**2. Expression atlases capture the dynamicity of transcriptome during seed development**

Seed development is a continuous process and is effected by the participation of many tissues that undergo various developmental changes over a course of time. Such dynamic alterations would be difficult to be depicted entirely by studying tissues in isolation. Gene expression atlases incorporate transcriptome profiles of a wide range of cell types and/ or developmental stages. Such global profiling studies become important when tracing the complex transcriptional changes associated with transition of tissues from one phase of development to another. Several high-throughput studies of this nature have been conducted in rice, employing MPSS, microarray and transcriptome sequencing, which span both vegetative and reproductive tissues [6, 9–11, 16, 17]. The primary information obtained from expression atlases is about the transcriptional status of the tissues/organs with respect to one another. For instance, the steady increase in the number of down regulated genes in seed tissues with respect to vegetative tissues indicates gradual decrease in transcriptional activity with the progression of seed development [6]. The similarity and disparity in the transcriptome profiles has also been used to assess the relatedness of tissues [16]. Through microarray analysis of 39 vegetative and reproductive tissue types in rice, it has been shown that rice endosperm forms a separate cluster and exhibits relatively lesser gene expression than other tissues including panicle stages. However, the expression levels of these genes are significantly high and a large portion of these are endosperm-specific. Also, most of the development related genes show variation in expression levels among different tissues revealing the fluctuations at the molecular level that these genes experience as they pass from one stage of development to another. These observations provide several important inferences regarding seed development, such as transcriptional dynamics and tissue-specificity. Also, an inevitable inference from here is that the transcriptome undergoes intense spatiotemporal reprogramming during transition from vegetative to seed development in order to manifest the expression of seed-specific/preferential genes [11]. Atlases also provide information about the contributions of various tissues in seed development. Transcriptome study encompassing various vegetative and reproductive tissues of rice indicate that out of the total seed-specific genes obtained, the proportion of endosperm-specific genes is higher than that of embryo-specific genes. This might imply that the endosperm has more disparate transcript profile shifting the balance towards the role of endosperm in seed development in comparison to embryo [10]. Nevertheless, conclusions from such studies can be subjective and will vary according to the tissues and developmental stages under investigation and the methods of data analysis. For instance, the discovery of seed-specific genes will be influenced by the variety of vegetative tissues that are being considered for assessing specificity or the parameters set to call a gene expressed or differentially expressed. In a study published by our group, encompassing 19 vegetative and reproductive tissues, the number of seed-specific genes has been found to vary when expression is considered against different vegetative controls such as root and mature leaf [6]. This indicates that a single transcriptome data can emanate various circumstantial biological interpretations. However, to minimize erroneous accounting it is necessary to exercise caution while sampling and have precise knowledge of the query that is being pursued.

embryo at maturity and the endosperm is consumed by the embryo during the course of seed development. The structure of monocot seed, such as rice, is different from a dicot seed by the presence of a starchy endosperm which occupies most of the space inside the seed coat and the embryo is positioned at the ventral side. Furthermore, the seed is covered entirely by the husk, which is formed by drying of the lemma and the palea. Seeds serve as the storage factories for synthesizing carbohydrates, proteins and lipid molecules, hence act as nutrition suppliers to the germinating seedling as well as to animals and humans. Rice seeds, in particular, are the major calorie providers constituting about 20% of the human nutrition worldwide [1, 2]. Therefore, it becomes imperative to understand seed development in rice to produce vari-

Seed development in rice incorporates development of the embryo and the endosperm and occurs in a systematic and sequential manner followed by desiccation and seed dormancy. The entire process of seed development in rice has been summated into five different stages from S1 to S5, categorized as 0–2, 3–4, 5–10, 11–20 and 21–29 days after pollination (DAP) seeds, respectively. Developmental period of the seed consisting of post-fertilization to middle globular embryo constitutes the first stage followed by embryo patterning and endosperm cellularization in second stage. The third stage is concerned with embryo morphogenesis, formation of a milky endosperm and initiation of endoreduplication. In the maturation phase, the milky endosperm transits from soft dough and hard dough stages in S4, and the seeds progress towards dormancy and desiccation in S5 stage [3, 4]. These developmental changes are channelized impeccably through the skillful operation of several genes and complex regulatory networks upon perception of internal and external stimuli [4–6]. Recent technological advances have facilitated the identification of genes responsible for guiding various steps of seed development. High-throughput mRNA profiling studies or transcriptomics is one such technology that has helped in deriving vital information about a myriad of molecular events that orchestrate seed development [7, 8]. Transcriptome profiling of a wide range of rice tissues, including vegetative and reproductive tissues, have proved beneficial in providing primary information about the genes expressed during seed development including their levels, patterns and molecular functions [6, 9–11]. With the aid of advanced bioinformatics platforms, transcriptome data is now being processed to derive more complex interpretations including pathways and regulatory networks that provide more complete picture of the

eties with improved nutritional content and yield.

26 Advances in Seed Biology

molecular changes regulating seed development [12–15].

**seed development**

**2. Expression atlases capture the dynamicity of transcriptome during**

Seed development is a continuous process and is effected by the participation of many tissues that undergo various developmental changes over a course of time. Such dynamic alterations would be difficult to be depicted entirely by studying tissues in isolation. Gene expression atlases incorporate transcriptome profiles of a wide range of cell types and/ or developmental stages. Such global profiling studies become important when tracing
