Legume Genomics and Genetics 2024, Vol.15, No.4, 187-198 http://cropscipublisher.com/index.php/lgg 188 This study aims to combine phylogenetic and genetic diversity approaches to better illustrate the origin, domestication history, and preserved germplasm of major legume crops. Specifically, the objectives are to elucidate the phylogenetic relationships among domesticated legumes using comprehensive genomic data, to assess the genetic diversity within and between different legume species, and to identify key genetic traits that have been selected during domestication. Additionally, the study seeks to provide insights into the potential for future crop improvement through the integration of phylogenetic and genetic diversity data, thereby enhancing the resilience and nutritional quality of legume crops. By achieving these objectives, this study will contribute to a deeper understanding of the evolutionary and genetic foundations of domesticated legumes, paving the way for more effective and sustainable agricultural practices. 2 Historical Perspective on Legume Domestication 2.1 Early domestication events The domestication of legumes began around 12 000 years ago, coinciding with the advent of Neolithic agriculture. This period marked the transformation of wild species into cultivated crops through human selection for desirable traits such as taste, yield, and ease of cultivation (Ambika et al., 2022; Bohra et al., 2022). Legumes were among the earliest domesticated plants, paralleling the domestication of cereals. Key legume crops such as soybean, lentil, chickpea, and pea were first cultivated in regions like the Fertile Crescent, China, and the Indian subcontinent (Smýkal et al., 2015). The domestication process involved significant genetic changes, including the loss of seed dormancy and shattering resistance, which were crucial for the development of stable and high-yielding crops (Rendón-Anaya et al., 2017). 2.2 Archaeological and historical evidence of legume cultivation Archaeological evidence provides critical insights into the history of legume domestication. For instance, lentils were first cultivated in Southwest Asia around 8 000~10 000 years ago, although the exact number of independent domestication events remains unclear (Liber et al., 2021). Similarly, the domestication of common beans in Mesoamerica and the Andes has been traced back through genetic and archaeological studies, revealing distinct domestication events in these regions (Nanni et al., 2011; Rendón-Anaya et al., 2017). The Indus Valley civilization also played a significant role in the domestication of various legumes, including pigeon pea and black gram (Figure 1) (Ambika et al., 2022). These findings are supported by radiocarbon dating of plant remains and the geographical distribution of wild relatives, which help reconstruct the domestication timeline and migration patterns of these crops (Fuller, 2007). Figure 1 Time divergence of major legume clades (Adopted from Ambika et al., 2022) Image caption: Values inside the brackets are the estimated time of divergence based on phylogenomic studies (Adopted from Ambika et al., 2022) 2.3 Evolutionary implications of domestication The domestication of legumes has had profound evolutionary implications. The process led to a severe genetic bottleneck, resulting in a significant loss of genetic diversity in domesticated varieties compared to their wild ancestors (Smýkal et al., 2015; Ambika et al., 2022). This reduction in genetic variability has implications for crop
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