Species & Dataset

  • Glycine max

  • Common name: Soybean

  • Family: Fabaceae

Foliar Ozone Injury

Glycine INJURY.jpeg

Experiment

  • Cultivar: Glycine max L.

  • Tissue: Seed coat

  • Ozone concentration: Ambient ozone (50.6 nL L−1)                   Elevated ozone (69.7 nL L−1 ± 1.3 nL L−1)

  • Ozone exposure: Throughout the  experiment (8 hours/day)

  • Platform: Hiseq 2000 (Illumina)

  • Year of study: 2017

  • Location: Urbana, USA

Title: Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress

 

Summary: Understanding how intensification of abiotic stress due to global climate change affects crop yields is important for continued agricultural productivity. Coupling genomic technologies with physiological crop responses in a dynamic field environment is an effective approach to dissect the mechanisms underpinning crop responses to abiotic stress. Soybean (Glycine max L. Merr. cv. Pioneer 93B15) was grown in natural production environments with projected changes to environmental conditions predicted for the end of the century, including decreased precipitation, increased tropospheric ozone concentrations ([O3]), or increased temperature.  All three environmental stresses significantly decreased leaf-level photosynthesis and stomatal conductance, leading to significant losses in seed yield. This was driven by a significant decrease in the number of pods per node for all abiotic stress treatments. To understand the underlying transcriptomic response involved in the yield response to environmental stress, RNA-Sequencing analysis was performed on the soybean seed coat, a tissue that plays an essential role in regulating carbon and nitrogen transport to developing seeds. Gene expression analysis revealed 49, 148 and 1,576 differentially expressed genes in the soybean seed coat in response to drought, elevated [O3] and elevated temperature, respectively. Elevated [O3] and drought did not elicit substantive transcriptional changes in the soybean seed coat. However, this may be due to the timing of sampling and does not preclude impacts of those stresses on different tissues or different stages in seed coat development. Expression of genes involved in DNA replication and metabolic processes were enriched in the seed coat under high temperate stress, suggesting that the timing of events that are important for cell division and proper seed development were altered in a stressful growth environment.

 

Data repository: Small Read Archive (http://www.ncbi.nlm.nih.gov/sra), SRA089043, BioProject number PRJNA207354.

Reference: Leisner, C.P., Yendrek, C.R. and Ainsworth, E.A., 2017. Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress. BMC plant biology, 17(1), pp.1-11.

