Legume Genomics and Genetics 2024, Vol.15, No.5, 244-256 http://cropscipublisher.com/index.php/lgg 245 This study evaluates the successes and challenges of translational genomics in legume breeding and proposes strategies for integrating genomic technologies into legume breeding programs to address biotic and abiotic stresses. It further emphasizes the potential socio-economic impacts of improving legume varieties for smallholder farmers and global food security. The aim is to understand the current state of legume genomics, its application in crop improvement, and to identify key genomic resources and tools that can be used to enhance the stress resistance and yield of legume crops. 2 Advances in Legume Genomics 2.1 Overview of genomic resources in legumes Recent advancements in genomics have significantly contributed to the development of extensive genomic resources for legume crops. These resources include large-scale sequence data, genome-wide molecular markers, genetic linkage maps, and trait mapping tools. Such developments have been pivotal in understanding genome architecture and dynamics, facilitating gene discovery, and enhancing crop productivity (Varshney et al., 2015; Afzal et al., 2019; Jha et al., 2022). The establishment of comprehensive transcriptome assemblies and genome sequences for major legume crops like chickpea, pigeonpea, and groundnut has transformed these species from 'orphan' crops to 'genomic resources rich' crops (Varshney et al., 2013). 2.2 Sequencing technologies and their impact on legume genomics The advent of next-generation sequencing (NGS) technologies has revolutionized legume genomics by enabling high-throughput genotyping and phenotyping. NGS has facilitated the sequencing and re-sequencing of important legume species, making structural variation and functional genomics studies feasible (Afzal et al., 2019; Salgotra and Stewart, 2022). These technologies have allowed for the accurate and accelerated delivery of genomic information, which is crucial for breeding programs aimed at improving legume crop yield and resilience (O’Rourke et al., 2014). The application of RNA sequencing (RNA-Seq) has provided considerable insights into gene characterization and expression profiling, especially in species with limited genomic information. 2.3 Key legume genome projects and achievements Several key genome projects have been undertaken to enhance our understanding of legume genomics. For instance, the genome sequencing of model legumes like Medicago truncatula has provided valuable insights into gene families of practical importance and facilitated marker development and gene discovery in related crop species (Young and Udvardi, 2009). The translational genomics approach has been successfully applied to place thousands of unigenes on the pea functional map, identifying candidate genes for important traits (Bordat et al., 2011). Additionally, comprehensive genome assemblies and resequencing efforts have been completed for various legume crops, aiding in the identification of genes underlying traits of breeding importance (Figure 1) (Jha et al., 2022). 2.4 Functional genomics approaches: gene annotation, expression profiling, and mutant libraries Functional genomics in legumes encompasses a range of approaches, including RNA transcription, protein expression, and metabolomics. The development of resources such as transcriptomes, proteomes, metabolomes, and mutant libraries has been instrumental in identifying genes that play essential roles in plant resistance to biotic and abiotic stresses, protein and oil accumulation in seeds, and beneficial plant-microbe symbiosis (Libault and Dickstein, 2014). Techniques like TILLING (Targeting Induced Local Lesions IN Genomes) have been employed to create mutant libraries, providing powerful tools for functional genomics studies. These approaches have already yielded valuable information for enhancing legume productivity and hold promise for future advancements. 3 Translational Genomics: From Model Legumes to Crops 3.1 Definition and scope of translational genomics Translational genomics involves the application of genomic insights and technologies from model organisms to improve and enhance the traits of crop species. This field bridges the gap between basic genomic research and practical agricultural applications, aiming to transfer knowledge gained from model species to economically
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