Figure 5

DNA polymorphisms associated with differential gene expression and seed size determination. (a) Number of seed-specific genes harboring promoter, non-synonymous and large-effect DNA polymorphisms that exhibit differential expression between the small and large-seeded cultivars at any of the seven stages of seed development, and higher expression at S3 and/or S5 stages of seed development in the large-seeded cultivar is shown. (b) Number of QTL-associated and non QTL-associated genes that show high expression at S3 and/or S5 stages of seed development in JGK 3 and harbor DNA polymorphisms, are given in the pie chart. Genes showing higher expression at S3 and/or S5 stages of seed development in JGK 3 harboring promoter, non-synonymous and/or large-effect DNA polymorphisms are categorized into genes encoding transcription factor or those involved in cell cycle, cell growth, endoreduplication or other processes. (c) Heatmaps showing presence of DNA polymorphism(s) (promoter, non-synonymous and large-effect) and gene expression of QTL-associated genes, and those involved in cell cycle, cell growth, endoreduplication and genes encoding transcription factors. Scale represents z-score based on FPKM expression values. JS3, JS5, HS3 and HS5 represent S3 and S5 stages of seed development in JGK 3 (JS3 and JS5) and Himchana 1, (HS3 and HS5), respectively. Labels on the left side indicate number of DNA polymorphisms. Gene identifiers and gene names are given on the right side.