Systems and evolutionary characterization of microRNAs and their underlying regulatory networks in soybean cotyledons

Authors: Goettel, Herbert; Liu, Zongrang; XIA, JING - Washington University; ZHANG, WEIXIONG - Washington University; ZHAO, PATRICK - Samuel Roberts Noble Foundation, Inc; An, Yong-Qiang - Charles

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/5/2013
Publication Date: 1/27/2014
Citation: Goettel, H.W., Liu, Z., Xia, J., Zhang, W., Zhao, P.X., An, Y. 2014. Systems and evolutionary characterization of microRNAs and their underlying regulatory networks in soybean cotyledons. PLoS One. doi: 10.1371/journal.pone.0086153.

Interpretive Summary: The value of soybean seeds is mainly determined by composition of protein and oil that is used for human consumption, animal feed and industrial feedstock. Cotyledons are the primary sink tissues for protein and oil reserve production and storage. Genetic engineering of the gene networks controlling cotyledon development, and protein and oil production to increase soybean yield and improve seed composition has been one of the major goals in soybean agricultural research. However, a lack of knowledge about the key regulatory components in these networks is one of the bottlenecks. MicroRNAs are a class of RNAs that have key regulatory functions in gene networks that control a variety of biological processes. To date, little is known about the microRNAs in soybean cotyledons. In this study, we applied a next generation DNA sequencing technology to produce 292 million small RNA sequences from soybean cotyledons representing six different soybean seed maturation stages. Using a computational approach, we identified 129 novel cotyledon specific microRNAs, and increased the number of currently known soybean miRNAs from 203 to 332. A total of 1180 genes that are potentially regulated by cotyledon microRNAs were identified. Twenty-six of the targeted transcripts are shown to be regulated by multiple miRNAs. Cotyledon miRNAs have higher rate of loss or gain than protein coding genes during plant evolution. We also identified a number of miRNAs thought to regulate genes related to protein and oil production and storage in cotyledons. These miRNAs could serve as potential targets for genetic engineering to improve seed quality and composition and will provide soybean breeders with new targets for soybean improvement strategies.

Technical Abstract: Soybean cotyledons have evolved as a sink organ to synthesize and deposit the storage protein and oil reserve over seed maturation. MicroRNAs represent a class of key components in gene regulatory networks underlying diverse biological processes. However, our understanding of the microRNAs in soybean cotyledon over seed maturation remains limited. In the study, we generated 292 million small RNA reads by sequencing 18 small RNA libraries from soybean cotyledon at six different stages of maturation. 129 novel cotyledon microRNAs and 93 novel miRNA families were identified. A total of 1193 cotyledon miRNA family-target transcript interaction were predicted. The targeted genes encode proteins with diverse biological functions, but preferentially encode proteins in pathways related to RNA metabolism, RNA transcription and protein degradation. Twenty-six of the transcripts are likely to be targeted by multiple miRNAs. Cotyledon miRNAs are preferentially transcribed in a coordinate orientation with their overlapping mRNA transcripts. Unlike the other plant miRNAs, a high percentage of soybean cotyledon miRNAs are intronic. Some of them are located in introns that are subjected to alternative splicing. The miRNA loci in duplicated genome segments from the recent Glycine whole genome replication have much higher loss/gain rate than the protein coding genes. The conserved miRNAs have lower loss/gain rate than non-conserved miRNAs.