Green fluorescent protein (GFP) ................................145,
160–162, 214, 215, 258, 259, 261–263, 265,
269, 276, 279–281, 283, 284, 305, 307,
324–326, 328, 332, 375, 380, 453–455
Growth conditions ............................................ 3, 5, 9–11,
14, 116, 151, 300, 329, 404
Guard cells .................................... 71, 306, 414–418, 421
H
High-pressure freezing .......................337–340, 342, 346
High-throughput sequencing ................................ 15, 25,
266, 268, 405, 453–460
Homologous recombination .........................32, 122, 123
I
Immunolabeling..................................339, 340, 342–346
Indentations ...................... 350, 352, 354, 359, 363, 365
In planta............................ 147, 310, 324, 326, 425–439
In vitro growth.............................................................. 169
L
Leaves...........................................19, 20, 76, 95, 97, 104,
115–118, 137, 141, 147, 158, 207, 208, 256,
258, 265, 270, 273, 283, 287, 295–300, 307,
326, 331, 332, 334, 346, 354, 356, 357, 366,
398, 416, 417, 421, 426, 433–435, 439
Library construction ............................................ 226, 227
Liquid-chromatography mass-spectrometry
(LC-MS) ......................................... 394, 396–398,
404, 405, 442, 447
Live-imaging......................................................... 295–301
Locus-Tagging .............................................................. 213
M
Mass spectrometry (MS)....................................... 4, 8, 15,
128, 137, 141, 148–151, 153, 154, 158, 159,
169–171, 215, 216, 273, 314, 327, 330, 338,
340, 354, 355, 396, 397, 402, 413–415,
417–419, 421, 426, 432, 434, 437–439, 441,
447–449
Mean square displacement (MSD)..............................214,
218–220, 222
Membrane protein–protein
interactions ..................... 158, 263, 323–334, 426
Metabolomics ..................................................8, 393–395,
398, 403–408, 413–423
Microscopy
atomic force .................................................... 349–367
fluorescence ............................................................. 158
structured Illumination.................................. 158, 159
Mobile signals.............................................. 113, 114, 117
N
Natural accessions ....................3, 19, 188–190, 193, 395
Natural variation ................................................... 93–109,
393–409
Network-based augmentation ............................. 187–208
Next-generation sequencing (NGS) ...........................226,
227, 247
Nucleotide diversity ................................................93–109
Nucleus ..................................53, 76, 213, 214, 216–219,
221, 222, 225, 259, 260, 263, 265, 268, 279,
280, 285, 342, 345, 372, 378, 453
P
Pavement cells ............................................. 214, 354, 366
Phosphoproteomics ..............................66, 441, 442, 448
Phytohormones ................................. 169, 170, 172, 175,
181, 182, 303, 305, 307
Pin-fasten grafting................................................ 115, 116
Plant membrane proteins .................................... 442, 443
Plants ................................................3–12, 15, 17–22, 25,
28, 30–32, 34, 37, 40, 41, 48, 52, 53, 55, 57, 59,
61, 63, 64, 66–68, 72–75, 79, 84, 93–95, 97,
99–105, 113–118, 121, 122, 124, 128, 137, 141,
144, 147, 148, 153, 157, 158, 163, 167–169,
187, 188, 207, 214–216, 221, 228, 241, 255,
256, 258–260, 263, 265, 267–269, 273–276,
279–281, 283, 286, 287, 295, 296, 300, 303,
305–307, 309–312, 314–316, 318, 324, 326,
327, 329, 331, 338, 340, 345, 349–368, 371,
376, 377, 382, 387, 388, 393–395, 397–399,
403, 404, 406, 408, 409, 413, 415–417, 421,
426, 429–431, 434, 438, 441–450, 454–459
Plant transformations.................................. 430, 433, 434
Pollen ...........................................15, 256, 268, 269, 272,
279, 281–284, 340, 342, 372–376, 378,
380–382, 387
Post-transcriptional ....................................................... 310
Promoter analyses .......................... 26, 46, 48, 50–53, 55
Protein complexes ................................................... 72, 74,
324, 341, 425–439
Protein-protein interactions ..................... 26, 66, 68, 426
Proteomics................................................. 32, 56, 64, 265
Protoplasts .................................................. 157–164, 168,
172, 179, 184, 256, 258, 259, 263, 265–270,
272, 273, 279, 281–285, 287, 324, 326, 426
Proximal proteins .......................................................... 426
Q
QTL analysis......................................................... 397, 404
Quantitative trait locus (QTL)............................... 93, 95,
97, 187, 397, 406, 407
