Molecular Plant Breeding 2024, Vol.15, No.5, 308-316 http://genbreedpublisher.com/index.php/mpb 311 Figure 2 Integration of GBS derived high density SNPs and multi-season phenotyping data for mapping of drought QTLs in rice (Adopted from Yadav et al., 2019) 3.3 Case studies Several studies highlight the practical applications of these QTLs in rice breeding. For instance, the identification of QTLs for yield components in the F2 and F3 populations has facilitated the development of rice varieties with improved yield stability across different environments. In another case, the validation of QTLs through SNP genotyping in the RIL population has enabled the identification of novel major effect QTLs with better resolution and precision, which can be utilized in the development of superior rice hybrids (Figure 3) (Kulkarni et al., 2020). Additionally, the use of meta-analysis to integrate QTL data from multiple studies has led to the identification of consensus QTL regions and candidate genes, which can be targeted for marker-assisted selection (MAS) to improve rice yield (Swamy and Sarla, 2011). 4 Key QTLs for Rice Quality 4.1 Major QTLs associated with grain quality traits Grain quality in rice is influenced by several quantitative trait loci (QTLs) that govern traits such as grain length, grain width, chalkiness, and milling quality. Notable QTLs identified for these traits include qGL5, qPGWC-5 and qHR. qGL5 is associated with grain length and is located on chromosome 5. It has been shown to significantly influence the grain length to width ratio (LWR) and grain thickness (GT) (Gao et al., 2016). qPGWC-5 is found on chromosome 5, this QTL controls the percentage of grain with chalkiness (PGWC), a critical trait affecting the visual quality of rice grains (Gao et al., 2016). qHR is linked to head-rice yield (HR), a key milling quality trait. It has been mapped in recombinant inbred lines (RILs) derived from a cross of L-204 and 01Y110, showing consistent expression across multiple environments (Nelson et al., 2012). 4.2 Mechanisms of action The mechanisms by which these QTLs influence grain quality traits involve various genetic and molecular pathways. qGL5 affects grain length by regulating cell division and elongation in the developing grain. The alleles at this locus contribute to variations in grain dimensions, which are crucial for market preferences and processing quality (Gao et al., 2016). The action of qPGWC-5 involves the regulation of starch synthesis and
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