Nematode Resistance in Soybean - Translational Genomics for Crop Breeding: Biotic Stress - page 107

which was previously reported to be associated
with resistance to SCN (Vuong et al. 2011).
Several genetic populations derived from new
RN resistance PIs have been developed and can
be utilized for the discovery of novel genomic
regions or genes underlying resistance to RN
using genotyping by sequencing (GBS) method.

Kim et al. (2010) identified the rhg1-b locus,
which is different from the previously pub-
lished rhg1 from PI 88788. Lately, the rhg1b
and R hg4 loci have been claimed to be cloned
with functional evidences. For rhg1b , three
genes—Glyma18g02580, Glyma18g02590, and
Glyma18g02610—are confirmed to be responsi-
ble for the rhg1b locus, which encode predicted
amino acid transporter, predicted alpha-SNAP
protein, and wound induced protein (Bent et al.
2012). For the Rhg4 locus, the gene that does not
encode any of the canonical classes of disease
resistance proteins in plant was cloned (Mitchum
et al. 2012). These remarkable findings enabled
soybean scientists to elucidate the mechanism
underlying nematode resistance in soybean and
also provided valuable tools to improve soybean
nematode resistance in the future.

Candidate Genes for HostPlant
Resistance and Host-Nematode
Interaction

Host Genes Involved in Nematode
Resistance

For decades, the utilization of resistant culti-
vars in combination with non-host crop rota-
tion and nematicide applications has been tra-
ditional methods to manage nematode problems
in soybean. Meanwhile, geneticists and molec-
ular biologists have been trying to identify the
resistance genes from host plants and to eluci-
date underlying resistance mechanism, aiming to
develop new varieties through advanced molec-
ular biotechnologies. The technologies that have
been demonstrated to be successful approaches
for the identification and characterization of can-
didate genes are reviewed in this section.

TranscriptomeAnalysesofNematode
ResistancesinSoybean

To elucidate how nematodes are established in
hosts, scientists have conducted large-scale anal-
yses of host or nematode gene expressions at the
time of infection to identify differentially regu-
lated genes and potential pathways involved. In
an earlier investigation, Hermsmeier et al. (1998)
used differential display of mRNA to detect host
gene expression changes during the early com-
patible interaction between soybean and SCN.
The authors identified 15 genes with different
expressions in SCN-infected versus uninfected
roots. Of those, the ADR12 gene was identi-
fied to be involved in soybean auxin down-
regulation, suggesting that the auxin pathway
may be involved in soybean-nematode interac-
tion (Hermsmeier et al. 1998).
Microarray gene expression profiling also
enables scientists to detect and compare tran-
scriptional changes of thousands of genes simul-
taneously when susceptible and non-host inter-
action happens. Using this method, a broader
study of the transcriptional changes associated
with both susceptible and non-host interactions
was conducted, which revealed important details

NematodeResistanceGenesClonedby
Map-BasedCloning

Map-based cloning, or positional cloning, is an
effective method to clone the genes controlling
the important agronomic traits in crop plants.
The most important genes conferring resistance
to SCN in soybean, rhg1 and Rhg4 , have been
claimed to have been cloned (Hauge et al. 2001;
Lightfoot and Meksem 2002). Both of them
encode the NBS-LRR protein, but no functional
evidence was provided to indicate successful
cloning of these genes. Recently, two groups
reported that the rhg1 and Rhg4 genes previ-
ously cloned are not really the genes respon-
sible for resistance to SCN in soybean (Liu
et al. 2011; Melito et al. 2010). Moreover,