Rice Genomics and Genetics 2024, Vol.15, No.3, 142-152 http://cropscipublisher.com/index.php/rgg 142 Research Report Open Access Nutrient Content and Yield in Rice: Genetic Intersections and Breeding Opportunities Yumin Huang School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China Corresponding email: hym@xmu.edu.cn Rice Genomics and Genetics, 2024, Vol.15, No.3 doi: 10.5376/rgg.2024.15.0015 Received: 12 May, 2024 Accepted: 14 Jun., 2024 Published: 25 Jun., 2024 Copyright © 2024 Huang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Huang Y.M., 2024, Nutrient content and yield in rice: genetic intersections and breeding opportunities, Rice Genomics and Genetics, 15(3): 142-152 (doi: 10.5376/rgg.2024.15.0015) Abstract The domestication of Oryza sativa, a staple food crop for over half the global population, is a pivotal event in agricultural history. This study synthesizes findings from multiple studies to elucidate the pathways of rice domestication from its wild ancestor, Oryza rufipogon. Phylogeographic analyses suggest that O. rufipogon exhibits a center of diversity in India and Indochina, with evidence supporting at least two independent domestication events leading to the major rice varieties, O. sativa indica and O. sativa japonica. Genome sequencing of a wide array of O. rufipogon and cultivated rice varieties has identified selective sweeps and domestication-associated traits, pinpointing the origin of O. sativajaponica to the Pearl River's middle area in southern China and the subsequent development of O. sativa indica from crosses between japonica and local wild rice. Furthermore, a comparative genomics study of Dongxiang wild rice and Nipponbare (O. sativa) has revealed significant structural variations and gene flow, highlighting the role of transposable elements and adaptations in the photophosphorylation and oxidative phosphorylation systems during domestication. This study integrates these insights to provide a comprehensive understanding of the genetic and evolutionary processes that have shaped the domestication of rice. Keywords Oryza sativa; Oryza rufipogon; Domestication; Phylogeography; Genome variation 1 Introduction Rice (Oryza sativa L.) is a fundamental staple food for more than half of the world's population, particularly in Asia, Africa, and Latin America. It provides a significant portion of the daily caloric intake and is a primary source of nutrition for billions of people (Yu et al., 2009). In many developing countries, rice contributes at least 20% of dietary protein and 3% of dietary fat, making it an essential component of the diet. Globally, rice is cultivated on approximately 166.1 million hectares, with an annual production of around 745.2 million tonnes (Gregorio, 2002). In India alone, rice is grown on 43.5 million hectares, producing 90 million tonnes annually, which accounts for 23% of the country's gross cropped area (Naik et al., 2020). These statistics underscore the critical role of rice in global food security and the agricultural economy. Rice is not only a staple food but also a significant source of essential nutrients. It provides 43% of the caloric requirement and 20%~25% of agricultural income in many regions (Xu et al., 2016). However, the nutritional quality of rice can be enhanced through breeding and genetic engineering to address micronutrient deficiencies, such as iron and zinc, which are crucial for human health. Biofortification efforts have shown promise in increasing the concentration of these essential minerals in rice grains (Naik et al., 2020). The economic impact of rice yield is profound, as it directly influences food security and the livelihoods of millions of farmers. High-yielding rice varieties are essential to meet the growing global demand and to ensure economic stability in rice-producing regions (Meena et al., 2023). The development of hybrid rice varieties has demonstrated significant yield increases, contributing to global food security (Das et al., 2020). Recent research has focused on the genetic relationship between grain yield and nutrient content in rice. Studies have identified quantitative trait loci (QTLs) that influence both yield and nutritional components, such as protein and fat content. The integration of genomics and metabolomics in breeding programs has further enhanced the
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