Fig. 5

The Circos diagram illustrates the positioning of MQTLs and GWAS-based SNPs associated with yield and drought tolerance (DT)-related traits under water deficit conditions on the physical map of Oryza sativa japonica (Nipponbare). a The twelve rice chromosomes are arranged in a clockwise direction. b The gene density on rice chromosomes shown in yellow to red scale for the lowest to the highest density in 500 kb windows. c The locations of identified MQTLs through comprehensive MQTL analysis on the physical map of each chromosome. d Position of the identified MQTLs for each distinct trait on the physical map of each chromosome. e Showing the genes locating inside both the SNP peak positions and the QTL-overview peaks for yield and DT-associated traits under drought stress conditions as novel candidate genes (Supplementary Table S7). f Points having various colors symbolize significant SNPs discovered through GWAS studies for yield and DT-associated traits under water deficit conditions. g The heatmap representing the Indels density in white to dark blue color scale for the lowest to the highest density. h The heatmap representing the structural variants (SV) density in white to dark red color scale for the lowest to the highest density. Physical positions of all markers (including those used in the flanking markers each MQT and map markers) were determined using the genome assembly IRGSP-1.0