Figure 4 : Genomic differentiation and selection between weedy and local cultivated rice.

From: Genomic variation associated with local adaptation of weedy rice during de-domestication

Figure 4

(a) Genomic distribution of population summary statistics of japonica (left) and indica type (right) weedy and local cultivated rice. The population parameters (π, Tajima’s D) in this study were estimated in a 100 Kb window size along the reference genome. Legends for circles from inside to outside: Tajima’s D of the LN1 (left) and GD1 (right) Tajima’s D of NX1 (left) and JS1 (right); Tajima’s D of TEJ (left) and IND (right); πJAP−πLN1 (left) and πIND−πGD1 (right), with inward present positive value; πJAP−πNX1 and πIND−πJS1 with inward present positive value; repeat density across the reference genome. (b) FST between weedy and cultivated rice from different locations. Japonica weedy rice from Ningxia (NX1) and Liaoning (LN1) and indica weedy rice from Jiangsu (JS1) and Guangdong (GD1) were illustrated, respectively. Some functionally known genes locating the significant divergent regions were shown. (c) A common genomic region with significant divergence in both indica and japonica weedy rice populations relative to their cultivated rice. The domestication gene Rc controlling pericarp colour and dormancy and a cluster of seed allergenic genes (RAL) locate in the region.