New research conducted at Southern University of Science and Technology (SUSTech) may have revealed the biogenesis mechanism of soybean 22-nt siRNA and its important role in regulating seed coat color.

On October 19, Associate Professor Jixian Zhai (Institute of Plant and Food Science, Department of Biology) led his research team to publish a ground-breaking paper in the high impact academic journal, The Plant Cell. The paper was titled “Soybean Dicer-Like 2 Regulates Seed Coat Color via Production of Primary 22-nt Small Interfering RNAs from Long Inverted Repeats“.

Small RNAs (sRNA), including microRNA (miRNA) and small interfering RNA (siRNAs), are produced by Dicer-like (DCL) protein and tend to be between 21-24 nucleotides (nt) long. sRNAs can cleavage the mRNAs and suppress the expression of target genes. In plants, sRNAs that are 22 nucleotides (nt) in length have the unique capacity to trigger the production of secondary small interfering RNAs (siRNAs) and further enhance silencing. While DCL2-dependent 22-nt siRNAs are rare in Arabidopsis and thought to have few functions except during viral infection, they are abundant in many major crops such as soybean and maize.

The researchers studied soybean 22-nt siRNAs by applying CRISPR-Cas9 genome editing technology to simultaneously knock out the two copies of soybean DCL2, GmDCL2a and GmDCL2b, in the Tianlong1 cultivar. sRNA sequencing revealed that the majority of 22-nt siRNAs are derived from long inverted repeats (LIRs) and disappeared in Gmdcl2a/2b double mutant. By de novo assembly of a Tianlong1 reference genome and transcriptome profiling, the researchers found an intron-located LIR formed by chalcone synthase (CHS) genes CHS1 and CHS3. This LIR is the source of the primary 22-nt siRNAs that target other CHS family genes and trigger the production of secondary 21-nt siRNAs. Disruption of this process in Gmdcl2a/2b substantially increased the level of CHS mRNAs in the seed coat, and changed the color from yellow to brown. The study demonstrated that endogenous LIR-derived transcripts in soybean are predominately processed by GmDCL2 into 22-nt siRNAs, and uncovered a previously overlooked role of DCL2 in regulating natural traits.

Figure: DCL2-dependent 22-nt siRNAs regulate seed coat color in soybean

Associate Professor Jixian Zhai at SUSTech and Professor Bin Liu at the Institute of Crop Sciences of the Chinese Academy of Agricultural Sciences are the corresponding authors. Research assistant professors Dr. Jinbu Jia at SUSTech and Dr. Ronghuan Ji at the Institute of Crop Sciences of the Chinese Academy of Agricultural Sciences are the co-first authors. Additional contributions came from the Donald Danforth Plant Science Center and South China Agricultural University.

The research paper received support from the National Key R&D Program of China Grant, the Program for Guangdong Introducing Innovative and Entrepreneurial Teams, the Shenzhen Sci-Tech Fund, the Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, the National Natural Science Foundation of China, the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences, and the Central Public-Interest Scientific Institution Basal Research Fund.

Paper link: http://www.plantcell.org/content/early/2020/10/19/tpc.20.00562