Systematic transcriptomic analysis provides insights into lotus (Nelumbo nucifera) seed development

Seed size is one of the most important determinants of yield in lotus (Nelumbo nucifera). The cotyledon, which is responsible for nutrient storage in the mature seed, is the major factor affecting seed size in this economically important crop. Here, transcriptome analysis on cotyledons were performed during the rapid expansion stage of two lotus cultivars with different seed size and yield, China Antique and Jianxuan-17, at 9, 12, and 15 days after pollination (DAP). We identified 22,549 genes, including 2414 novel genes. Among them, 8437 genes were differentially expressed between CA and JX from 9 to 15 DAP. Gene ontology analysis suggested that these DEGs were significantly enriched in cell proliferation and gene expression. Dozens of DEGs are involved in brassinosteroids (BRs) biosynthesis and signaling pathway. Nine genes controlling seed size by cell number and size were candidate genes regulating lotus seed size. There was a notable difference in the expression patterns and level of starch-synthesis genes between two cultivars. NNU_20629 and NNU_05331 were likely responsible for the difference in starch accumulation between CA and JX, which might lead to their different yield. Pairwise comparisons of our transcriptome data provide insights into lotus seed development, which could facilitate projects aimed at breeding lotus with improved traits.