Legume Genomics and Genetics 2024, Vol.15, No.4, 176-186 http://cropscipublisher.com/index.php/lgg 178 GS has been successfully applied in pulse crop breeding to improve traits such as yield, disease resistance, and stress tolerance. By integrating genomic data into breeding programs, researchers can make more informed decisions and accelerate the development of improved varieties. For example, the use of GBS in GS has enabled the efficient genotyping of large populations, facilitating the identification of superior genotypes for breeding. The implementation of GS in pulse crops holds great promise for enhancing productivity and sustainability in these important food crops. 3 Advancements in Pulse Crop Genomics 3.1 Genetic mapping and quantitative trait loci (QTL) analysis The advent of next-generation sequencing (NGS) technologies has revolutionized QTL mapping by providing high-resolution genetic maps and enabling the rapid identification of QTLs. Techniques such as QTL-seq, which involves whole-genome resequencing of DNA from bulked populations, have significantly accelerated the process of QTL identification. This method has been successfully applied in various crops, including rice, to identify QTLs for traits like disease resistance and seedling vigor (Figure 1) (Takagi et al., 2013). Additionally, the integration of NGS with traditional bulk-segregant analysis (BSA) has enhanced the resolution of QTL mapping, facilitating the detection of causative genes (Nguyen et al., 2019). Recent studies have identified numerous QTLs associated with key agronomic traits in pulse crops. For instance, in sorghum, an ultra-high-density linkage map constructed using SNPs from high-throughput sequencing revealed 57 major QTLs for traits such as plant height, flowering time, and grain yield under different photoperiods (Zou et al., 2012). Similarly, in cassava, QTL mapping has identified loci associated with productivity and plant architecture traits, highlighting the potential for marker-assisted selection to improve crop yields (Okogbenin and Fregene, 2003). These findings underscore the importance of QTL analysis in understanding the genetic basis of complex traits and enhancing pulse crop productivity. 3.2 Transcriptomics and gene expression profiling RNA sequencing (RNA-seq) has emerged as a powerful tool for transcriptomic analysis in pulse crops. This technology allows for the comprehensive profiling of gene expression, providing insights into the molecular mechanisms underlying various traits. RNA-seq has been instrumental in identifying differentially expressed genes and understanding their roles in stress responses, growth, and development (Kumar et al., 2017). Transcriptomic studies have yielded significant findings that contribute to our understanding of pulse crop biology. For example, RNA-seq has been used to identify genes involved in drought tolerance, disease resistance, and nutrient uptake. These studies have revealed the complex regulatory networks that govern these traits and have identified potential targets for genetic improvement. The integration of transcriptomic data with QTL mapping has further enhanced the identification of candidate genes and their functional validation (Shariatipour et al., 2021). 3.3 Functional genomics The CRISPR-Cas9 system has revolutionized functional genomics by enabling precise gene editing in pulse crops. This technology allows for the targeted modification of specific genes, facilitating the study of gene function and the development of improved crop varieties. CRISPR-Cas9 has been successfully used to knock out genes associated with undesirable traits and to introduce beneficial alleles, thereby enhancing crop performance (Xu et al., 2017). Functional genomics approaches, such as gene knockout and overexpression studies, have provided valuable insights into the roles of specific genes in pulse crops. These studies have identified key genes involved in traits such as yield, stress tolerance, and nutrient content. For instance, the overexpression of certain genes has been shown to improve drought tolerance and increase biomass production, while gene knockout studies have elucidated the functions of genes involved in disease resistance (Yang et al., 2012). These findings highlight the potential of functional genomics to drive the development of high-yielding, resilient pulse crop varieties.
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