Determination of candidate genes for root-length QTLs by integrated analyses of GWAS, linkage mapping and pooled-χ2-tests.

(A) Heat map showing significant differences in long-root allele frequencies at 230 SNPs in 85 genes in 18 GWAS detected root-length QTL regions of the two extreme phenotypic pools (long-root vs short-root varietal pools) within rice populations (S1 Table), in which different colors show different long-root allele frequencies; rows of the heat map are SNP sites and QTLs; columns are long-root allele frequencies in different populations (japonica, long-root japonica, short-root japonica, indica, long-root indica and short-root indica); red arrows and stars show QTLs with known genes and candidate genes identified and confirmed for root length in this study. Identification of candidate genes in regions of (B) qRL8-2 and (C) qRL11-1. The top of each panel shows the entire QTL region identified by GWAS using the whole population and CMLM, and X-axis indicates the physical position (Mb) of the QTL regions in the rice genome. Negative log10-transformed P values are plotted on the vertical axis, in which dots show positions and -log(P) values of all significant SNPs in the QTL region and the red points indicate SNPs with significant differences in allele frequency of GWAS detected QTLs between the root-length pools and differential alleles between parents in previously reported bi-parental mapping populations; pink points represent SNPs with significant differences in allele frequency between pools, when the QTL was mapped only in our GWAS; and skyblue points show others. At the bottom of each panel, annotated genes are indicated by skyblue boxes; candidate genes are colored in red. Functional genes verified are red-labeled.