Plant Gene and Trait 2024, Vol.15, No.2, 85-96 http://genbreedpublisher.com/index.php/pgt 89 Furthermore, the integration of multiple QTLs through pyramiding strategies poses a challenge due to potential epistatic interactions and the need for precise marker-assisted selection. Despite these challenges, ongoing advancements in genomic tools and mapping techniques continue to improve our ability to accurately map and utilize QTLs for enhancing rice grain quality. 4 Case Studies of QTL Application 4.1 Case study 1: impact of specific QTLs on rice grain texture The texture of rice grains is a critical quality trait that significantly influences consumer preference and market value. Several studies have identified and mapped QTLs associated with grain texture, providing insights into the genetic control of this trait. For instance, Zhou et al. (2019) study identified 36 QTLs for grain shape and weight, with qGL1.3 being a major QTL contributing significantly to grain length and weight. This QTL was fine-mapped to a 350 kb region on chromosome 1, laying the groundwork for its potential use in breeding programs aimed at improving grain texture (Figure 3). Figure 3 Fine mapping of qGL1.3 and its genotypic effects on grain length and thousand-grain weight (Adopted from Zhou et al., 2019) Image caption: The numbers below the bar indicate the number of recombinants between qGL1.3 and molecular markers. Values of grain length and 1000-grain weight are shown for representative BC1F3 lines (Y1-Y14). Each recombinant was progeny tested to deduce the qGL1.3genotype (Adopted from Zhou et al., 2019) Rahimsoroush et al. (2021) focused on the eating and cooking quality (ECQ) of rice, identifying 17 main QTLs with additive effects on traits such as amylose content, gelatinization temperature, and gel consistency. The study highlighted the importance of QTL clusters on chromosomes 6, 7, 8, and 9, which may control multiple ECQ traits through pleiotropic effects. These findings underscore the complexity of grain texture traits and the potential for QTL-based breeding to enhance rice quality. 4.2 Case study 2: QTLs influencing aromatic compounds in rice varieties Aroma is another key quality trait in rice, highly valued in premium varieties such as Basmati and Jasmine rice. The genetic basis of aroma in rice has been explored through QTL mapping, revealing several loci associated with this trait. Arikit et al. (2019) study identified QTLs for grain elongation, a trait often correlated with aromatic varieties, using bulk-segregant analysis and whole-genome sequencing. The study pinpointed QTLs on chromosomes 4 and 6, near genes involved in starch synthesis, which may indirectly influence aromatic compound production.
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