Fig. 6: Tandem duplication of the VumCYP78A6 gene associated with seed yield traits. | Nature Communications

Fig. 6: Tandem duplication of the VumCYP78A6 gene associated with seed yield traits.

From: Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

Fig. 6

a GWAS using the 2020 and 2021 Nanning datasets, indicating that the strongest association signals for hundred seed weight (HSW) and seed length (SL) traits all located at Chr9: 29,030,437–29,126,729. b Local Manhattan plot of HSW (top), the gene models (middle), and pairwise linkage disequilibrium heat map (bottom) at Chr9: 29,030,437–29,174,247. The two tandemly duplicated VumCYP78A6 genes (VumCYP78A6-1 and VumCYP78A6-2) are shown with the red dashed triangles. In a and b, the red horizontal dashed lines indicated the Bonferroni-corrected significance thresholds of GWAS (α = 1). c The HSW distributions of landraces carrying distinct copy numbers of the VumCYP78A6 gene. The number (n) of landraces carrying distinct copy numbers is shown below. d Bar plot showing the relative expression levels of VumCYP78A6 in the pods at 16 DAP (days after pollination) from the long-seed landrace S28 (carrying two gene copies) and the short-seed landrace S33 (carrying one gene copy). e Light microscope images (top) and cell number per square millimeter (bottom) of the cross-sections of the pod wall for the S28 and S33 landraces at 16 DAP. Scale bar, 100 μm. In the box plots of c and e, central line: median values; bounds of box: 25th and 75th percentiles; whiskers: 1.5*IQR (IQR: the interquartile range between the 25th and 75th percentile). f Silique (left) and seed (right) morphology of the wild type (Col-0) and two independent Arabidopsis thaliana transformants overexpressing the VumCYP78A6-2 gene (OE1 and OE2). Scale bar: 5 mm for silique and 1 mm for seed. g The bar plots of thousand seed weight (TSW), silique length, silique width, and SL for Col-0, OE1, and OE2. P values are 1.07 × 10−4, 1.11 × 10−2, 2.36 × 10−8, 4.18 × 10−6, 1.44 × 10−2, 5.25 × 10−3, 1.88 × 10−7, and 1.94 × 10−6. The significance was tested using the two-sided Student’s t-test in c, d, e, and g. *P < 0.05, **P < 0.01, ***P < 0.001 in (g). The data in d and g are shown as mean ± SE. In d, e, and g, the number (n) of each independent experiment is shown below. Source data are provided as a Source Data file.

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