Legume Genomics and Genetics 2024, Vol.15, No.6, 291-302 http://cropscipublisher.com/index.php/lgg 296 transcriptome profiling using RNA-Seq can identify differentially expressed genes (DEGs) under drought conditions, providing insights into the genetic mechanisms underlying drought tolerance and identifying potential candidate genes for marker development (Aleem et al., 2020). 5.2 High-throughput sequencing technologies and genotyping High-throughput sequencing technologies, such as Whole-Genome Resequencing (WGRS) and RNA-Seq, have revolutionized the field of genotyping and marker development. WGRS allows for the comprehensive analysis of genetic variation across the entire genome, facilitating the identification of SNPs and structural variants associated with drought tolerance (Patil et al., 2016). This technology has been used to identify high-quality SNP markers that can be employed in marker-assisted selection (MAS) programs to develop drought-tolerant soybean cultivars. RNA-Seq, on the other hand, provides a detailed view of the transcriptome, enabling the identification of DEGs under drought stress. This approach has been used to compare root transcriptome profiles of drought-tolerant and drought-sensitive soybean genotypes, leading to the identification of key genes and pathways involved in drought response (Aleem et al., 2020). The integration of high-throughput sequencing data with phenotypic data allows for the precise mapping of QTLs and the development of robust molecular markers for drought tolerance. 5.3 Importance of genome-wide association studies (GWAS) and linkage mapping Genome-Wide Association Studies (GWAS) and linkage mapping are critical tools in the identification of genetic loci associated with drought tolerance in soybean. GWAS leverages the natural genetic variation present in diverse germplasm collections to identify significant associations between genetic markers and drought tolerance traits. This approach has been used to identify numerous QTLs and candidate genes associated with drought tolerance in soybean. The use of multi-locus multi-allele GWAS has further enhanced the resolution and accuracy of QTL mapping, providing a comprehensive understanding of the genetic architecture of drought tolerance (Wang et al., 2020). Linkage mapping, on the other hand, involves the use of bi-parental populations to map QTLs associated with drought tolerance. This method has been successfully employed to identify QTLs related to various drought tolerance traits, such as relative water content, root length, and grain yield, in soybean (Can, 2011). The integration of GWAS and linkage mapping results can provide a more complete picture of the genetic basis of drought tolerance, facilitating the development of effective MAS programs for breeding drought-tolerant soybean cultivars. 6 Marker-Assisted Breeding Programs in Soybean 6.1 Overview of MAS breeding programs targeting drought tolerance in soybean Marker-Assisted Selection (MAS) has emerged as a powerful tool in the breeding of drought-tolerant soybean varieties. This approach leverages molecular markers to identify and select for desirable traits, thereby accelerating the breeding process and improving the precision of selection. The application of MAS in soybean breeding programs has focused on identifying quantitative trait loci (QTLs) associated with drought tolerance and introgressing these traits into elite cultivars. Several studies have demonstrated the effectiveness of MAS in improving drought tolerance in various crops, which provides a strong foundation for its application in soybean. For instance, MAS has been successfully used to improve drought adaptation in maize by introgressing favorable alleles at target regions involved in yield components and flowering traits, resulting in significant yield improvements under water-limited conditions (Ribaut and Ragot, 2006). Similarly, in common bean, MAS has been employed to identify RAPD markers associated with drought resistance, leading to improved performance under stress conditions. These successes highlight the potential of MAS to enhance drought tolerance in soybean by targeting specific QTLs and genes associated with drought resistance. In soybean, the identification of QTLs related to drought tolerance has been a key focus. For example, a study identified multiple QTLs associated with drought tolerance in a Recombinant Inbred Line (RIL) population, which could be utilized in MAS to develop drought-tolerant soybean varieties (Dhungana et al., 2021).
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