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.
