Advances in Genetics and Breeding of Rice: An Overview

Rice (Oryza sativa L.) is life for more than half of the human population on Earth. In the history of rice breeding, two major yield breakthroughs or leaps occurred, which phenomenally revolutionized rice breeding: the Green Revolution in the 1960s and hybrid technology in the 1970s. However, the fruits of these technologies have not spread globally to all rice-growing areas, especially African countries, for diverse reasons. It is estimated that at least 50% more rice yield is needed to feed the anticipated nine billion people by 2050. This clearly warrants another breakthrough in rice. It is apparent that the currently used conventional and molecular marker-assisted methods need to be updated with multi-pronged approaches involving innovative cutting-edge technologies for achieving the next breakthrough in rice. Here, we attempt to discuss the exciting avenues for the next advances in rice breeding by exploiting cutting-edge technologies.

Green Super Rice (GSR) Traits: Breeding and Genetics for Multiple Biotic and Abiotic Stress Tolerance in Rice

The frequent fluctuations in global climate variability (GCV), decreases in farmland and irrigation water, soil degradation and erosion, and increasing fertilizer costs are the significant factors in declining rice productivity, mainly in Asia and Africa. Under GCV scenarios, it is a challenging task to meet the rice food demand of the growing population. Identifying green traits (tolerance of biotic and abiotic stresses, nutrient-use efficiency, and nutritional grain quality) and stacking them in high-yielding elite genetic backgrounds is one promising approach to increase rice productivity. To this end, the Green Super Rice (GSR) breeding strategy helps to pool multi-stress-tolerance traits by stringent selection processes and to develop superior GSR cultivars within a short span of 4–5 years. In the crossing and selection process of GSR breeding, selective introgression lines (SILs) derived from sets of early backcross BC1F2 bulk populations through both target traits and non-target traits were selected. Genotyping of SILs with high-density SNP markers leads to the identification of a large number of SNP markers linked with the target green traits. The identified SILs with superior trait combinations were used for designed QTL pyramiding to combine different target green traits. The GSR breeding strategy also focused on nutrient- and water-use efficiency besides environment-friendly green features primarily to increase grain yield and income returns for resource-poor farmers. In this chapter, we have highlighted the GSR breeding strategy and QTL introgression of green traits in rice. This breeding strategy has successfully dissected many complex traits and also released several multi-stress-tolerant varieties with high grain yield and productivity in the target regions of Asia and Africa.

Doubled Haploids in Rice Improvement: Approaches, Applications, and Future Prospects

Exploitation of biotechnological tools in conventional breeding strategies is the need of the hour for overcoming limitations in rice production and productivity. In addition, improvement in quantity and quality along with resistance to climatic and disease stress in rice require immediate attention. Anther culture has proven its efficiency by instantaneously fixing homozygosity through diploidization of regenerated haploid plants. Therefore, androgenesis provides an efficient platform for developing inbred lines in a short period of time. Although anther culture shows its efficiency in speeding up breeding in several crop species, including rice, associated limitations still prevent the exploitation of its optimum potential. Although anther culture is well exploited in japonica rice breeding, its application in indica rice is limited because of inherent recalcitrant genetic backgrounds. The success of anther culture is determined by several factors that limit the efficiency of androgenesis. Identified constraints are early anther necrosis, poor-callus response, and proliferation, and low green-plant regeneration, along with the most frustrating albinism associated with indica rice, which has been considerably clarified. This chapter details the method of androgenesis and scope for improving the applicability of anther culture producing doubled haploids of rice in order to use it as a complementary tool for precision breeding.

