GWAS identification of candidate genes for variation in alfalfa root traits. (IMAGE)
Caption
GWAS identification of candidate genes for variation in alfalfa root traits. (A) Circular Manhattan plots of the association analysis for the six root system architecture (RSA) traits using Blink. The dotted red line indicates the significance threshold of a P-value of 1 × 10−5. ①–⑥ represent different traits: ① RN, root number; ② TRD, taproot diameter; ③ SRD, secondary root diameter; ④ RDW, root dry weight; ⑤ RL, root length; and ⑥ SRP, secondary root position. ⑦ distribution of SNP markers on eight chromosomes in the association pool. The color represents the density of the SNP markers. (B) GO enrichment analysis of 308 GWAS candidate genes. These candidate genes were identified in our GWAS results within 50 kb of the significant SNPs. (C and D) GWAS identification of MsMKK6 and MsVTI13 (significant SNP located within the gene) as candidate genes for RSA variation. Each set of plots comprises a partial Manhattan plot (top left), the candidate gene structure, an LD heat map (bottom left), and the phenotype values of different haplotypes (right). (E and F) GWAS identification of MsLBD2 and MsP4H5 (significant SNP located within the LD block) as candidate genes for RSA variation. Each set of plots comprises a partial Manhattan plot (top left), the distribution of genes within the LD block, an LD heat map (bottom left), and the phenotype values of different haplotypes separated using the top significant SNP (right). In each box, asterisks denote significant differences between haplotype groups (t-test, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001). “n” in C–F denotes the number of genotypes in each haplotype group, and each point represents the mean value of six clone plants of each genotype.
Credit
Horticulture Research
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