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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.

The plastid is an organelle vital to all photosynthetic and some non-photosynthetic eukaryotes. In the model plant Arabidopsis thaliana, a number of nuclear genes encoding plastid proteins have been found to be necessary for embryo development. However, the exact roles of plastids in this process remain largely unknown. Here we use publicly available datasets to obtain insights into the relevance of plastid activities to A. thaliana embryogenesis. By searching the SeedGenes database (http://www.seedgenes.org) and recent literature, we found that, of the 339 non-redundant genes required for proper embryo formation, 108 genes likely encode plastid-targeted proteins. Nineteen of these genes are necessary for development of preglobular embryos and/or their conversion to globular embryos, of which 13 genes encode proteins involved in non-photosynthetic metabolism. By contrast, among 38 genes which are dispensable for globular embryo formation but necessary for further development, only one codes for a protein involved in metabolism. Products of 21 of the 38 genes play roles in plastid gene expression and maintenance. Examination of RNA profiles of embryos at distinct growth stages obtained in laser-capture microdissection coupled with DNA microarray experiments revealed that most of the identified genes are expressed throughout embryo morphogenesis and maturation. These findings suggest that metabolic activities are required at preglobular and throughout all stages of embryo development, whereas plastid gene expression becomes necessary during and/or after the globular stage to sustain various activities of the organelle including photosynthetic electron transport.

White mold is caused by the fungal pathogen Sclerotinia sclerotiorum and leads to rapid and significant loss in plant yield. Among its many brassicaceous hosts, including Brassica napus (canola) and Arabidopsis, the response of individual tissue layers directly at the site of infection has yet to be explored. Using laser microdissection coupled with RNA sequencing, we profiled the epidermis, mesophyll, and vascular leaf tissue layers of B. napus in response to S. sclerotiorum. High-throughput tissue-specific mRNA sequencing increased the total number of detected transcripts compared with whole-leaf assessments and provided novel insight into the conserved and specific roles of ontogenetically distinct leaf tissue layers in response to infection. When subjected to pathogen infection, the epidermis, mesophyll, and vasculature activate both specific and shared gene sets. Putative defense genes identified through transcription factor network analysis were then screened for susceptibility against necrotrophic, hemi-biotrophic, and biotrophic pathogens. Arabidopsis deficient in PR5-like RECEPTOR KINASE (PR5K) mRNA levels were universally susceptible to all pathogens tested and were further characterized to identify putative interacting partners involved in the PR5K signaling pathway. Together, these data provide insight into the complexity of the plant defense response directly at the site of infection. [ABSTRACT FROM AUTHOR]

We examined the dynamic cellular changes that occur in Brassica napus L. funiculus histology and ultrastructure over developmental time by using light and transmission electron microscopy. Over the course of development, the funiculus significantly increased in size. This was a result of increased cell numbers as well as the deposition of additional wall material in the epidermis and vasculature layers of the funiculus. Conversely, the intermediate cortex layer broke down, detached from adjacent tissues, and developed large intercellular spaces. There was a loss of cytoplasm in the epidermis although this tissue remained intact. This cellular degeneration was correlated with a reduction in starch and other changes in organelle features. A pronounced increase in the number of vascular elements, both in the xylem and phloem tissues, also occurred as the funiculus matured. We present the first detailed histological examination of the funiculus in B. napus, one of the most economically important crops in Canada, and discuss the importance of cellular changes required for development as they relate to the three primary tissue systems of the plant. Key words: Brassica napus, funiculus, histology, microscopy, seed, ultrastructure. Resume : A l'aide de la microscopie photonique et electronique par transmission, les auteurs ont examine la chronosequence des changements de la dynamique cellulaire, de l'histologie et de l'ultrastructure du funicule chez le Brassica napus. Au cours du developpement, la dimension du funicule augmente significativement. Ceci resulte d'une augmentation du nombre de cellules ainsi que de la deposition de materiel parietal supplementaire dans l'epiderme et les couches vascularisees du funicule. Au contraire, la couche de cortex intermediaire se rupture, se detache des tissus adjacents et forme de grands espaces intercellulaires. On observe une perte de cytoplasme dans l'epiderme, bien que ce tissu demeure intact. Cette degenerescence cellulaire correspond a une reduction de l'amidon et autres changements dans les caracteristiques des organelles. On observe egalement une forte augmentation du nombre d'elements vasculaires, a la fois dans le xyleme et le phloeme, au cours de la maturation du funicule. Les auteurs presentent la premiere description histologique detaillee du funicule du B. napus, une des plantes cultivees les plus importantes au Canada. On discute finalement l'importance des changements cellulaires requis pour le developpement en relation avec les trois systemes histologiques primaires de la plante. [Traduit par la Redaction] Mots-cles: Brassica napus, funicule, histologie, microscopie, graines, ultrastructure., Introduction In flowering plants, seeds originate from structures of the ovule and undergo dramatic morphological and anatomical changes over the course of the plant lifecycle. In several plant systems, seed [...]

SUMMARY: We profiled the global gene expression landscape across the reproductive lifecycle of Brassica napus. Comparative analysis of this nascent amphidiploid revealed the contribution of each subgenome to plant reproduction. Whole‐genome transcription factor networks identified BZIP11 as a transcriptional regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in a similar reduction in gene activity of predicted gene targets, and a reproductive‐lethal phenotype. Global mRNA profiling revealed lower accumulation of Cn subgenome transcripts relative to the An subgenome. Subgenome‐specific transcription factor networks identified distinct transcription factor families enriched in each of the An and Cn subgenomes early in seed development. Analysis of laser‐microdissected seed subregions further reveal subgenome expression dynamics in the embryo, endosperm and seed coat of early stage seeds. Transcription factors predicted to be regulators encoded by the An subgenome are expressed primarily in the seed coat, whereas regulators encoded by the Cn subgenome were expressed primarily in the embryo. Data suggest subgenome bias are characteristic features of the B. napus seed throughout development, and that such bias might not be universal across the embryo, endosperm and seed coat of the developing seed. Transcriptional networks spanning both the An and Cn genomes of the whole B. napus seed can identify valuable targets for seed development research and that ‐omics level approaches to studying gene regulation in B. napus can benefit from both broad and high‐resolution analyses. Significance Statement: Global gene expression profiling and laser microdissection of the B. napus seed identifies subgenome bias and spatial distribution of biological processes and transcription factor networks. [ABSTRACT FROM AUTHOR]