Plant Gene and Trait 2024, Vol.15, No.5, 230-242 http://genbreedpublisher.com/index.php/pgt 230 Feature Review Open Access Genetic Basis of Rice Grain Shape and Palatability: A Genome-Wide Study Review Nant Nyein Zar Ni Naing1,4, Chunli Wang1,3, Cui Zhang1,3, Junjie Li 1,3, JuanLi 1,2,3, QianZhu1,2,3, Lijuan Chen1,2,3 , Dongsun Lee 1,2,3 1 Rice Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 2 The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 3 State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 4 Department of Plant Breeding, Physiology and Ecology, Yezin Agricultural University (YAU), Nay Pyi Taw, 15013, Myanmar Corresponding email: chenlijuan@hotmail.com Plant Gene and Trait, 2024, Vol.15, No.5 doi: 10.5376/pgt.2024.15.0023 Received: 19 Aug., 2024 Accepted: 22 Sep., 2024 Published: 30 Sep., 2024 Copyright © 2024 Ni Naing et al., 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: Ni Naing N.N.Z., Wang C.L., Zhang C., Li J.J., Li J., Zhu Q., Chen L.J., and Lee D.S., 2024, Genetic basis of rice grain shape and palatability: a genome-wide study review, Plant Gene and Trait, 15(5): 230-242 (doi: 10.5376/pgt.2024.15.0023) Abstract The genetic basis of grain shape and palatability of rice is complex, involving multiple genes and QTLs. The combination of Genome-wide association study (GWAS) and functional genomics has greatly improved researchers' understanding of these traits. GWAS has identified important loci and candidate genes that regulate grain shape, including GS3, GW5, and qSW5, and discussed natural variation and artificial selection of these key genes, which play a critical role in the formation of grain size and quality during evolution. This paper highlights the importance of allelic combination and haplotype analysis in understanding the genetic structure of grain shape and palatability, and these findings provide a strong framework for future rice breeding programs to improve grain yield and quality. This paper is expected to provide a comprehensive review of the genetic basis of rice grain shape and palatability through genome-wide analysis, and to identify key genes and quantitative trait loci (QTLs) that influence these traits, thereby offering valuable insights for rice breeding programs. Keywords Rice grain shape; Quantitative trait loci (QTLs); Genome-wide association study (GWAS); Genetic variation; Rice breeding 1 Introduction Rice (Oryza sativa L.) is a staple food for over half of the world's population, making its yield and quality critical for global food security. Among the various factors influencing rice quality, grain shape and palatability are paramount. Grain shape, which includes attributes such as grain length, width, and thickness, significantly affects both the yield potential and market value of rice (Wang et al., 2012; Jahani et al., 2013; Niu et al., 2020). Palatability, encompassing taste, texture, and overall eating quality, is equally important for consumer acceptance and marketability. Grain shape is controlled by multiple QTLs and genes, making it a complex trait to study and manipulate. Advances in genomics and molecular biology have facilitated the identification of numerous QTLs and genes associated with grain shape, providing valuable insights for rice breeding programs aimed at improving both yield and quality (Huang et al., 2013; Zheng et al., 2015; Nawaz et al., 2015). Recent advancements in high-throughput sequencing technologies and genomics have further elucidated the genetic basis of these traits (Zhang et al., 2020). GWAS have become a powerful tool for uncovering the genetic basis of complex traits in rice, including grain shape and palatability. The 3 000 Rice Genomes Project (3K RGP) has been instrumental in this regard, enabling the discovery of valuable genetic variants and resources for grain weight and shape (Niu et al., 2020; Niu et al., 2021). Through GWAS, researchers have identified numerous QTLs and candidate genes that play crucial roles in determining grain shape and quality (Huang et al., 2016; Niu et al., 2020; Meng et al., 2022). For instance, recent studies have identified several novel QTLs and candidate genes associated with grain weight and shape, such as qTGW3.1, qTGW9, qTGW11, qGL4/qRLW4, qGL10, and qRLW1 (Niu et al., 2020; Niu et al., 2021). These
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