Legume Genomics and Genetics 2024, Vol.15, No.4, 187-198 http://cropscipublisher.com/index.php/lgg 189 resilience and adaptability. However, the identification of domestication-responsive loci and the use of modern genomic tools, such as whole genome sequencing and gene-editing technologies, offer opportunities to reintroduce genetic diversity and improve crop traits (Bohra et al., 2022). Additionally, the study of phylogenetic relationships among legume species has revealed complex evolutionary histories, including instances of polyploidy and hybridization, which have contributed to the diversification and success of legume crops (Delêtre et al., 2017; Koenen et al., 2020). Understanding these evolutionary processes is crucial for developing strategies to enhance the genetic diversity and resilience of modern legume cultivars. 3 Phylogenetic Relationships among Domesticated Legumes 3.1 Methods for constructing phylogenetic trees Molecular markers and DNA sequencing are fundamental tools in constructing phylogenetic trees. Various types of molecular markers, such as microsatellites (SSR) and single nucleotide polymorphisms (SNPs), are used to assess genetic diversity and relationships among legume species. For instance, microsatellite markers have been effectively used to evaluate the genetic diversity of Vigna stipulacea, revealing significant variation and clustering accessions into distinct clades (Gore et al., 2022). Additionally, sequencing of specific genes, such as the plastid matK gene, has provided high-resolution phylogenetic trees for legumes, supporting well-resolved subclades within the family (Wojciechowski et al., 2004). Computational approaches play a crucial role in analyzing large-scale genomic data to infer phylogenetic relationships. Methods such as maximum likelihood, Bayesian inference, and multispecies coalescent models are commonly employed. For example, a study utilizing 72 chloroplast genes and 7 621 nuclear-encoded proteins across 157 taxa employed these computational methods to resolve deep divergences in the legume phylogeny, despite challenges like incomplete lineage sorting (Figure 2) (Koenen et al., 2019). These approaches help in constructing robust phylogenetic frameworks and understanding evolutionary processes. 3.2 Phylogenetic analysis of major domesticated legume species The common bean has been extensively studied for its phylogenetic relationships and genetic diversity. Genotyping-by-sequencing (GBS) has revealed the presence of two major gene pools, Mesoamerican and Andean, with evidence of hybridization events between them (Lioi et al., 2019). Additionally, the assembly of the common bean genome and comparison with the soybean genome have provided insights into the genetic changes associated with domestication (Schmutz et al., 2014). Chickpea phylogenetic studies often focus on its genetic diversity and domestication history. Molecular markers and sequencing data have been used to trace the evolutionary relationships and divergence times within the species, contributing to a better understanding of its domestication and adaptation processes (Smýkal et al., 2015). Lentil phylogenetic analysis involves the use of molecular markers to assess genetic diversity and relationships among different accessions. These studies help in identifying key traits and understanding the evolutionary history of lentils, which is crucial for breeding and conservation efforts. Soybean phylogenetic studies have utilized both molecular markers and whole-genome sequencing. Comparative genomic analyses between soybean and other legumes, such as Medicago truncatula, have highlighted the conservation and divergence of genomic regions, providing insights into the evolutionary history and domestication of soybean (Choi et al., 2004; Pfeil et al., 2005). 3.3 Phylogenetic insights into legume evolution Phylogenetic studies have provided significant insights into the divergence times and evolutionary relationships among legume species. For example, the simultaneous origin of all six subfamilies of legumes suggests a rapid speciation event, challenging the traditional view of basal and early-diverging subfamilies (Koenen et al., 2019). Additionally, the reconstruction of ancestral genomes has revealed the chromosomal evolution history of legumes, indicating a common ancestor with nine chromosomes (Ren et al., 2019). The phylogenetic insights gained from these studies have important implications for the classification and taxonomy of legumes. For instance, the reestablishment of the tribe Diocleae within the Millettioid clade based on molecular phylogenetic analysis has clarified the higher-level phylogeny and generic relationships within this
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