Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (Glycine max) Tissues during Early Seed Development.

Shuo Sun,James Whelan,Shoudong Wang,Jing Ma,Huixia Shou,Mathew G Lewsey,Changyu Yi,Marta Peirats-Llobet

doi:10.3390/ijms21207603

Abstract

Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.

Highlights

Soybean [Glycine max (L.) Merr.] is one of the most economically important cultivated plants
We obtained RNA-seq data of soybean seeds (Williams 82) during early seed development from the Gene Networks in Seed Development project [16]. These data were obtained from eight seed compartments over three stages of early seed development using laser capture microdissection (LCM) (Figure 1A)
We analyzed a transcriptomic dataset from 8 seed tissues at 3 developmental stages during soybean seed morphogenesis (Figure 1)

Summary

Introduction

Soybean [Glycine max (L.) Merr.] is one of the most economically important cultivated plants. Soybean belongs to the Fabaceae family, one of the largest and most diverse families of flowering plants. Legumes, as this family is known colloquially, have been used extensively as model species in plant biology and historically, soybean and other close relatives have been used as model species to study seed and embryo development [1,2,3,4,5,6]. Seed development is triggered by the double fertilization of the egg cell and central cells that leads to the differentiation of the seed tissues, embryo, endosperm and seed coat [5,7]. As a result of the developmental process, the mature seed will consist of a number of different gene expression programs occurring at the same time in the different compartments (e.g., embryo, endosperm, seed coat) as well as within specific regions and tissues (e.g. embryo proper, suspensor, epidermis) [6]

Methods

Results

Conclusion