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 is easily broken due to long planting of same cultivars. Therefore, it is urgent to gain more understanding of resistance mechanism to develop multi-resistance gene resources and breed multi-resistance varieties.

The third-generation full-length transcriptome sequencing technology （FLTS）can directly read the full-length sequence of the RNA molecule without interruption, and accurately identify those that cannot be accurately identified by the second-generation sequencing technology (NGS), such as alternative splicing (AS), alternative polyadenylation (APA), fusion gene, long non-coding RNA (lncRNA) and other structures, and has the advantages of quantitative analysis of genes and transcripts at the same time. FLTS for inferring an improving gene model and identifying novel genes has been reported on rice, wheat, maize and others but not on soybean.

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 utilize FITS to investigate SCN resistance in soybean. This study was published in Frontiers in Plant Science.

The researches 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 1117 new genes and 41,096 novel transcripts; the structural analysis of the novel transcripts found that post-transcriptional modification, such as AS, APA, fusion genes and lncRNA, involved in defense response.

The GO and metabolic pathway KEGG enrichment analysis of differentially expressed genes (DEGs) indicated 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 are involved in the susceptible response, while the phenylpropane biosynthesis pathway is involved in both resistant and susceptible response.

Protein-protein interaction analysis combined with 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.

This finding show that full-length transcriptome sequencing provides a powerful tool to study plant defense mechanism in the levels of transcription and post-transcriptional modifications (such as AS, APA, lncRNA, etc.). The established new model will help to analyze the resistance mechanism between other plant-nematode interactions. The identified candidate genes provide new resistance gene resources for disease resistance breeding and engineering resistance.

Contact: WANG Congli

Northeast Institute of Geography and Agroecology

E-mail: wangcongli@iga.ac.cn