Legume Genomics and Genetics 2024, Vol.15, No.3, 105-117 http://cropscipublisher.com/index.php/lgg 113 9 Challenges and Future Directions 9.1 Gaps in current genomic knowledge Despite significant advancements in pea genomics, several gaps remain. The first annotated chromosome-level reference genome for pea has provided a foundation for understanding legume genome evolution and the molecular basis of agronomically important traits (Kreplak et al., 2019). However, the complexity of the pea genome, characterized by intense gene dynamics and large genome size, poses challenges for comprehensive genomic studies. Additionally, while translational genomics has identified numerous candidate genes and syntenic relationships, the functional characterization of these genes remains incomplete (Bordat et al., 2011). The integration of different genotyping-by-sequencing datasets has expanded our understanding of pea biodiversity, yet the loss of information during this process indicates that more comprehensive datasets are needed (Pavan et al., 2022). Furthermore, the identification of genomic regions under selection in domesticated pea groups suggests that there are still undiscovered genetic bases of domestication (Hellwig et al., 2022). 9.2 Integrating genomics with phenomics The integration of genomic data with phenomic data is crucial for advancing our understanding of pea domestication and diversity. Recent studies have highlighted the importance of combining genomic and phenomic resources to elucidate the genetic architecture of complex traits (Turner-Hissong et al., 2019). Advanced molecular technologies, such as genome-wide association studies and population genetic screens, have revealed diverse mutations affecting domestication traits (Olsen and Wendel, 2013). However, the challenge lies in effectively integrating these genomic insights with phenotypic data to inform breeding strategies. The development of high-density SNP arrays and consensus genetic maps has provided valuable tools for genotyping and mapping, but their application in phenomic studies is still in its early stages (Tayeh et al., 2015). Moreover, the identification of genomic hotspots of differentiation in pea aphid host races underscores the potential for similar approaches in pea to uncover adaptive divergence and ecological isolation (Nouhaud et al., 2018). 9.3 Prospects for future research and crop improvement Future research in pea genomics should focus on addressing the existing gaps and enhancing the integration of genomics with phenomics. One promising direction is the use of genomic selection (GS) to improve breeding accuracy and efficiency. Studies have shown that GS can significantly enhance the prediction accuracy of important traits, such as seed weight and flowering time, by leveraging genome-wide molecular marker data (Tayeh et al., 2015). Additionally, the development of community resources and collaborative efforts will be essential for advancing pea genomics. The creation of comprehensive genomic databases and bioinformatics tools, such as the translational toolkit for pea, will facilitate the identification and functional characterization of candidate genes (Bordat et al., 2011). Furthermore, the application of precision gene editing technologies holds great potential for targeted crop improvement by leveraging the genetic insights gained from evolutionary genomics studies (Turner-Hissong et al., 2019). Overall, the integration of advanced genomic and phenomic approaches, coupled with collaborative research efforts, will pave the way for significant advancements in pea domestication and crop improvement. 10 Concluding Remarks The evolutionary genomics of peas (Pisum sativumL.) has provided significant insights into their domestication and genetic diversity. The integration of genotyping-by-sequencing (GBS) data from different germplasm collections has allowed for a comprehensive analysis of pea biodiversity, revealing geographic patterns of genetic variation and identifying selective sweeps associated with domestication and breeding. The development of the GenoPea 13.2 K SNP Array and high-density genetic maps has further elucidated the structure and organization of the pea genome, facilitating the identification of important agronomic traits. Despite the challenges posed by the large and repetitive nature of the pea genome, significant progress has been made in understanding its evolution and the genetic basis of key traits. Studies on genetic diversity and population structure have highlighted the substantial variation within the cultivated genepool and the potential of wild material to introduce novel traits.
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