Gene Chip representing 61K probe sets is frequently being used for transcriptome
analysis of soybean RNA samples under drought stress (Haerizadeh et al. 2011; Le
et al. 2012). The normalized expression data generated using the Affymetrix Gene
Chip can be utilized to compare soybean experiments performed across the
world. RNA-seq, another cost-effective and high-throughput technique, analyzes
transcriptome by sequencing. The RNA-seq approach has several advantages over
the microarray technology where available genomic information is used. For
Table 4.5 List of differentially expressed genes (DEGs) related to drought tolerance in soybean
Genotype
name
Number of
DEGs/
candidate
genes
Putative functions
Platform used
References
Glycine
max
L. Merr
9148 genes
Genes related to membrane
transport, defense signaling,
metabolism associated with
roots
Affymetrix
chips
containing
37,500 probe
sets
Haerizadeh
et al. (2011)
Williams
82
3276 for V 6
3270 for R 2
Expression of many GmNAC
and hormone-related genes
61 K
Affymetrix
Soybean Array
GeneChip
Le et al.
(2012)
DT 2008
and W82
822 and
632 genes
Genes related to osmoprotectant
biosynthesis cell wall-related
proteins phosphatase 2C
proteins TFs (NAC, AP2)
66 K
Affymetrix,
Soybean Array
GeneChip
Ha et al.
(2015)
Pana and
PI 567690
1914 and
670
Hydrolase activity
carbohydrate/lipid metabolism
apoplast, and chlorophyll a/b
binding proteins xyloglucan
endo-transglycosylases
–
Prince et al.
(2015b)
Williams
82
6609
Genes related to cell wall
modification, lipid metabolism,
carbohydrate metabolism,
hormonal pathways, and TFs
Illumina
HiSeq 2000
Song et al.
(2016)
Glycine
max
L. Merr
49, 148, and
1576 genes,
respectively
RNASeq analysis was
performed on seed coat which
plays a crucial role in
controlling carbon and nitrogen
transfer to developing seed set
RNASeq
Leisner
et al. (2017)
Williams
82
GmWRKY12 Increase in proline (Pro) content
and decreased malondialdehyde
content
RNA-Seq,
qRT-PCR
Shi et al.
(2018)
Williams
NAC4,
NAC29,
NAC25,
NAC72
2771 DEGs 1798 genes were
upregulated and 973 were
downregulated and related to
ABA biogenesis, secondary
metabolite synthesis, etc.
RNA-Seq,
HiSeq4000
Xu et al.
(2018)
102
G. K. Satpute et al.
analysis of soybean RNA samples under drought stress (Haerizadeh et al. 2011; Le
et al. 2012). The normalized expression data generated using the Affymetrix Gene
Chip can be utilized to compare soybean experiments performed across the
world. RNA-seq, another cost-effective and high-throughput technique, analyzes
transcriptome by sequencing. The RNA-seq approach has several advantages over
the microarray technology where available genomic information is used. For
Table 4.5 List of differentially expressed genes (DEGs) related to drought tolerance in soybean
Genotype
name
Number of
DEGs/
candidate
genes
Putative functions
Platform used
References
Glycine
max
L. Merr
9148 genes
Genes related to membrane
transport, defense signaling,
metabolism associated with
roots
Affymetrix
chips
containing
37,500 probe
sets
Haerizadeh
et al. (2011)
Williams
82
3276 for V 6
3270 for R 2
Expression of many GmNAC
and hormone-related genes
61 K
Affymetrix
Soybean Array
GeneChip
Le et al.
(2012)
DT 2008
and W82
822 and
632 genes
Genes related to osmoprotectant
biosynthesis cell wall-related
proteins phosphatase 2C
proteins TFs (NAC, AP2)
66 K
Affymetrix,
Soybean Array
GeneChip
Ha et al.
(2015)
Pana and
PI 567690
1914 and
670
Hydrolase activity
carbohydrate/lipid metabolism
apoplast, and chlorophyll a/b
binding proteins xyloglucan
endo-transglycosylases
–
Prince et al.
(2015b)
Williams
82
6609
Genes related to cell wall
modification, lipid metabolism,
carbohydrate metabolism,
hormonal pathways, and TFs
Illumina
HiSeq 2000
Song et al.
(2016)
Glycine
max
L. Merr
49, 148, and
1576 genes,
respectively
RNASeq analysis was
performed on seed coat which
plays a crucial role in
controlling carbon and nitrogen
transfer to developing seed set
RNASeq
Leisner
et al. (2017)
Williams
82
GmWRKY12 Increase in proline (Pro) content
and decreased malondialdehyde
content
RNA-Seq,
qRT-PCR
Shi et al.
(2018)
Williams
NAC4,
NAC29,
NAC25,
NAC72
2771 DEGs 1798 genes were
upregulated and 973 were
downregulated and related to
ABA biogenesis, secondary
metabolite synthesis, etc.
RNA-Seq,
HiSeq4000
Xu et al.
(2018)
102
G. K. Satpute et al.