The June 2020 Editor’s pick for MPMI is “RNA Sequencing-Associated Study Identifies GmDRR1 as Positively Regulating the Establishment of Symbiosis in Soybean” with corresponding authors Dawei Xin and Qingshan Chen from the Northeast Agricultural University in Harbin, China. To read more about Dawei you can find his bio here.

RNA Sequencing-Associated Study Identifies GmDRR1 as Positively Regulating the Establishment of Symbiosis in Soybean

Submitted by Dawei Xin and Qingshan Chen

Soybean is one of the most important crops in the world, supplying protein and oil to humans and animals. Symbiosis is a special characteristic of legumes that allows them to fix nitrogen from the air. However, chemical nitrogen fertilization is still the main source utilized in legume crops, which causes serious pollution in the environment. Too little is understood about the mechanism of symbiosis, which impedes utilization of symbiosis in agriculture. The benefits of symbiosis encourages us to become more familiar with the molecular mechanism of legume–Rhizobium interaction. The genes of Rhizobium sp. and host both play a pivotal role in symbiosis establishment.

In recent decades, type Ⅲ effector (T3E) was found and identified as playing a pivotal role in nodule formation. To date, there is no gene has been identified in a legume host that directly interacts with T3E. Our lab has been working to identify the genes that might interact with T3E and the soybean response mechanism to Rhizobium spp. Considering the complex genetic background of soybean, we selected a genetic population to identify the genes underlying symbiosis and the response to T3E. Chromosome segment substituted lines (CSSL) with wild soybean genomic sequences are an ideal genetic material to locate quantitative trait loci (QTL) and mining genes in the target chromosome regions.

Identifying special soybean lines

To identify the chromosome region that might underlie symbiosis and the response to T3E during symbiosis establishment, we screened the CSSL population, first to compare the nodule-related phenotype and genotype of CSSL. After inoculation with wild-type Rhizobium sp., two lines of CSSL were identified. One line can form more nodules than the recurrent parent, and other can form fewer nodules than the recurrent parent. This supports the hypothesis that substituted chromosome segments play a role in the identified phenotype. The substituted segments on the chromosome were detected by resequencing the genome of two identified lines of CSSL and the recurrent parent.

Mining the response of candidate genes to Rhizobium sp. and T3E

As there are no single substituted segments on the chromosome, we needed to identify the target region to reduce our workload. To accomplish this, we used CSSL to map the QTL underlying nodule number after inoculation with a wild Rhizobium sp. and derived T3E mutant. At the same time, RNA sequencing was performed to detect the gene expression pattern located in the substituted segment of chromosome. We used a wild-type Rhizobium sp. and T3E mutant strain to inoculate the two identified CSSL lines and the recurrent parent. Many different expression genes were found. To delimitate the region on the chromosome, we used the QTL assistant to find the chromosome region. Because the length of substituted segments can be identified by genomic resequencing and molecular analysis, we can narrow down the chromosome region to a shortened region. This was a great help to us in identifying the candidate for further work. Now, several candidate genes that can interact with T3E have been identified, and we have designed a more detailed experiment to elucidate the interaction mechanism.

We are pleased that our work was accepted for publication by MPMI and that we could share our findings with other researchers who we followed during manuscript preparation.

We duly acknowledge funding from the Nature Science Foundation of China and the graduate students of our lab at Northeast Agricultural University.

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