Rice Genomics and Genetics 2024, Vol.15, No.3, 94-105 http://cropscipublisher.com/index.php/rgg 100 both Asian and African rice underwent convergent yet independent selection of a common set of genes during their domestication processes (Wang et al., 2014). Genome-wide analyses have identified several selective sweeps that occurred during the domestication of rice. For instance, 55 selective sweeps were identified in the genome of Oryza sativa, highlighting regions that underwent strong artificial selection (Huang et al., 2012). Similarly, population genomics analyses of Oryza glaberrima and its wild progenitor Oryza barthii have detected evidence for artificial selection at a genome-wide scale, further supporting the theory of independent domestication in African rice (Figure 3) (Wang et al., 2014). These genomic signatures of selection provide insights into the evolutionary pressures that shaped the domesticated rice varieties. The figure from Wang et al. (2014) illustrates the phylogenetic relationships and geographical distribution of Oryza glaberrima and its wild progenitor Oryza barthii. Panel (a) indicates that O. glaberrima shares a close genetic relationship with O. barthii from the OB-V group, suggesting that O. glaberrima was domesticated from O. barthii within this genetic group. Panel (b) maps the geographical distribution of O. barthii accessions, supporting the hypothesis that O. glaberrima was domesticated in this region. This phylogeographic pattern underlines the significance of West Africa as the center of domestication for O. glaberrima and provides insights into the spread of genetic diversity within the species. The findings emphasize the role of geographical isolation and local adaptation in the domestication process. Figure 3 Identification of the domestication center of O. glaberrima(Adopted from Wang et al., 2014) Image caption: (a) NJ phylogenetic tree of 20 O. glaberrima and 94 O. barthii accessions. All but one of the O. glaberrima accessions (black) are clustered with O. barthii accessions from group OB-V (green). (b) The proportion of each group of O. barthii accessions originating from different countries in Africa. All O. barthii accessions collected from the countries in the proposed domestication center (highlighted in black) are from the OB-V and OB-IV admixture groups. The proportion of O. barthii from the OB-V and OB-IV admixture groups found in each country decreased with distance from the domestication center, whereas the O. barthii accessions from other subgroups showed the opposite trend (Adopted from Wang et al., 2014) 5.3 Impact of domestication on phylogenetic structure Comparative genomic studies between wild and cultivated rice species have elucidated the impact of domestication on the phylogenetic structure of the genus Oryza. The analysis of 13 reference genomes spanning the Oryza species tree has shown that despite few large-scale chromosomal rearrangements, rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons and potential new coding and noncoding genes. This comparative approach has resolved controversial areas of the Oryza phylogeny and highlighted the complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species (Stein et al., 2018).
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