Species & Dataset

  • Phaseolus vulgaris

  • Common name: Common bean

  • Family: Fabaceae

Foliar Ozone Injury

Phaseolus injury.jpg

Experiment

  • Cultivar: Phaseolus vulgaris L.

  • Tissue: Shoot leaves

  • Ozone concentration: Ambient ozone (12.5 nL L−1 ± 0.96 nL L−1)

  •  Elevated ozone (151.2 nL L−1 ± 0.72 nL L−1)

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

  • Sampling time: 11-13 days after planting

  • Platform: Hiseq 2000 (Illumina)

  • Year of study: 2015

  • Location: Urbana, USA

Title: A comparative analysis of transcriptomic, biochemical, and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crop 

Summary: Current concentrations of tropospheric ozone ([O3]) pollution negatively impact plant metabolism, which can result in decreased crop yields. Interspecific variation in the physiological response of plants to elevated [O3] exists; however, the underlying cellular responses explaining species-specific differences are largely unknown. Here, a physiological screen has been performed on multiple varieties of legume species. Three varieties of garden pea (Pisum sativum L.) were resilient to elevated [O3]. Garden pea showed no change in photosynthetic capacity or leaf longevity when exposed to elevated [O3], in contrast to varieties of soybean (Glycine max (L.) Merr.) and common bean (Phaseolus vulgaris L.). Global transcriptomic and targeted biochemical analyses were then done to examine the mechanistic differences in legume responses to elevated [O3]. In all three species, there was an O3-mediated reduction in specific leaf weight and total non-structural carbohydrate content, as well as increased abundance of respiration-related transcripts. Differences specific to garden pea included a pronounced increase in the abundance of GLUTATHIONE REDUCTASE transcript, as well as greater contents of foliar glutathione, apoplastic ascorbate, and sucrose in elevated [O3]. These results suggest that garden pea may have had greater capacity for detoxification, which prevented net losses in CO2 fixation in an elevated [O3] environment

 

Data repository: NCBI [GenBank: SRP009826]

Reference: Yendrek, C.R., Koester, R.P. and Ainsworth, E.A., 2015. A comparative analysis of transcriptomic, biochemical, and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crops. Journal of experimental botany, 66(22), pp.7101-7112.