Gene
logFC
p-value
FDR p-value
Functional Annotation
Glyma14g39930
0.948097498
0.00025872
0.085574935
alpha-amylase-like 2
Glyma07g01400
2.576431338
0.000259466
0.085574935
phosphate starvation-induced gene 2
Glyma06g17760
1.401452601
0.000259593
0.085574935
Major facilitator superfamily protein
Glyma08g26150
0.885683765
0.000265609
0.086613151
Sec14p-like phosphatidylinositol transfer family protein
Glyma13g36780
2.787841014
0.000267844
0.086613151
late embryogenesis abundant domain-containing protein / LEA domain-containing protein
Glyma09g29630
-1.114994313
0.000271544
0.08674887
Kinase interacting (KIP1-like) family protein
Glyma14g06600
0.81731602
0.000273374
0.08674887
Transmembrane amino acid transporter family protein
Glyma11g32600
2.595503231
0.000280189
0.086765776
cysteine-rich RLK (RECEPTOR-like protein kinase) 2
Glyma12g06820
-1.151763157
0.000282008
0.086765776
actin-11
Glyma15g41970
0.734618182
0.000284372
0.086765776
Eukaryotic aspartyl protease family protein
Glyma06g09660
2.513315131
0.000285642
0.086765776
hydroxyproline-rich glycoprotein family protein
Glyma08g38840
-0.637672673
0.000286204
0.086765776
phosphate transporter 2;1
Glyma13g25900
1.339003899
0.0002938
0.088280319
alpha/beta-Hydrolases superfamily protein
Glyma13g31595
3.362012078
0.0003021
0.089683271
Glyma17g05450
-1.244314062
0.000303751
0.089683271
GDSL-like Lipase/Acylhydrolase superfamily protein
Glyma03g40021
1.047744527
0.000312643
0.091117647
GDSL-like Lipase/Acylhydrolase superfamily protein
Glyma04g00570
1.65301341
0.000313977
0.091117647
actin depolymerizing factor 5
Glyma13g09620
-0.738648023
0.000316682
0.091124006
Protein kinase protein with adenine nucleotide alpha hydrolases-like domain
Glyma13g00590
0.676514355
0.000321216
0.09165194
OSBP(oxysterol binding protein)-related protein 4B
Glyma17g02600
2.356529683
0.000331899
0.092316985
Uncharacterised protein family (UPF0497)
Glyma18g25160
-0.637249666
0.000336613
0.092316985
expansin A4
Glyma11g00710
1.85126222
0.000336683
0.092316985
Major facilitator superfamily protein
Glyma09g00550
-0.733696966
0.000341042
0.092316985
beta glucosidase 13
Glyma11g14040
-2.886636614
0.000342104
0.092316985
Integrase-type DNA-binding superfamily protein
Glyma03g26640
2.07578139
0.000345215
0.092316985
Auxin efflux carrier family protein
Glyma20g36880
-0.714051932
0.000352349
0.092316985
winged-helix DNA-binding transcription factor family protein
Glyma19g41550
0.659923453
0.000353334
0.092316985
Nucleotide-diphospho-sugar transferases superfamily protein
Glyma13g19800
-1.019410515
0.000355865
0.092316985
Glyma08g40100
0.883732946
0.000358229
0.092316985
Xanthine/uracil permease family protein
Glyma18g19670
-0.837910206
0.000359759
0.092316985
Pectin lyase-like superfamily protein
Glyma18g41650
2.989735105
0.000362181
0.092316985
HSP20-like chaperones superfamily protein
Glyma18g18060
0.939218194
0.000362272
0.092316985
Xanthine/uracil permease family protein
Glyma15g16260
1.206571212
0.00036334
0.092316985
ethylene-responsive element binding protein
Glyma05g01920
-1.008624952
0.000366436
0.092316985
RHO-related protein from plants 10
Glyma19g45230
1.179723547
0.000367881
0.092316985
GDSL-motif lipase 5
Glyma18g08930
-1.018255927
0.000371083
0.092316985
cytochrome P450, family 71, subfamily B, polypeptide 34
Glyma12g04850
1.786641992
0.000375041
0.092316985
Glyma12g02300
-0.507951095
0.000375206
0.092316985
ABC-2 type transporter family protein
Glyma04g02621
1.055264589
0.000388936
0.095006723
Glyma07g37270
2.594283009
0.000397862
0.096399208
MLP-like protein 423
Glyma17g29060
-1.060735172
0.000400315
0.096399208
Cellulose-synthase-like C5
Glyma02g45810
0.784795839
0.000406828
0.096477714
alpha-crystallin domain 32.1
Glyma10g37400
0.951133071
0.000407056
0.096477714
VIRB2-interacting protein 1
Glyma06g15411
2.139348794
0.000411735
0.096477714
Glyma10g30820
2.151822002
0.000412006
0.096477714
plasmodesmata-located protein 2
Glyma03g07590
2.649396916
0.000420774
0.097855893
Homeodomain-like superfamily protein
Glyma12g34370
-1.167958058
0.000424796
0.098119271
histone H2A 2
Glyma19g41410
7.779243067
9.59E-05
0.060913048
