A Transcriptome Profile for Developing Seed of Polyploid Cotton

Cotton ranks among the world's important oilseed crops, yet relative to other oilseeds there are few studies of oil-related biosynthetic and regulatory pathways. We present global transcriptome analyses of cotton seed development using RNA-seq and four developmental time-points. Because Upland cotton (Gossypium hirsutum L.) is an allopolyploid containing two genomes (A/D), we partitioned expression into the individual contributions of each homeologous gene copy. Data were explored with respect to genic and subgenomic patterns of expression, globally and with respect to seed pathways and networks. The most dynamic period of transcriptome change is from 20-30 d postanthesis (DPA), with about 20% of genes showing homeolog expression bias. Co-expression analysis shows largely congruent homeolog networks, but also homeolog-specific divergence. Functional enrichment tests show that flavonoid biosynthesis and lipid related genes were significantly represented early and later in seed development, respectively. An involvement of new features in oil biosynthesis was found, like the contribution of DGAT3 (diacylglycerol acyltransferase) to the total triglyceride expression pool. Also, catechin-based and epicatechin-based proanthocyanidin expression are reciprocally biased with respect to homeolog usage. This study provides the first temporal analysis of duplicated gene expression in cotton seed and a resource for understanding new aspects of oil and flavonoid biosynthetic processes.