**Acknowledgements**

**8. Summary and concluding remarks**

38 Advances in Seed Biology

accumulation of storage reserves and programmed cell death.

Expression profiling studies performed till now have provided information about important genes and pathways, interrelatedness of various processes and cross talks between the key players. Nevertheless, obtaining a fully functional knowledge of this complex development

Transcriptome studies have gained momentum in the last decade by the advancements in sequencing techniques, bioinformatics tools and functional genomics. This has strengthened our knowledge of the seed development program by boosting data generation and interpretation. The outlook from these high-throughput studies is predominantly determined by the tissues under investigation. Seed development process can be studied in entirety through expression atlases. They provide information about the dynamics and specificity of transcriptomes across a range of tissues/organs associated with the growth and development of rice seed. Larger proportion of endosperm-specific genes obtained in comparative studies between vegetative and seed stages indicate the amount of reprogramming happening at the molecular level. The extent of involvement of various tissues in seed development as well as their molecular relatedness can also be assessed by means of transcript profiling of tissues in groups. This helps in visualizing the molecular changes occurring during progression of development in rice seed through subsequent stages by highlighting the factors that undergo change or remain constant. Several TFs and hormone-related genes show specific or preferential expression in seed tissues indicating their active involvement with the process. Molecular interactions between tissues, such as cross talk between embryo and endosperm, can also be revealed by transcriptome atlases. However, for obtaining detailed information about the developmental changes related to a particular tissue, it will be beneficial to study that tissue in isolation, as it will be cost effective and less time consuming. Transcriptome studies of rice embryo and endosperm have identified the genes and pathways that control various phases of their development. Several MTases, including MET1, genes associated with DNA/chromatin remodeling and homeobox TFs are up regulated in the initial stages of embryo development indicating induction of genes associated with zygotic development and organ formation. Polarized expression of various TFs, TRs and phytohormones, including auxin, GA and cytokinin, suggests their role in establishing apical-basal polarity in the embryo. In the early and middle stages of embryo development, pathways related to amino acid metabolism, lipid and energy metabolism, nucleic acid replication/processing and signal transduction are up regulated, while in the later stages, pathways related to starch biosynthesis and protein modification are up regulated. Also, up regulation of ABA biosynthesis and down regulation of ethylene biosynthesis in later stages suggests their antagonistic role in embryo maturation. Endosperm development starts little later than embryo in seed development. Higher expression of cell cycle related genes in the initial stages suggest that early endosperm development is mostly concerned with cell division and expansion. Variable expression pattern of TFs, such as MADS, AP2-EREBP, NACs and CCAAT, throughout different stages of endosperm development emphasizes their specific roles throughout the process. Up regulation of PCD related genes, starch and storage protein synthesis genes and carbohydrate and energy metabolism genes in the middle and later stages suggests that these stages of endosperm development are active in

IEM and AM acknowledge the Junior and Senior Research Fellowship from University Grants Commission (UGC). PA thanks the Department of Biotechnology (DBT), India for grants supporting research and NIPGR core grant.
