Legume Genomics and Genetics 2024, Vol.15, No.3, 105-117 http://cropscipublisher.com/index.php/lgg 106 genome assemblies, genotyping-by-sequencing, and comparative genomics, this study will highlight key discoveries and their implications for pea breeding and crop improvement. The scope of the study encompasses the genetic architecture of domestication traits, the identification of selective sweeps, and the application of genomic tools in pea research and breeding. Through this synthesis, the study aims to advance our understanding of pea evolution and support ongoing efforts to enhance the genetic potential of this important crop. 2 Genomic Structure and Evolution 2.1 Basic genome structure of peas The pea (Pisum sativumL.) genome is characterized by its large size and high content of repetitive DNA elements. The first annotated chromosome-level reference genome assembly for pea has provided significant insights into its genomic structure. This reference genome revealed that the pea genome is dominated by LTR-retrotransposons, particularly Ty3/gypsy elements, which are less diverse but more abundant than Ty1/copia elements. Notably, Ogre-like retrotransposons alone constitute over 20% of the genome. Additionally, the genome contains novel satellite repeats and variants of telomeric sequences, further contributing to its complexity (Macas et al., 2007; Kreplak et al., 2019). 2.2 Comparative genomics with related legumes Comparative genomics has been instrumental in understanding the evolutionary relationships between peas and other legumes. Syntenic relationships between pea and other legume genomes, such as Medicago truncatula and soybean, have been established, revealing blocks of synteny that provide insights into the evolution of chromosome structure in legumes (Bordat et al., 2011; Smýkal et al., 2012; Tayeh et al., 2015). The development of the GenoPea 13.2 K SNP Array and high-density genetic maps has further facilitated the identification of syntenic networks and the localization of important agronomic traits (Tayeh et al., 2015). Additionally, a hierarchical alignment of legume genomes has illustrated genomic fractionation and gene loss patterns following polyploidization events, highlighting the evolutionary divergence among legume species (Wang et al., 2017). 2.3 Major evolutionary events in pea genomics The evolutionary history of peas has been shaped by several major events, including genomic rearrangements, translocations, and transpositions. Phylogenetic analyses have shown that the pea genome has undergone significant gene dynamics, likely associated with genome size expansion during the divergence of the Fabeae tribe from its sister tribes (Figure 1) (Kreplak et al., 2019). The integration of genotyping-by-sequencing data from different germplasm collections has provided a comprehensive view of pea biodiversity and population structure, reflecting genetic variation based on geographic patterns and identifying putative selective sweeps associated with domestication and breeding (Pavan et al., 2022). Furthermore, the discordant evolution of organellar genomes in peas, driven by hybridization events and plastid-nuclear incompatibility, has contributed to the complex evolutionary landscape of the species (Bogdanova et al., 2018; Bogdanova et al., 2020). In summary, the genomic structure and evolution of peas have been shaped by a combination of repetitive DNA accumulation, syntenic relationships with related legumes, and significant evolutionary events such as genomic rearrangements and hybridization. These insights not only enhance our understanding of pea genomics but also provide valuable information for crop improvement and conservation efforts. 3 Domestication of Peas 3.1 Historical perspectives on pea domestication Pea (Pisum sativum L.) is one of the oldest domesticated crops, with a history that dates back to the Neolithic period. The domestication of peas is believed to have occurred in the Fertile Crescent, a region known for the early development of agriculture. Historical evidence suggests that peas were among the first crops to be cultivated by humans, alongside other staple crops such as wheat and barley (Pavan et al., 2022; Hellwig et al., 2022). The spread of pea cultivation from its center of origin to other parts of the world followed a pattern similar to other domesticated crops, facilitated by human migration and trade.
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