Fig. 5: Allelic classification of HWS1/HWS2 combination and verification of the functional SNP in HWS1 locus. | Nature Communications

Fig. 5: Allelic classification of HWS1/HWS2 combination and verification of the functional SNP in HWS1 locus.

From: Dysfunction of duplicated pair rice histone acetyltransferases causes segregation distortion and an interspecific reproductive barrier

Fig. 5

a Case/control test for SNPs in the 4.6 kb fine-mapped region around the HWS1 locus and expression level using a standard one-degree-of-freedom allelic Chi-square test in Plink. Local Manhattan plot (top), gene structure (middle), and LD heatmap (bottom) surrounding HWS1 are shown. The red diamond in the Manhattan plot shows the position of the proposed causative mutation SNP (SNP1_7385301). P values and identified SNPs are presented in Supplementary Data 3. b Activity analysis of HWS1 promoter. Upper part: schematic diagram of the pGREENII 0800-LUC vector fused with HWS1 promoter. Leftward part: a series of constructs with site-directed mutation HWS1 promoter. S1, 3000-bp promoter region of HWS1CG14, S2, T to C point mutation of S1; S3, 3000-bp promoter region of hws1WYJ7; S4, C to T point mutation of S3. Rightward part: expression levels of firefly luciferase normalized by Renilla luciferase. c Haplotypes of HWS1 of various germplasm. The identified SNPs in a associated with HWS1 expression are arranged in the table (bottom), and the leading SNP variant is marked with a red arrowhead and asterisk. Hybrid combinations between SG178 and seven cultivars including four japonica varieties (d–g) and three indica varieties (h–j). The plants in parts d–j shown in the right panels exhibited typical sterile and dwarf phenotypes compared with the F2 control individuals shown on the left. Scale bars = 5 cm (top), 5 cm (bottom). k Allele frequencies of the causal polymorphisms in HWS1/HWS2 in the three groups comprising 133 AA-genome Oryza accessions. The total number and proportion of accessions in each class and population are given beneath each pie chart. The blank grid indicates that there were no varieties in this Class. All rice accessions are listed in Supplementary Data 1. Data in b are means ± SEM (n = 3 biological replicates). Different letters denote significant differences (p < 0.05, one-way ANOVA with two-sided Tukey’s HSD test). P values for b are adjusted and shown in the Source Data file.

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