Gene id
log2FC
Ambient RPKM
Elevated RPKM
Gene Annnotation
Phvul.004G013500.1
-0.7
8.23
4.83
CARBONIC ANHYDRASE
Phvul.009G178900.1
1.09
4.22
8.59
CARBONIC ANHYDRASE
Phvul.004G013500.3
-0.7
48.05
28.16
CARBONIC ANHYDRASE
Phvul.006G192400.1
2.41
3.61
18.12
NADH-DEHYDROGENASE [type II, external]
Phvul.002G223400.1
1.57
8.87
25.19
NADH-DEHYDROGENASE [type II, internal matrix]
Phvul.002G175300.1
-2.41
27.98
4.98
NADH-DEHYDROGENASE [type II, internal matrix]
Phvul.008G260300.1
0.7
13.07
20.23
NADH-DEHYDROGENASE [type II, internal matrix]
Phvul.011G058400.1
0.76
14.56
23.66
CYTOCHROME C
Phvul.004G070000.1
-1.24
5.2
2.1
CYTOCHROME C OXIDASE
Phvul.003G219400.1
0.59
26.82
38.78
Fermentation: LACTATE DEHYDROGENASE
Phvul.008G243200.1
0.6
51.66
74.7
Fermentation: PYRUVATE DECARBOXYLASE
Phvul.008G095400.1
-0.86
16.98
8.95
Fermentation: PYRUVATE DECARBOXYLASE
Phvul.002G072100.1
1.52
43.7
118.31
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.002G314000.1
0.7
80.61
124.69
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.004G162300.1
1.88
1.75
6.01
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.009G226700.1
0.96
32.31
59.73
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.003G199100.2
0.8
1.49
2.49
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.003G209100.1
2.68
13.39
80.64
Gluconeogenesis / glyoxylate cycle: CITRATE SYNTHASE
Phvul.002G007700.1
-3.37
4.42
0.39
Gluconeogenesis / glyoxylate cycle: MALATE DEHYDROGENASE
Phvul.002G139200.1
2.19
40.07
173.5
Gluconeogenesis / glyoxylate cycle: PEPCK
Phvul.011G105500.1
9.52
0.17
117.68
Gluconeogenesis / glyoxylate cycle: ISOCITRATE LYASE
Phvul.009G049200.1
-0.89
8.15
4.16
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONOLACTONASE
Phvul.004G150100.1
0.81
27.24
45.36
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONATE DEHYDROGENASE
Phvul.006G127500.1
0.94
3.99
7.23
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONATE DEHYDROGENASE
Phvul.008G023700.2
0.73
2.41
3.87
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONATE DEHYDROGENASE
Phvul.004G046100.1
-1.99
13.36
3.18
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONATE DEHYDROGENASE
Phvul.002G281000.1
1.94
0.25
0.97
Pentose phosphate pathway, non-reductive: TRANSALDOLASE
Phvul.008G003600.1
0.64
103.8
153.64
Pentose phosphate pathway, non-reductive: TRANSALDOLASE
Phvul.006G122300.1
-0.69
25.67
15.23
Pentose phosphate pathway, non-reductive: RIBOSE 5-PHOSPHATE ISOMERASE
Phvul.002G234600.1
-0.62
43.54
27.05
Pentose phosphate pathway, non-reductive: RIBOSE 5-PHOSPHATE ISOMERASE
Phvul.006G011600.1
1.11
22.53
46.41
ASCORBATE OXIDASE [cell wall]
Phvul.006G011700.1
-1.92
19.68
4.94
ASCORBATE OXIDASE [cell wall]
Phvul.011G071300.1
0.19
386.48
421.5
ASCORBATE PEROXIDASE 1 [cytoplasm]
Phvul.002G107000.1
-2.32
4.79
0.9
ASCORBATE PEROXIDASE 3 [microsome]
Phvul.011G035000.1
0.08
16.76
16.88
ASCORBATE PEROXIDASE 3 [microsome]
Phvul.009G093000.1
-0.88
43.84
22.66
ASCORBATE PEROXIDASE 6 [cytoplasm]
Phvul.009G126500.1
-0.65
2.99
1.8
ASCORBATE PEROXIDASE [thylakoid]
Phvul.009G126500.2
0.18
13.97
15.1
ASCORBATE PEROXIDASE [thylakoid]
Phvul.009G011100.1
0.07
571.15
572.24
CATALASE 2
Phvul.001G001000.1
0.07
54.47
54.3
CATALASE 2
Phvul.007G009800.1
-0.03
57.96
54.31
DEHYDROASCORBATE REDUCTASE 2
Phvul.001G230400.1
0.24
87.11
98.06
DEHYDROASCORBATE REDUCTASE 3 [chloroplast]
Phvul.002G322400.1
0.46
93.4
122.63
GLUTATHIONE PEROXIDASE 3
Phvul.002G288700.1
1.34
173.55
417.89
GLUTATHIONE PEROXIDASE 6
Phvul.004G083600.1
0.3
81.55
95.88
GLUTATHIONE REDUCTASE [cytoplasm]
Phvul.004G083700.1
0.21
65.64
72.45
GLUTATHIONE REDUCTASE [cytoplasm]
Phvul.007G177200.1
-0.05
99.64
91.6
GLUTATHIONE REDUCTASE [chloroplast]
Phvul.007G230300.1
0.1
284.07
289.11
MONODEHYDROASCORBATE REDUCTASE 1
Phvul.008G155600.1
-0.37
78.86
58.21
MONODEHYDROASCORBATE REDUCTASE 4
Phvul.006G097000.1
-0.14
169.55
146.36
SUPEROXIDE DISMUTASE 1 [Cu,Zn]
Phvul.011G086300.1
-0.6
202.81
127.54
SUPEROXIDE DISMUTASE 2 [Cu,Zn]
Phvul.004G081000.1
-0.19
39.31
32.83
SUPEROXIDE DISMUTASE 3 [Cu,Zn]
Phvul.007G135400.1
1.16
35.61
75.98
SUPEROXIDE DISMUTASE 2 [Fe; chloroplast]
Phvul.007G135400.2
0.74
2.32
3.72
SUPEROXIDE DISMUTASE 2 [Fe; chloroplast]
Phvul.006G010800.1
-0.33
20.79
15.9
SUPEROXIDE DISMUTASE 3 [Fe; chloroplast]
Phvul.009G141600.1
0.28
106.03
123.09
SUPEROXIDE DISMUTASE 1 [Mn]
Phvul.001G249200.1
-1.34
13.23
5.01
?-GLUTAMYL TRANSPEPTIDASE
Phvul.002G289200.1
0.18
67.27
72.48
GLUTAMATE-CYSTEINE LIGASE
Phvul.006G094500.1
-0.06
55.27
50.65
GLUTATHIONE SYNTHETASE
Phvul.006G145300.1
-2.03
5.13
1.19
PHOSPHOFRUCTOKINASE [cytoplasm]
Phvul.001G259000.1
0.65
66.79
99.89
GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE [cytoplasm]
Phvul.004G127500.1
0.74
3.76
6
ENOLASE [cytoplasm]
Phvul.004G078400.1
-1.43
0.98
0.34
PYRUVATE KINASE [cytoplasm]
Phvul.003G024800.1
-1.64
4.22
1.29
PHOSPHO-ENOL-PYRUVATE CARBOXYLASE [cytoplasm]
Phvul.005G066400.1
1.55
9.89
27.84
PHOSPHO-ENOL-PYRUVATE CARBOXYLASE [cytoplasm]
Phvul.002G096000.1
-1.63
113.76
35.36
PHOSPHOGLUCOMUTASE [plastid]
Phvul.008G180200.1
-0.6
54.4
34.26
GLUCOSE-6-PHOSPHATE ISOMERASE [cytoplasm]
Phvul.002G306800.1
1.41
9.8
24.99
PHOSPHOFRUCTOKINASE [plastid]
Phvul.011G090600.1
-0.68
76.49
45.67
PHOSPHOGLYCERATE MUTASE [localization unclear]
Phvul.003G106700.1
0.9
24.42
43.35
PYRUVATE DEHYDROGENASE [E2]
Phvul.008G239900.1
0.58
8.33
11.91
ISOCITRATE DEHYDROGENASE
Phvul.003G253200.1
0.78
56.15
91.95
SUCCINATE DEHYDROGENASE
Phvul.009G111500.2
2.56
0.16
0.9
MALATE OXIDOREDUCTASE
Phvul.010G094700.1
0.83
43.82
74.55
MALATE OXIDOREDUCTASE
Phvul.005G166400.1
0.87
72.66
126.61
MALATE OXIDOREDUCTASE
Phvul.005G043500.1
-0.85
29.78
15.81
ATP-CITRATE LYASE
Phvul.005G048000.1
0.66
53.29
80.23
Misc. organic acid transformatons
Phvul.005G048300.1
0.67
42.24
63.98
Misc. organic acid transformatons
Phvul.002G071200.1
-1.37
12.74
4.7
CARBONIC ANHYDRASE
Phvul.008G181400.2
2.33
0.41
2
CARBONIC ANHYDRASE