Fig. 5: The molecular basis and selection history of stem determinacy in cultivated rice bean. | Nature Communications

Fig. 5: The molecular basis and selection history of stem determinacy in cultivated rice bean.

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

Fig. 5

a InDel-based GWAS result from the analysis of data for stem determinacy measured at the Nanning site in 2020. The peak InDel is indicated by the red circle. The red horizontal dashed line indicated the Bonferroni-corrected significance thresholds of GWAS (α = 1). b A 2-bp causative deletion (the peak InDel) introduced a premature termination codon in the first exon of the TFL1 gene. Ref reference, Del deletion. c The frequency distributions of three types of stem growth habit (indeterminate (Indet), semi-determinate (Semi-det), and determinate (Det)) among three groups comprising landraces carrying the homologous reference alleles (designated as Ref), heterozygous (Ref/Del) or homologous mutation (2-bp deletion) alleles (Del), respectively. Two-sided Fisher’s exact tests were used to assess the significance of the differences in the proportion of the determinate type of stem growth habit between landraces carrying Ref and Del alleles and between landraces carrying Ref/Del and Del alleles. d The geographical distributions of the 32 landraces carrying Del alleles from Southern-Central China. The map was created using the map_data() function in the R package ggplot2. HB Hubei province, HN Hunan province, CQ Chongqing province, GZ Guizhou province, GX Guangxi province. e There was a significant improvement for the 32 landraces carrying Del alleles compared with the landraces carrying Ref alleles in the SC group for multiple human-desired traits including flowering time (DAE, days after emergence), branch number, seed length, and HGW (hundred seed weight). Significance was tested with two-sided Wilcoxon tests. In the box plots, central line: median values; bounds of the box: 25th and 75th percentiles; whiskers: 1.5*IQR (IQR: the interquartile range between the 25th and 75th percentile). f Divergence time of the 32 landraces carrying Del alleles with the landraces carrying Ref alleles in the SC group, inferred using the SMC++ program66, under a mutation rate μ = 1.5 × 10–8 per site per generation140, and a generation time of one year. Source data are provided as a Source Data file.

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