exploitation of host plant resistance is considered the most effective, economical, and environmentally safe measure for controlling BLB in combination with management practices (Singh et al., 2015).

Symptoms
Bacterial leaf blight is a vascular disease caused by Xanthomonas oryzae pv. oryzae can significantly affect the crop production and overall yield. The pathogens can enter the host through openings like hydathodes and also through wounds present on the plant surface. BLB pathogens cannot enter through stomata. It divides in number in the epitheme cell and move to the xylem vessel. Kresek and leaf blight are the major symptoms observed in the affected crops. Kresek is usually seen in the tillering stage. In kresek phase due to blockage of nutrient transfer from root to different parts of plant resulting in pale yellow symptoms appears and finally wilting of the plant (Shekhar et al., 2020). High humidity, rainfall and high temperature are favourable conditions for the occurrence of leaf blight. The most favourable temperatures for Xoo growth ranges from 26-30°C and 20°C is ideal temperature for initial multiplication and growth (Shekhar et al., 2020).  The symptoms for leaf blight start as small water-soaked stripes from the tips where water pores are found and rapidly enlarge in length and width, forming a yellow lesion with a wavy margin along the edge (Shekhar et al., 2020). The sign of Xanthomonas oryzae pv. oryzae is bacterial ooze and can be seen on the margins or veins of the freshly infected leaf under moist conditions in morning hours and a source of secondary inoculums (Nino liu et al., 2006). This disease is more likely to occur during the monsoon season of the south-east Asian and Indian oceans particularly from June to September (Shekhar et al., 2020). 

Leaf Blight Resistance in Rice

Several management practices like pesticide application, crop rotation, balanced fertilizer application, field sanitation, etc have been utilised to control BLB but none of these were 100% effective. This is the main reason for which the idea of developing new resistant varieties of rice have come into light. There are more than 40 resistance genes (R genes) that have been identified to dominate BLB of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Representatives of a major class of resistance genes (R genes) against the disease that are prominent in rice are given the prefix Xa for Xanthomonas (Shekhar et al., 2020). The R gene Xa21, originated from the wild rice species Oryzae longistaminata, has provided potential resistance against the bacterial pathogen Xanthomonas oryzar pv. oryzae. Over inducing this Xa21 gene in rice plants builds resistance at both seedling and adult stages of plant lifecycle.

Although it has been well known that most plant R genes are dominant, recessive genes have also been recognized in many host-pathogen interactions. Of these, 3 (xa5, xa8 and xa13) occur naturally and confer race-specific resistance (Shekhar et al., 2020). The alleles of the recessive resistance gene xa13 identified by gene map- based cloning, occurs naturally for resistance to Xoo isolates (Yang et al., 2006). Genotypes carrying the Xa21 and xa13 resistance genes has successfully shown low disease incidence and superior grain protein quality. By developing resistant varieties with the help of resistant gene combinations like Xa4 + xa5, xa5 + xa21 and xa4 + xa5+ xa2l can be a mindful strategy to tackle the problems of bacterial leaf blight disease. Marker-assisted breeding strategy has also been found advantageous in enhancing the resistance of elite cultivars (viz. Swarna and IR 64) to bacterial leaf blight by pyramiding a few specific resistance genes (xa5, xa13 and Xa21) through backcrossing (Shekhar et al., 2020). The resistance gene xa13, originally derived from landrace BJ1 from the Indian subcontinent, is effective individually as well as in combination with Xa21, xa5, Xa4, and Xa2 against many pathotypes of Xoo (Lore et al., 2011).

The major constraint after deployment of these R genes is the fact that pathogen populations evolve rapidly in order to overcome the resistance (Shekhar et al., 2020). Therefore, it is important to continue finding measures to control bacterial leaf blight disease in the rice crop. IRBB60 variety of rice developed by IRRI, incorporates four BLB resistance genes (Xa21, xa13, xa5, Xa4).

As discussed in this study, enhancing grain nutritional quality—such as increasing protein content and enriching micronutrients like iron and zinc—alongside developing resistance to bacterial leaf blight (BLB) is crucial for both the quantitative and qualitative improvement of rice crop production. These advancements are essential to ensure national food security and to deliver better dietary value for improving public health. High-quality rice grain is a vital source of carbohydrates, proteins, fiber, vitamins, and minerals, contributing significantly to balanced diets and overall nutritional well-being. Among the different types, colored rice varieties are superior to non-colored ones in terms of nutritional composition, as they contain a higher concentration of micronutrients and antioxidant compounds. Several studies suggest that black rice exhibits higher scavenging activity compared to red rice, while non-colored varieties possess relatively lower levels of phenolic content and antioxidant activity (Veni, 2019). Developing resistance to BLB, caused by Xanthomonas oryzae pv. oryzae (Xoo)—one of the most destructive rice diseases—is essential for minimizing economic losses and maintaining consistent crop yields. The integration of genetic resistance strategies offers a sustainable and environmentally friendly solution for managing BLB while simultaneously improving grain quality. In conclusion, the dual approach of enhancing grain nutrition and BLB resistance can significantly benefit consumers through better health, support farmers by increasing income stability, reduce the risk of crop failure, and contribute to national food security.

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