How does nematode infection activate plant defense response in soybean?

Soybean cyst nematode (SCN) is one of the devastating diseases in soybean worldwide. Host-plant resistance is the most economical and effective method to control SCN disease.  

However, SCN resistance is a multigenic and quantitative trait in soybean, and most resistance sources are easily broken due to long-time planting of the same cultivars. Therefore, it is urgent to deeply understand the resistance mechanism, develop multi-resistance gene resources, and breed multi-resistance varieties.

A research team led by Prof. WANG Congli from the Northeast Institute of Geography and Agroecology of the Chinese Academy of Sciences, for the first time, utilized full-length transcriptome sequencing (FITS) technology to investigate SCN resistance in soybean.

This study was published in Frontiers in Plant Science.

The third-generation FLTS technology can directly read the full-length sequence of the RNA molecule without interruption. It also has the advantages of quantitative analysis of genes and transcripts at the same time.

The researchers confirmed a new soybean breeding genotype 09-138 (rhg1a + Rhg4b), which is resistant to the highly toxic SCN race 4 (SCN4) but susceptible to SCN5 with less virulence.  

The FLTS analysis of 9 cDNA libraries of 09-138 with SCN4, SCN5 and control treatments demonstrated an average of 6.1Gbp of clean data for each library, a total of 1,117 new genes and 41,096 novel transcripts.  

Through structural analysis of the novel transcripts, the researchers found that post-transcriptional modification, such as alternative splicing (AS), alternative polyadenylation (APA), fusion genes and long non-coding RNA (lncRNA), were involved in defense response.

The researchers found that stress response elements, plant hormone signal transduction pathway and plant-pathogen interaction pathway were involved in resistance defense responses, cell wall modifications and metabolic pathways related to carbohydrate biological processes were involved in the susceptible response, while the phenylpropane biosynthesis pathway was involved in both resistant and susceptible response.

Protein-protein interaction analysis combined with differentially expressed genes (DEGs) displayed, for the first time, that SCN4 incompatible response activated the interactions among the kinases MAPK/KK/KKK, the transcription factor WRKY, and the calmodulin VQ to regulate resistance defense. A defense model associated with MAPK-WRKY-VQ was established for SCN resistance in soybean.

These findings show that full-length transcriptome sequencing provides a powerful tool to study plant defense mechanism in the levels of transcription and post-transcriptional modifications.