464
ARABIDOPSIS PROTOCOLS
Index
160–162, 214, 215, 258, 259, 261–263, 265,
269, 276, 279–281, 283, 284, 305, 307,
324–326, 328, 332, 375, 380, 453–455
Growth conditions ............................................ 3, 5, 9–11,
14, 116, 151, 300, 329, 404
Guard cells .................................... 71, 306, 414–418, 421
H
High-pressure freezing .......................337–340, 342, 346
High-throughput sequencing ................................ 15, 25,
266, 268, 405, 453–460
Homologous recombination .........................32, 122, 123
I
Immunolabeling..................................339, 340, 342–346
Indentations ...................... 350, 352, 354, 359, 363, 365
In planta............................ 147, 310, 324, 326, 425–439
In vitro growth.............................................................. 169
L
Leaves...........................................19, 20, 76, 95, 97, 104,
115–118, 137, 141, 147, 158, 207, 208, 256,
258, 265, 270, 273, 283, 287, 295–300, 307,
326, 331, 332, 334, 346, 354, 356, 357, 366,
398, 416, 417, 421, 426, 433–435, 439
Library construction ............................................ 226, 227
Liquid-chromatography mass-spectrometry
(LC-MS) ......................................... 394, 396–398,
404, 405, 442, 447
Live-imaging......................................................... 295–301
Locus-Tagging .............................................................. 213
M
Mass spectrometry (MS)....................................... 4, 8, 15,
128, 137, 141, 148–151, 153, 154, 158, 159,
169–171, 215, 216, 273, 314, 327, 330, 338,
340, 354, 355, 396, 397, 402, 413–415,
417–419, 421, 426, 432, 434, 437–439, 441,
447–449
Mean square displacement (MSD)..............................214,
218–220, 222
Membrane protein–protein
interactions ..................... 158, 263, 323–334, 426
Metabolomics ..................................................8, 393–395,
398, 403–408, 413–423
Microscopy
atomic force .................................................... 349–367
fluorescence ............................................................. 158
structured Illumination.................................. 158, 159
Mobile signals.............................................. 113, 114, 117
N
Natural accessions ....................3, 19, 188–190, 193, 395
Natural variation ................................................... 93–109,
393–409
Network-based augmentation ............................. 187–208
Next-generation sequencing (NGS) ...........................226,
227, 247
Nucleotide diversity ................................................93–109
Nucleus ..................................53, 76, 213, 214, 216–219,
221, 222, 225, 259, 260, 263, 265, 268, 279,
280, 285, 342, 345, 372, 378, 453
P
Pavement cells ............................................. 214, 354, 366
Phosphoproteomics ..............................66, 441, 442, 448
Phytohormones ................................. 169, 170, 172, 175,
181, 182, 303, 305, 307
Pin-fasten grafting................................................ 115, 116
Plant membrane proteins .................................... 442, 443
Plants ................................................3–12, 15, 17–22, 25,
28, 30–32, 34, 37, 40, 41, 48, 52, 53, 55, 57, 59,
61, 63, 64, 66–68, 72–75, 79, 84, 93–95, 97,
99–105, 113–118, 121, 122, 124, 128, 137, 141,
144, 147, 148, 153, 157, 158, 163, 167–169,
187, 188, 207, 214–216, 221, 228, 241, 255,
256, 258–260, 263, 265, 267–269, 273–276,
279–281, 283, 286, 287, 295, 296, 300, 303,
305–307, 309–312, 314–316, 318, 324, 326,
327, 329, 331, 338, 340, 345, 349–368, 371,
376, 377, 382, 387, 388, 393–395, 397–399,
403, 404, 406, 408, 409, 413, 415–417, 421,
426, 429–431, 434, 438, 441–450, 454–459
Plant transformations.................................. 430, 433, 434
Pollen ...........................................15, 256, 268, 269, 272,
279, 281–284, 340, 342, 372–376, 378,
380–382, 387
Post-transcriptional ....................................................... 310
Promoter analyses .......................... 26, 46, 48, 50–53, 55
Protein complexes ................................................... 72, 74,
324, 341, 425–439
Protein-protein interactions ..................... 26, 66, 68, 426
Proteomics................................................. 32, 56, 64, 265
Protoplasts .................................................. 157–164, 168,
172, 179, 184, 256, 258, 259, 263, 265–270,
272, 273, 279, 281–285, 287, 324, 326, 426
Proximal proteins .......................................................... 426
Q
QTL analysis......................................................... 397, 404
Quantitative trait locus (QTL)............................... 93, 95,
97, 187, 397, 406, 407
464
ARABIDOPSIS PROTOCOLS
Index