Glycosyl hydrolase superfamily protein
Glyma08g16850
1.244810629
9.65E-05
0.060913048
Glyma14g36380
1.626280768
9.85E-05
0.060913048
hydroxyproline-rich glycoprotein family protein
Glyma15g08860
3.837779631
0.00010149
0.060913048
Dof-type zinc finger DNA-binding family protein
Glyma13g19200
-1.031202737
0.000101574
0.060913048
Protein of unknown function (DUF3741)
Glyma0220s50
1.075172804
0.000101725
0.060913048
Disease resistance protein (TIR-NBS-LRR class) family
Glyma04g37320
2.134352425
0.000102257
0.060913048
Major facilitator superfamily protein
Glyma14g38101
1.316516593
0.000105101
0.06152769
O-methyltransferase family protein
Glyma08g25520
1.897500118
0.000109523
0.062437197
kunitz trypsin inhibitor 1
Glyma13g01560
-0.696400067
0.000111821
0.062437197
Fatty acid hydroxylase superfamily
Glyma17g33370
1.096069703
0.000112171
0.062437197
Concanavalin A-like lectin protein kinase family protein
Glyma10g01610
1.193331683
0.00011416
0.062518974
CP12 domain-containing protein 2
Glyma07g03220
-0.75291091
0.000118481
0.062644865
Inorganic H pyrophosphatase family protein
Glyma18g10930
1.126087164
0.000119002
0.062644865
Protein of unknown function, DUF584
Glyma09g22306
1.7468551
0.000119924
0.062644865
Caleosin-related family protein
Glyma10g41531
-1.516355211
0.000136788
0.068456619
Zinc finger C-x8-C-x5-C-x3-H type family protein
Glyma08g37240
-0.614045364
0.000137386
0.068456619
beta HLH protein 93
Glyma11g12810
-2.541197175
0.000138469
0.068456619
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein
Glyma10g35550
-0.593858643
0.000140061
0.068456619
PATATIN-like protein 6
Glyma04g03130
1.240609371
0.000142339
0.068456619
cytokinin oxidase 5
Glyma18g08550
-0.614549089
0.000144558
0.068456619
acyl-CoA synthetase 5
Glyma05g32700
0.636035507
0.000147067
0.068456619
Copine (Calcium-dependent phospholipid-binding protein) family
Glyma03g39620
-0.737997479
0.00014718
0.068456619
Actin-binding FH2 (formin homology 2) family protein
Glyma13g31290
0.935198139
0.000166704
0.076165927
phosphate 2
Glyma02g41150
1.176263009
0.000171655
0.076165927
HSP20-like chaperones superfamily protein
Glyma02g38250
1.846081264
0.00017237
0.076165927
hydroxyproline-rich glycoprotein family protein
Glyma20g27180
-1.592431552
0.000172954
0.076165927
CYCLIN D1;1
Glyma19g41930
0.852361019
0.00017497
0.076165927
F-box family protein
Glyma08g44190
-0.750661712
0.000179048
0.076719739
acyl-CoA synthetase 5
Glyma15g42140
-0.80291347
0.000180762
0.076719739
ATP-citrate lyase A-1
Glyma18g02980
1.758546342
0.000192247
0.080302655
Plant protein of unknown function (DUF828)
Glyma18g03550
-0.767450547
0.000201593
0.080302655
Protein of unknown function (DUF620)
Glyma11g08830
0.791872976
0.000202164
0.080302655
Vacuolar iron transporter (VIT) family protein
Glyma17g09110
-1.265270988
0.000203132
0.080302655
strictosidine synthase 2
Glyma12g29010
-2.193933014
0.000204847
0.080302655
homeobox protein 21
Glyma11g06611
1.414499279
0.000206698
0.080302655
Protein of unknown function, DUF547
Glyma20g36690
-0.76692641
0.00020803
0.080302655
NIMA-related kinase 2
Glyma02g39370
-0.840673397
0.000209628
0.080302655
potassium transporter 1
Glyma10g26740
1.462971436
0.000210489
0.080302655
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein
Glyma15g42050
-2.825562596
0.000216576
0.080374645
NAC (No Apical Meristem) domain transcriptional regulator superfamily protein
Glyma17g09310
-0.807034969
0.000217171
0.080374645
myb domain protein 86
Glyma19g32070
-0.667664049
0.000217779
0.080374645
magnesium-chelatase subunit chlH, chloroplast, putative / Mg-protoporphyrin IX chelatase, putative (CHLH)
Glyma06g36590
-1.737059521
0.000228173
0.082638179
early nodulin-like protein 1
Glyma04g40580
-0.793335672
0.00022878
0.082638179
O-methyltransferase 1
Glyma09g41000
-0.840212589
0.000240322
0.085039577
Glycosyl hydrolase superfamily protein
Glyma04g37391
1.305448334
0.000243067
0.085039577
Squamosa promoter-binding protein-like (SBP domain) transcription factor family protein
Glyma08g08200
-1.002550435
0.000243967
0.085039577
senescence-associated gene 29
Glyma02g00440
0.721375861
0.00024658
