Identification of temporal regulatory modules associated with proliferation and differentiation in early maize endosperm development

Endosperm is a product of double fertilization and functions as a nutritive tissue in the angiosperm seed to support the growth of the embryo or the germinating seedling. In cereal grains, endosperm comprises a large proportion of the mature seed and contains large amounts of carbohydrates and proteins. To identify a high-resolution temporal transcriptome of the earliest stages of endosperm development, we used laser-capture microdissection to isolate and profile mRNA populations of a developmental series of the endosperm from 0 to 4 DAP in maize inbred B73. These stages comprise the initial period of proliferation of the triploid endosperm coenocyte through cellularized endosperm that shows an overall polarity and indications of early cell differentiation. Using computational tools, we identified distinct temporal co-expression modules during this period of development. Analysis of the co-expressed transcription-factor genes and the associated cis-regulatory elements allowed us to hypothesize gene regulatory networks involved in early endosperm development in maize. mRNA populations of a developmental series of the central cell and endosperm from 0 to 4 days after pollination (DAP) (0, 1, 2, 3, and 4 DAP), and the whole embryo at 4 DAP in triplicates (18 samples) in maize inbred B73 were isolated using laser-capture microdissection and sequenced using an Illumina HiSeq 2500 platform.