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United States Department of Agriculture

Agricultural Research Service


Location: Plant Genetics Research

2011 Annual Report

1a. Objectives (from AD-416)
Objective 1: Analyze mRNA and storage oil profiles of cotyledons over the course of seed maturation to infer biological networks underlying soybean seed oil composition and content, and to predict their key gene candidates. Objective 2: Analyze small RNA profiles of cotyledons over course of the seed maturation, and further predict small RNA candidates regulating soybean seed oil composition and content.

1b. Approach (from AD-416)
Objective 1: Soybean oil synthesis and deposition occur mainly in cotyledons and are differentially regulated over the course of seed maturation. The oil synthesis and deposition are accomplished through the concerted activities of many gene products and biological pathways that are primarily regulated at transcription levels. Gene expression patterns change very quickly over the course of an organism’s evolution if it is not subjected to functional constraints. Although it is not a universal rule, evidence suggests that expression patterns of many genes are intended to co-evolve with their biological functionalities. The co-evolution is reflected by a correlation of gene expression pattern with the related biological functions, and co-expression of functionally related genes such as those that encode proteins that reside in the same metabolic or signal pathways, or in the same cellular complexes under a variety of biological conditions (Stuart et al., 2003; Wei et al., 2006). The expression pattern correlation is widely used as criteria to predict biological functions of genes, functional relatedness between genes, and gene regulatory networks (Horan et al., 2008). We have examined transcriptomes and storage lipid profiles of cotyledons at six distinct developmental stages over the course of seed maturation. Objective 2: We have conducted deep sequencing of small RNA populations in the same RNA preparations used for transcriptome analysis. It is believed that miRNAs function as master regulators in gene regulatory networks underlying diverse biological processes in Arabidopsis. However, much less is known about soybean miRNA species and their accumulation patterns over the course of seed maturation. As part of our effort to delineate regulatory networks and identify key genetic components controlling oil composition and content, we will conduct genome-wide characterization of small RNAs, particularly miRNAs, in cotyledons over the course of seed maturation. We will use a bioinformatic approach to analyze the small RNA sequences we have conducted to discover miRNA species and their accumulation patterns. MiRNA species recognize their target mRNA by high sequence complementation, and function mainly as suppressors of the accumulation of the target mRNA by directing the degradation of its functional target mRNAs in plants. Sequence complementarities and negative correlation of mRNA and miRNA accumulation patterns should offer a more effective approach to identify the functional target genes, and can be used to delineate the topology of small RNAs in the TF networks inferred in Objective 1. The miRNA species that locate in TF networks enriched with oil related genes or target oil related genes would be strong candidates for future investigations for oil composition and content improvement.

3. Progress Report
Soybean seed oil composition and content are important agronomic traits, and determine soybean oil nutritional values and its use in biodiesel production and other industrial applications. Production of storage oil in seeds requires concerted expression of many genes and biological pathways over the course of seed maturation. However, the lack of knowledge of the intricate structure of this biological network and the availability of its key regulatory components has been a bottleneck in the effective application of both breeding and biotechnological approaches for soybean oil quality improvement. Recent developments in large-scale “-omics” technologies and the public availability of many large-scale biological datasets provide an unprecedented opportunity to delineate the biological networks and discover the key regulatory components. To address this problem an ARS scientist in St. Louis, MO has undertaken a multi-faceted approach to determine profiles of message ribonucleic acids (RNAs), small RNAs (RNAs that often play a master role in controlling gene expression), and major lipid species in soybean cotyledons at six distinct developmental stages over the course of seed maturation. We have determined which biological pathways the transcriptional factor regulatory networks identified in earlier studies, potentially regulate. Forty-one gene regulatory networks potentially involved in oil production were also identified. Bioinformatic analysis of 292 million sequenced small RNAs identified 129 novel cotyledon miRNAs, and increased the total number of currently discovered soybean miRNA families to 222. We demonstrated that cotyledon miRNAs are preferentially transcribed in a coordinate orientation to their overlapping mRNA transcripts. Unlike the other plant miRNAs, the majority of cotyledon miRNAs are intronic. Four miRNAs that potentially regulate oil composition and content were identified for further functional validation. The project also predicted the genes and biological pathways that other miRNAs potentially regulate, and further mapped those miRNAs and their target genes on the soybean genome to integrate with the other soybean genomic and genetic data to maximize their application in soybean research.

4. Accomplishments

Last Modified: 10/16/2017
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