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Fig. 5 | Genome Biology

Fig. 5

From: Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

Fig. 5

GWAS and identification of candidate genes responsible for seed size in castor bean. ad Manhattan plots for GWAS of seed length (SL, MLMM model), seed width (SW, MLM model), seed thickness (ST, MLM model), and seed area (SA, MLMM model). Two shared GWAS signals (SZ1 and SZ3) are shown. The dashed horizontal line indicates the threshold for GWAS (−logP = 7.67). e QTL mapping analysis of seed size (including SL, SW, ST, SSW) using recombination inbred lines (RILs) from a cross between landrace Rc250 with large seeds with the cultivar Rc249 with small seeds. The common QTL that overlapped with GWAS signal SZ3 on chromosome 3 is displayed. The dashed horizontal line indicates the LOD threshold for QTLs (LOD = 2.5). f Manhattan plots for GWAS of single seed weight (SSW, MLMM model). The dashed horizontal line indicates the threshold for GWAS (−logP = 7.67). The SZ1 signal (see panels ad) was identified and two candidate genes are shown. g A non-synonymous SNP in ARPN and heatmap of LD. The black triangle indicates the positions of an LD block which contains two genes MYB52 (Rc02G003980) and ARPN (Rc02G003981). The color key indicates r2 values in the LD region. h Comparisons of SSW between haplotypes in the GWAS populations. Those carrying the haplotype AA exhibit significantly lighter seeds than those carrying the alternate haplotypes. i Allelic distribution surrounding the significant SNP on chromosome 2 in WE, WK, and LC population. The pie charts indicate that the wild populations (WE and WK) contained only a few accessions carrying the haplotypes for large seeds, while the domesticated population (LC) contains many accessions carrying the haplotype for large seeds but some for small seeds

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