Crop Establishment in Direct-Seeded Rice: Traits, Physiology, and Genetics

The changing climate and water availability strongly affect the current state of agricultural production. While the global temperature rises, the occurrence of extreme climatic conditions becomes erratic. This current scenario has driven the development of rice varieties and cultivation practices that require less water and favor mechanization. Although puddled transplanted rice has been more widely used in the past, direct seeding has been gaining popularity in recent years, especially due to its water- and labor-saving features. This technique allows full crop establishment from seeds that were directly sown in the field, thus avoiding puddling, transplanting, and maintaining standing water. Consequently, it offers promising positive environmental effects including decreasing the release of greenhouse gases and increasing water-use efficiency. Historically, rice varieties bred for transplanting are also used in direct seeding, which limits the maximum yield potential of field trials. The success of direct seeding relies strongly on the development of rice varieties with robust crop establishment. Anaerobic germination, seed longevity, and early seedling vigor are the key traits required to achieve this. This chapter expounds on the physiology, molecular mechanisms, genetics, and relevance of the enumerated traits for direct seeding. A brief discussion of breeding for rice varieties with improved germination under direct seeding is also provided.

Arsenic Stress Responses and Accumulation in Rice

Rice (Oryza sativa L.) is one of the world’s most vital staple grains, and 90% of it is produced and consumed in Asia alone. It plays a significant role in the entry of mineral nutrients into the food chain. Arsenic (As) is a toxic heavy metal that threatens the major rice-growing regions in the world, particularly in Asia. Arsenic is ubiquitously present in moderate concentrations in the environment because of natural geological processes and anthropogenic impacts. However, rapid industrialization and excessive use of arsenic-rich groundwater are further fueling the increased arsenic concentration in agricultural topsoil. Arsenic accumulation in rice plants has a significant adverse effect on plant, human, and livestock health. Although arsenic contamination in rice is well documented, its interaction and accumulation in rice are poorly understood. So far, no candidate genes or QTLs associated with arsenic interaction are used in breeding programs for the development of low-arsenic-accumulating rice varieties. The development and adaptation of new low-arsenic-accumulating rice cultivars resilient to arsenic toxicity constitute safe ways to mitigate arsenic contamination in rice. Recent scientific advances in rice genetics, genomics, and physiology have opened up new opportunities to speed up the process of developing low-arsenic-accumulating rice cultivars for the rapidly growing human population.

Strategies for Engineering Photosynthesis for Enhanced Plant Biomass Production

Crop productivity would have to increase by 60–110% compared with the 2005 level by 2050 to meet both the food and energy demands of the growing population. Although more than 90% of crop biomass is derived from photosynthetic products, photosynthetic improvements have not yet been addressed by breeding. Thus, it has been considered that enhancing photosynthetic capacity is considered a promising approach for increasing crop yield. Now, we need to identify the specific targets that would improve leaf photosynthesis to realize a new Green Revolution. This chapter summarizes the various genetic engineering approaches that can be used to enhance photosynthetic capacity and crop productivity. The targets considered for the possible candidates include Rubisco, Rubisco activase, enzymes of the Calvin–Benson cycle, and CO2 transport, as well as photosynthetic electron transport. Finally, it describes the importance of considering ways to improve photosynthesis not under the stable environmental conditions already examined in many studies with the aim of improving photosynthetic capacity, but under natural conditions in which various environmental factors, and especially irradiation, continually fluctuate.

Growing Rice with Less Water: Improving Productivity by Decreasing Water Demand

Rice is a staple food for more than half of the global population. With the increasing population, the yield of rice must correspondingly increase to fulfill the requirement. Rice is cultivated worldwide in four different types of ecosystems, which are limited by the availability of irrigation water. However, water-limiting conditions negatively affect rice production; therefore, to enhance productivity under changing climatic conditions, improved cultivation practices and drought-tolerant cultivars/varieties are required. There are two basic approaches to cultivation: (1) plant based and (2) soil and irrigation based, which can be targeted for improving rice production. Crop plants primarily follow three mechanisms: drought escape, avoidance, and tolerance. Based on these mechanisms, different strategies are followed, which include cultivar selection based on yield stability under drought. Similarly, soil- and irrigation-based strategies consist of decreasing non-beneficial water depletions and water outflows, aerobic rice development, alternate wetting and drying, saturated soil culture, system of rice intensification, and sprinkler irrigation. Further strategies involve developing drought-tolerant cultivars through marker-assisted selection/pyramiding, genomic selection, QTL mapping, and other breeding and cultivation practices such as early planting to follow escape strategies and decreasing stand density to minimize competition with weeds. Similarly, the identification of drought-responsive genes and their manipulation will provide a technological solution to overcome drought stress. However, it was the Green Revolution that increased crop production. To maintain the balance, there is a need for another revolution to cope with the increasing demand.

