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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #352537

Research Project: Defining the Genetic Diversity and Structure of the Soybean Genome and Applications to Gene Discovery in Soybean, Wheat and Common Bean Germplasm

Location: Soybean Genomics & Improvement Laboratory

Title: Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing

Author
item CHEN, LINFENG - Nanjing Agricultural University
item DING, XIANLONG - Nanjing Agricultural University
item ZHANG, HAO - Nanjing Agricultural University
item HE, TINGTING - Nanjing Agricultural University
item LI, YANWEI - Nanjing Agricultural University
item WANG, TANLIU - Nanjing Agricultural University
item LI, XIAOQIANG - Nanjing Agricultural University
item JIN, LIN - Nanjing Agricultural University
item Song, Qijian
item YANG, SHOUPING - Nanjing Agricultural University
item GAI, JUNYI - Nanjing Agricultural University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/3/2018
Publication Date: 9/12/2018
Citation: Chen, L., Ding, X., Zhang, H., He, T., Li, Y., Wang, T., Li, X., Jin, L., Song, Q., Yang, S., Gai, J. 2018. Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing. BMC Genomics. 9(1):663.

Interpretive Summary: Heterosis in plants refers to the existence of superior levels of biomass, stature, growth rate and/or fertility in hybrid progeny compared to their parents. The discovery of heterosis in maize a century ago has revolutionized plant and animal breeding and production. Heterosis may be useful for improving soybeans in the future, but this will require breeding hybrid soybeans. Hybrid soybeans can be made from plants with cytomplasmic male sterility (CMS). CMS soybeans do not produce pollen, but they can be pollenated by other non-CMS soybean. The molecular control of CMS involves chloroplast, mitochondrial and nuclear genes, but the regulation of these genes is not completely understood. In this study, we evalutated the presence of circular RNAs (circRNAs) in CMS soybeans. We observed that differentially expressed circRNAs are related to genes that control flower and pollen development, male sterility and cell death in the CMS line. The study provides new knowledge for understanding the molecular mechanisms controlling CMS. This study may provide plant breeders at universities, companies and government agencies with new knowledge to utilize crop heterosis for the production of high-yield hybrid soybean seed.

Technical Abstract: Cytoplasmic male sterility (CMS) is a natural phenomenon of pollen abortion caused by the interaction between cytoplasmic and nuclear genes. CMS is a simple and effective pollination control system, and plays an important role in crop heterosis utilization. Circular RNAs (circRNAs) are a vital type of non-coding RNAs, which can control microRNAs (miRNAs) function and post-transcription. To explore the expression profile and possible functions of circRNAs in the soybean CMS line NJCMS1A and CMS maintainer NJCMS1B, high-throughput sequencing coupled with RNase R enrichment strategy was conducted. CircRNA libraries were constructed from the flower buds of NJCMS1A and NJCMS1B with three biological replicates. A total of 2867 circRNAs were identified, with 1009 circRNAs differentially expressed between NJCMS1A and NJCMS1B. Different expression levels of 12 randomly selected circRNAs were tested by quantitative real-time PCR, of which 10 showed consistent expression patterns with the high-throughput sequencing results. Tissue specific expression patterns were also verified by quantitative real-time PCR. Most parental genes of differentially expressed circRNAs were involved in biological processes such as metabolic process, biological regulation, and reproductive process. Moreover, 83 miRNAs were predicted from differentially expressed circRNAs, some of which were closely related to pollen development and male fertility; The functions of miRNA targets were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and the target mRNAs were significantly enriched in signal transduction and programmed cell death. Furthermore, a total of 165 soybean circRNAs were predicted to contain at least one internal ribosome entry site (IRES) element and an open reading frame, indicating their potential to encode polypeptides or proteins. Our study indicated that the circRNAs might participate in the regulation of flower and pollen development, which could provide a new insight into the molecular mechanisms of CMS in soybean.