0.085039577
S-adenosyl-L-methionine-dependent methyltransferases superfamily protein
Glyma15g41130
1.043409475
0.000247951
0.085039577
SAUR-like auxin-responsive protein family
Glyma05g07630
-1.171589929
0.000258488
0.085574935
Calcium-dependent phosphotriesterase superfamily protein
Glyma07g31630
1.588263727
3.33E-08
0.001130314
phosphate 2
Glyma14g04940
-1.826402686
1.14E-07
0.001931761
Glycosyl hydrolase family protein
Glyma07g06750
3.285695425
4.05E-07
0.004588966
BCL-2-associated athanogene 6
Glyma07g31790
5.950924294
9.45E-07
0.008018868
ralf-like 19
Glyma19g22790
7.074291378
1.62E-06
0.010125767
Plant invertase/pectin methylesterase inhibitor superfamily
Glyma02g42000
4.110033116
1.79E-06
0.010125767
HSP20-like chaperones superfamily protein
Glyma14g17863
2.814959307
4.35E-06
0.018686449
phytochromobilin:ferredoxin oxidoreductase, chloroplast / phytochromobilin synthase (HY2)
Glyma06g47750
3.62223386
4.40E-06
0.018686449
Glyma07g01250
-0.86823461
5.30E-06
0.020013724
beta galactosidase 1
Glyma13g07735
-1.096291989
8.19E-06
0.027557896
phosphoglycerate kinase 1
Glyma14g05760
4.631255685
8.93E-06
0.027557896
Glyma14g04700
-3.888879694
1.00E-05
0.028363232
GroES-like zinc-binding dehydrogenase family protein
Glyma12g07841
2.636875995
1.19E-05
0.031074547
Glyma19g42240
-1.00090825
1.35E-05
0.032737445
histone H2A 7
Glyma13g24810
1.134721578
1.63E-05
0.034238471
phosphate 2
Glyma06g17640
2.285878771
1.70E-05
0.034238471
fatty acyl-ACP thioesterases B
Glyma10g36790
-1.563055892
1.74E-05
0.034238471
cellulose synthase 6
Glyma12g06010
-3.799446476
1.82E-05
0.034238471
Integrase-type DNA-binding superfamily protein
Glyma20g28640
4.676482564
1.94E-05
0.034685961
cupin family protein
Glyma02g00260
0.901435485
2.44E-05
0.04046263
AUX/IAA transcriptional regulator family protein
Glyma09g36830
-1.970666828
2.50E-05
0.04046263
Galactosyltransferase family protein
Glyma03g14150
0.875682966
2.73E-05
0.042097856
plasma membrane intrinsic protein 1;4
Glyma09g03042
3.348067663
3.23E-05
0.047720121
Glyma12g29840
-1.35363226
3.47E-05
0.048235338
cyclic nucleotide-gated channel 15
Glyma17g37800
-1.081129772
3.55E-05
0.048235338
Pathogenesis-related thaumatin superfamily protein
Glyma08g00535
1.455024787
3.82E-05
0.049856805
fatty acid amide hydrolase
Glyma17g08310
-1.041848828
4.46E-05
0.054886027
aldehyde dehydrogenase 11A3
Glyma05g02550
-0.872715275
4.53E-05
0.054886027
myb domain protein 86
Glyma14g06900
3.532111557
4.90E-05
0.05615386
HSP20-like chaperones superfamily protein
Glyma04g08410
3.384433577
5.07E-05
0.05615386
BURP domain-containing protein
Glyma11g12460
-4.923561249
5.13E-05
0.05615386
RAD-like 6
Glyma09g12252
3.56746704
5.46E-05
0.057579699
Glyma08g28050
-3.706970173
5.60E-05
0.057579699
Glyma13g13300
-2.544744194
5.97E-05
0.058361276
GDSL-like Lipase/Acylhydrolase superfamily protein
Glyma03g03360
3.871108585
6.02E-05
0.058361276
Plant invertase/pectin methylesterase inhibitor superfamily
Glyma06g12150
2.818503434
6.37E-05
0.060063995
beta-galactosidase 16
Glyma17g16160
2.355567878
7.16E-05
0.060913048
Plant invertase/pectin methylesterase inhibitor superfamily protein
Glyma01g02330
2.261560618
7.23E-05
0.060913048
phosphoenolpyruvate carboxykinase 1
Glyma02g42627
3.207132747
7.49E-05
0.060913048
Glyma06g03110
3.568453911
7.50E-05
0.060913048
Integrase-type DNA-binding superfamily protein
Glyma11g34740
-0.98481775
7.58E-05
0.060913048
Protein of unknown function (DUF620)
Glyma17g12910
-0.615020885
7.63E-05
0.060913048
pleiotropic drug resistance 4
Glyma18g44053
-0.928970863
8.01E-05
0.060913048
SCAR homolog 2
Glyma12g13130
-2.011280155
8.09E-05
0.060913048
early nodulin-like protein 1
Glyma14g06230
0.944377523
8.11E-05
0.060913048
Leucine-rich repeat protein kinase family protein
Glyma15g01690
1.986390588
8.64E-05
0.060913048
Coatomer, beta\' subunit
Glyma07g28610
3.266634164
8.76E-05
0.060913048
Glyma19g42230
-0.684837581
8.78E-05
0.060913048
Actin-binding FH2 (formin homology 2) family protein
Glyma13g24210
-5.040055537
9.55E-05
0.060913048
O-methyltransferase family protein
Glyma04g42520
2.504514646
9.56E-05
0.060913048
amino acid permease 3