Figure 2.

Functional Analysis of Genes with and without LoF Variants.

(A) Genes from larger gene families tend to have LoF variants based on the Col-0 genome. In the boxplot, the box equals the difference between the 75th and 25th percentiles. The thick line indicates the median. The two whiskers indicate 1.5 interquartile range of the lower quartile or the upper quartile. Outliers are plotted as individual points. ***P < 0.001.

(B) LoF mutations are under-represented in lethal genes in Arabidopsis. <0.005 indicates MAF less than 0.5%, <0.05 indicates MAF < 5%, and >0.05 indicates MAF > 5%.

(C) GO enrichment analysis of genes with LoF, with different LoF allele frequencies, and those without LoF variants across the 1071 genomes. Colors indicate P-values of GO enrichment analysis.

(D) Expression level variation between alleles with and without LoF variants of genes with significant GWAS signals based on RNA-seq data for 541 accessions. NS, insignificant difference.

(E) Expression level variation between alleles with and without LoF variants (6675 genes) based on RNA-seq data for 541 accessions. NS, insignificant difference.

(F) GWAS of stop-gain variants of KUK with regard to precipitation in the wettest month. Chr, chromosome.