Plant Gene and Trait 2024, Vol.15, No.5, 230-242 http://genbreedpublisher.com/index.php/pgt 232 in genomics have facilitated the identification of key genes such as GS3, GW5, and qSW5, which play significant roles in determining grain shape (Niu et al., 2020; Meng et al., 2022). Recent studies have also identified new QTLs and candidate genes through GWAS, further expanding researchers’ understanding of the genetic architecture underlying grain shape. For example, GWAS has uncovered QTLs such as qTGW3.1, qTGW9, and qGL4, which are involved in regulating grain size and shape (Feng et al., 2016; Zhou et al., 2019; Niu et al., 2021). Moreover, advanced populations such as the MAGIC have provided deeper insights into the genetic diversity governing grain traits (Ponce et al., 2020), enabling the discovery of multiple alleles that contribute to grain shape variation. The integration of these genetic insights into breeding programs holds promise for the development of rice varieties with optimized grain shapes tailored to specific market preferences (Misra et al., 2018; Kang et al., 2021). 3 Palatability of Rice: Factors and Attributes 3.1 Defining rice palatability and its importance in breeding programs Rice palatability refers to the sensory attributes that determine the acceptability and preference of rice by consumers. These attributes include texture, flavor, appearance, and aroma which together create the overall eating experience. A key component affecting palatability is the amylose content, which significantly influences the texture of cooked rice. Higher amylose content results in firmer, less sticky rice, while low amylose varieties tend to be softer and more adhesive (Misra et al., 2018). Textural attributes such as adhesiveness, hardness, springiness, and cohesiveness are vital in determining how rice feels in the mouth, making texture one of the most critical aspects of palatability (Huang et al., 2013). In addition to texture, aroma plays a significant role in consumer preference, especially in aromatic rice varieties such as Jasmine and Basmati. These varieties possess 2-acetyl-1-pyrroline (2-AP), a compound that imparts a distinct, appealing fragrance (Buttery et al., 1983). The integrated value of organoleptic evaluation, which includes luster and tenderness, also plays a crucial role in determining the overall palatability of rice (Wan et al., 2004). Palatability is a critical factor in rice breeding programs because it directly impacts consumer acceptance and market value. Breeding for improved palatability involves selecting desirable textural properties and other sensory attributes that meet consumer preferences. The identification of QTLs associated with palatability traits enables breeders to use marker-assisted selection to develop rice varieties with enhanced eating quality (Wan et al., 2004; Tang et al., 2005). Consistently producing rice varieties with improved palatability not only increases consumer satisfaction but also boosts economic returns for farmers and producers, making it a critical focus in modern rice breeding (Wan et al., 2004; Huang et al., 2013; Misra et al., 2018). 3.2 Genetic factors influencing palatability The genetic basis of rice palatability is complex and involves multiple genes and QTLs. Studies have identified several QTLs that influence various aspects of rice palatability, such as amylose content, adhesiveness, and other textural properties. A GWAS identified significant QTLs on chromosome 6 that are associated with amylose content and adhesiveness, which are key determinants of rice texture and palatability (Misra et al., 2018). Additionally, QTLs for luster, tenderness, and the integrated value of organoleptic evaluation have been mapped to specific regions on chromosomes 6 and 8, indicating their importance in rice quality improvement (Wan et al., 2004). The identification and validation of these QTLs provide valuable resources for breeding programs aimed at enhancing rice palatability (Wan et al., 2004; Tang et al., 2005; Misra et al., 2018). 4 Methodologies in Genome-Wide Studies of Rice 4.1GWAS GWAS are a powerful tool used to identify genetic loci associated with specific traits in rice. This method involves scanning the entire genome for single nucleotide polymorphisms (SNPs) that occur more frequently in individuals with a particular trait. For instance, a study utilized multiple GAPIT models and high-density SNP chip DNA markers (Figure 1) to identify QTLs associated with grain shape and size in rice. The study revealed significant associations between SNP markers and QTLs for grain length, width, and thickness across various chromosomes, explaining a substantial portion of the phenotypic variance (Kabange et al., 2023). Another study
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