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

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.

Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model

“…Other parameters of GENIE3 were set as the default values. Prior to the analysis, we filtered out all the genes with low variance across samples as in Sun et al (2020) by using the filterGenes function in the DGCA R package ( Mckenzie et al, 2016 ). Because we only constructed tissue-specific GRNs, for each tissue only tissue-specific genes were considered, resulting in 660, 632, 737, and 582 genes left for leaf, root, seed, and nodule, respectively.…”

“…Moreover, by systematically analyzing 1,270 microarray samples generated with Affymetrix gene chips, a nodulation-related co-expression module was uncovered ( Wu et al, 2019 ). More recently, researchers ( Sun et al, 2020 ) identified key regulators and hub genes in each tissue by analyzing a genome-wide transcriptome dataset from eight tissues at three different seed development stages. To elucidate the dynamics of transcriptional regulation across the broad range of samples, tissues, and cultivars, 1,298 publicly available soybean transcriptome samples were collected and analyzed by Machado et al (2020) .…”

Gene mining of 100‐grain weight and the number of four‐seed pods in soybean (Glycine max)

“…One of the first studies in soybean seed development used RNA‐seq to develop an atlas during seed development (Severin et al, 2010; Sun et al, 2020). With the development of high‐throughput sequencing technology, the application of whole genome resequencing and transcriptome sequencing data to genetic map traits associated with soybean pods and seeds has been ongoing (Teng et al, 2019; Wang et al, 2015).…”

Physiological and Environmental Regulation of Seed Germination: From Signaling Events to Molecular Responses

“…The specific functions of the different seed tissues, as well as their functional interactions, have been paid increasing attention and bridge seed development and seed germination processes over space and time [3]. These issues are addressed in a review article by Miray et al [8] and in a research article by Sun et al [9]. Miray and collaborators present an exhaustive overview of how oil metabolism is controlled in the endosperm during seed development [8].…”

“…Importantly, they bring evidence that the functions of oils stored in endosperm exceed in fueling seedling metabolism and cover problematic aspects as diverse as seed dispersal, seed imbibition and the regulation of seed germination in relation to ROS signaling. For its part, the study by Sun and colleagues [9] revealed the specific gene expression profiles of height different tissues during early soybean seed development. The data obtained further evidence of the determinant weight of tissue specificity compared to developmental stage specificity in the determination of expression profile during seed development.…”