Fig. 8.

Domestication and diversification of C1 and A1. (A) Allele frequency analysis of C1 and A1. A total 342 rice varieties were identified for functional and non-functional alleles at C1 and A1. In this panel, 143 landraces and 199 improved rice varieties were further grouped as indica and japonica, respectively. Numbers of functional and non-functional alleles of C1 or A1 were used to compute the allele frequency of each gene in four distinct groups. Pie charts above the horizontal line represent landraces whereas improved varieties are shown below the line. (B) Phylogenic tree of rice varieties. The color strip in the inner part of the circle represents the taxonomic subgroup. Dark blue indicates wild rice from China; light-blue represents wild rice outside of China. The colored spots at the outer parts of the tree represent the phenotype of different accessions. (C) A minimum spanning tree of C1 and A1 combinations. Circle size is proportioned to the number of accessions with a given haplotype. Black circles on the lines represent mutational steps between alleles. Hatching (for wild rice) within circles indicate the place of origin of the varieties: blue horizontal lines represent accessions from Yangtze and Pearl River valleys; wild rice accessions originating from the Indochinese Peninsula are labeled with pink back-slashes, from South Asia with pink forward slashes, and from the Malay Archipelago with pink vertical lines. Landraces are represented by dark gray and improved rice varieties are represented by pale gray. The thick purple line separates the color phenotypes of varieties; accessions above the line have purple or brown color in their hulls or apiculi, and those below the line have no color. Accessions with brown hulls or apiculi are circled by a brown box. The series of circles located in the lower right corner represent reference scales. Arabic numeral in each circle indicates the number of materials represented by the circle of this size.