Genetics and Breeding of Low-Temperature Stress Tolerance in Rice

Low-temperature stress (LTS) is one of the major abiotic stresses that affect crop growth and ultimately decrease grain yield. The development of rice varieties with low-temperature stress tolerance has been a severe challenge for rice breeders for a long time. The lack of consistency of the quantitative trait loci (QTLs) governing LTS tolerance for any given growth stage over different genetic backgrounds of mapping populations under different low-temperature stress conditions remains a crucial barrier for adopting marker-assisted selection (MAS). In this review, we discuss the ideal location and phenotyping for agromorphological and physiological parameters as indicators for LTS tolerance and also the traits associated with QTLs that were identified from biparental mapping populations and diverse rice accessions. We highlight the progress made in the fields of genome editing, genetic transformation, transcriptomics, and metabolomics to elucidate the molecular mechanisms of cold tolerance in rice. The stage-specific QTLs and candidate genes for LTS tolerance brought out valuable information toward identifying and improving LTS tolerance in rice varieties. We showed 578 QTLs and 38 functionally characterized genes involved in LTS tolerance. Among these, 29 QTLs were found to be colocalized at different growth stages of rice. The combination of stage-specific QTLs and genes from biparental mapping populations and genome-wide association studies provide potential information for developing LTS-tolerant rice varieties. The identified colocalized stage-specific LTS-tolerance QTLs will be useful for MAS and QTL pyramiding and for accelerating mapping and cloning of the possible candidate genes, revealing the underlying LTS-tolerance mechanisms in rice.

Molecular Approaches for Disease Resistance in Rice

Rice production needs to be sustained in the coming decades, with changing climatic conditions becoming more conducive to the prevalence of disease outbreaks. Major rice diseases collectively cause enormous economic damage and yield instability. Breeding for disease-resistant rice varieties could be one of the best options to counter these disease outbreaks. Disease-screening protocols and newer technologies are essential for effective phenotyping and would aid in gene discovery and function. Understanding the genetics of disease mechanisms and stacking of broad-spectrum disease-resistance genes could lead to faster development of rice varieties with multiple disease resistance. New molecular breeding approaches are discussed for the development of these varieties. The molecular biology of disease resistance is now better understood and could be well manipulated for improved resilience. Transgenic approaches for disease resistance are discussed. Genome-editing tools for the development of disease-resistant rice varieties are thoroughly discussed. The use of bioinformatics tools to speed up the process and to obtain a better understanding of molecular genetics mechanisms of disease resistance is explained.

Biofortification of Rice Grains for Increased Iron Content

Dietary iron (Fe) deficiency affects 14% of the world population with significant health impacts. Biofortification is the process of increasing the density of vitamins and minerals in a crop, through conventional breeding, biotechnology approaches, or agronomic practices. This process has recently been shown to successfully alleviate micronutrient deficiency for populations with limited access to diverse diets in several countries (https://www.harvestplus.org/). The Fe breeding target in the HarvestPlus program was set based on average rice consumption to fulfil 30% of the Estimated Average Requirement of Fe in women and children. In this review, we present the reported transgenic approaches to increase grain Fe. Insertion of a single or multiple genes encoding iron storage protein, metal transporter, or enzyme involved in the biosynthesis of metal chelator in the rice genome was shown to be a viable approach to significantly increase grain-Fe density. The most successful approach to reach the Fe breeding target was by overexpression of multiple genes. Despite this success, a significant effort of 8–10 years needs to be dedicated from the proof of concept to varietal release. This includes large-scale plant transformation, event selection, collection of data for premarket safety assurance, securing biosafety permits for consumption and propagation, and collection of data for variety registration.