Plant Gene and Trait 2024, Vol.15, No.2, 85-96 http://genbreedpublisher.com/index.php/pgt 85 Feature Review Open Access From QTLs to Field: Mapping the Genetic Determinants of Rice Grain Quality Jianquan Li Hier Rice Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: jianquan.li@hitar.org Plant Gene and Trait, 2024, Vol.15, No.2 doi: 10.5376/pgt.2024.15.0010 Received: 09 Mar., 2024 Accepted: 13 Apr., 2024 Published: 21 Apr., 2024 Copyright © 2024 Li, 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: Li J.Q., 2024, From QTLs to field: mapping the genetic determinants of rice grain quality, Plant Gene and Trait, 15(2): 85-96 (doi: 10.5376/pgt.2024.15.0010) Abstract Rice grain quality is a critical determinant of market value and consumer preference, necessitating the identification and mapping of quantitative trait loci (QTLs) associated with key quality traits. This study synthesizes recent advancements in high-resolution QTL mapping and genetic analysis to elucidate the genetic determinants of rice grain quality. Studies employing genotyping-by-sequencing and next-generation sequencing have identified numerous QTLs linked to traits such as grain shape, chalkiness, and cooking quality. For instance, high-density genetic maps have facilitated the discovery of novel QTLs for grain transparency and chalkiness, with significant phenotypic variation explained by these loci. Meta-analyses have further refined these findings, pinpointing meta-QTLs associated with essential micronutrients like iron and zinc, which are crucial for biofortification efforts. Additionally, fine mapping of specific QTLs has revealed candidate genes that play pivotal roles in grain quality traits, offering new genetic resources for breeding programs. This study underscores the importance of integrating high-resolution mapping techniques and functional genomics to accelerate the genetic improvement of rice grain quality. Keywords Quantitative trait loci (QTL); Rice grain quality; Genotyping-by-sequencing; Chalkiness; Biofortification 1 Introduction Rice (Oryza sativa L.) is a staple food for more than half of the world’s population, making its grain quality a critical factor in global food security and market value. The quality of rice grains encompasses various attributes, including cooking and eating quality, nutritional content, and physical appearance, all of which are influenced by genetic and environmental factors (Raza et al., 2019; Zhang et al., 2020; Jin et al., 2023). As consumer preferences and nutritional demands evolve, improving rice grain quality has become a primary objective for breeders worldwide (Chen et al., 2012; Das et al., 2020). Grain quality in rice is a multifaceted trait that significantly impacts its marketability and consumer acceptance. Key quality attributes include amylose content, gelatinization temperature, gel consistency, grain size, and chalkiness (Qin et al., 2015; Zhu et al., 2018; Zhang et al., 2020). For instance, amylose content and gelatinization temperature are crucial for determining the texture and cooking properties of rice, which vary according to regional preferences (Chen et al., 2012; Zhang et al., 2020). In addition, the nutritional quality of rice, such as its iron and zinc content, is vital for addressing micronutrient deficiencies in developing countries (Raza et al., 2019; Das et al., 2020). Therefore, enhancing grain quality not only meets consumer demands but also contributes to nutritional security and economic value. Quantitative Trait Loci (QTLs) are genomic regions that contribute to the variation in complex traits, such as grain quality in rice. Identifying and mapping QTLs associated with grain quality traits enable breeders to understand the genetic basis of these traits and facilitate marker-assisted selection (MAS) (Wang et al., 2021; Sharma et al., 2021; Jin et al., 2023). High-resolution QTL mapping and genome-wide association studies (GWAS) have identified numerous QTLs linked to key quality traits, including grain size, chalkiness, and nutritional content (Qiu et al., 2015; Zhu et al., 2018; Jin et al., 2023). For example, the Wx locus is a well-known QTL that influences amylose content and gel consistency, while novel QTLs such as qGC10 and qGL11 have been identified for gel consistency and grain length, respectively (Zhang et al., 2020; Wang et al., 2021). These discoveries provide valuable genetic resources for improving rice grain quality through breeding programs.
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