Fig. 1

Ho-LAMap accelerated the identification of grain size loci in rice. a Comparison of GWAS results for grain length among the full, indica, and japonica populations using the GLM (Q) model. Arrows indicate the physical positions of known grain length genes overlapping with the QTL. Vertical dashed lines represent QTL co-localized with linkage mapping. Blue dots indicate QTL overlapping with the published QTL. b Venn diagram showing numbers of unique and shared QTL mapped by GWAS among the full, indica, and japonica populations. c Heat map for effect of grain length QTL mapped by four linkage populations and GWAS. Rows in the heat map correspond to the 14 QTL for grain length. d Identification of causal SNPs in QTL qGL3-1 using Ho-LAMap, a novel method, which combined linkage mapping and association mapping for grain length. Manhattan plot for candidate region association mapping for qGL3-1 (top) and Ho index plots of qGL3-1 (middle). Red regression lines were obtained by averaging SNP indices from a moving window of two consecutive SNPs, and shifting the window one SNP at a time. The bottom part corresponds to annotated genes in this region, with the purple arrow representing GS3. e Minor allele frequency influence on effectiveness of Ho-LAMap