Genomic dissection of the seed

Abstract

Seeds play an integral role in the global food supply and account for more than 70% of the calories that we consume on a daily basis. To meet the demands of an increasing population, scientists are turning to seed genomics research to find new and innovative ways to increase food production. Seed genomics is evolving rapidly, and the information produced from seed genomics research has exploded over the past two decades. Advances in modern sequencing strategies that profile every molecule in every cell, tissue, and organ and the emergence of new model systems have provided the tools necessary to unravel many of the biological processes underlying seed development. Despite these advances, the analyses and mining of existing seed genomics data remain a monumental task for plant biologists. This review summarizes seed region and subregion genomic data that are currently available for existing and emerging oilseed models. We provide insight into the development of tools on how to analyze large-scale datasets.

Keywords: Arabidopsis; RNA seq; next generation sequencing; oilseed; seed; soybean; transcriptome.

FIGURE 1

Development and biological functions of Arabidopsis seed subregions. (A) Representation of seed subregions in Arabidopsis from the preglobular to mature green stages of development. Green, embryo proper (EP); dark pink, micropylar endosperm (MCE); light pink, peripheral endosperm (PEN); orange, chalazal endosperm (CZE); purple, chalazal seed coat(CZSC); blue, seed coat (SC). (B) Heat map visualization of representative Gene Ontology terms, biological processes, and metabolic pathways found in different subregions of the seed discussed in the review. Preglobular (pg); globular (g); heart (h); linear cotyledon (lc); mature green (mg). Dark green color represents activity in a particular subregion of the seed over developmental time.

FIGURE 2

Cumulative seed related Sequence Read Archive (SRA) submissions in Arabidopsis (orange), Brassica (yellow), and soybean (gray) from 2008 to 2014 (April 13) through the National Center for Biotechnology Information.

FIGURE 3

Predicted bZIP-regulated seed maturation network. bZIP TFs (blue squircles) are predicted (dashed lines) or known (solid lines) to bind to DNA sequence motifs (green diamonds) within the 1 kb upstream region of the transcription start site in genes associated with enriched GO terms like lipid storage, nutrient reservoir activity and seed oilbody biogenesis (P < 0.001, hypergeometric distribution, purple circles). Genes associated with the network are co-expressed during seed maturation (orange hexagons). Modified from Belmonte et al. (2013).

FIGURE 4

Predictive transcriptional circuits in subregions of the Arabidopsis seed. (A) MINISEED3 (MINI3)-W-box transcriptional circuit in the micropylar endosperm (MCE) regulating processes like the endomembrane system. (B) A CIRCADIAN CLOCK ASSOCIATED1 (CCA1) module in the chalazal endosperm (CZE) of heart-stage seeds. (C) A MYB transcriptional module in the mature green (mg) seed coat (SC) predicted to control processes like proanthocyanidin metabolism and ovule and carpel development. TFs (blue squircles) are predicted (dashed lines) or known (solid lines) to bind to DNA sequence motifs (green diamonds) within the 1 kb upstream region of the transcription start site in genes associated with enriched (P < 0.001, hypergeometric distribution) GO terms (purple circles) within patterns of co-expressed gene sets (orange hexagons). All networks are modified from Belmonte et al. (2013).