Legume Genomics and Genetics 2024, Vol.15, No.4, 176-186 http://cropscipublisher.com/index.php/lgg 179 Figure 1 QTL-seq applied to rice F2 progenyidentifies quantitative trait loci (QTLs) involvedin seedling vigor (Adopted from Takagi et al., 2013) Image caption: (a) Seedlings of Hitomebore and Dunghan Shali10 days after water imbibition. Dunghan Shalishows higher seedling vigor compared with Hitomebore. (b) Frequency distribution of seedling height in 531 F2 progenies 14 days after water imbibition. H and D indicate the average seedling height of Hitomebore and Dunghun Shali, respectively.We selected 50 F2 progeny shorter than 18 cm to make Low (L-) bulk and 50 progeny taller than 24 cm to make High (H-) bulk, and applied to QTL-seq using the Hitomebore reference genome sequence. (c) Results of QTL-seq for chromosome 3 (left) and 1 (right). The D (SNP-index) plot (top) with statistical confidence intervals under the null hypothesis of no QTL (gray, P < 0.1; green, P< 0.05; pink, P< 0.01) and log of odds (LOD)score plot of QTL controlling plant height as obtained by classical QTL analysis of 250 recombinant inbred lines of the F7 generation (bottom) (Adopted from Takagi et al., 2013) 4 Case Study: Enhancing Drought Tolerance in Soybeans Using Genomic Approaches 4.1 Introduction to drought stress in soybeans Drought stress is a significant environmental factor that adversely affects soybean productivity, leading to substantial yield losses. Soybeans are particularly sensitive to water-deficit conditions, which limit their growing area and overall production stability (Fuganti-Pagliarini et al., 2017; Shahriari et al., 2022). The increasing frequency and intensity of drought events due to climate change further exacerbate this issue, making it crucial to develop drought-tolerant soybean cultivars (Valliyodan et al., 2016; Dubey et al., 2019). 4.2 Genomic strategies for improving drought tolerance The identification of drought-responsive genes is a critical step in understanding and improving drought tolerance in soybeans. Comprehensive RNA-seq analyses have revealed numerous differentially expressed genes (DEGs) associated with drought tolerance. For instance, a study identified 4 850 and 6 272 DEGs in drought-tolerant and drought-sensitive soybean genotypes, respectively, highlighting genes involved in water and auxin transport, cell wall/membrane integrity, antioxidant activity, and transcription factor activities (Aleem et al., 2020). Another study identified 2 168 significant DEGs and core modules involved in key biological processes such as photosynthesis and cytokinin dehydrogenase activity, which are crucial for drought tolerance (Shahriari et al., 2022). Marker-assisted selection (MAS) and breeding strategies have been employed to enhance drought tolerance in soybeans. Genomic resources, including whole-genome sequences and high-throughput marker genotyping platforms, have facilitated the discovery of quantitative trait loci (QTLs) associated with drought tolerance traits such as root system architecture and nitrogen-fixation efficiency (Figure 2) (Valliyodan et al., 2016). Additionally,
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