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2/26/2014
Maize Phenotyping under the Seeds of Discovery
Initiative: The Brute Force Method
Martha C. Willcox
Maize Landrace
Improvement Coordinator
Coauthors:
CIMMYT:Juan Burgueno, Armando Guadarrama, Daniel
Chepetla, Enrique Rodriguez, Dan Jeffers, George Mahuku,
Iván Ortiz-Monasterio, Natalia Palacios, Félix San Vicente,
Rosemary Shrestha, Samuel Trachsel, Sarah Hearne, Peter
Wenzl
INIFAP: Noel Gómez, Alejandro Ortega, Ernesto Preciado,
Víctor Vidal
Pioneer-Mexico: Fernando González, Heriberto Torres, Marco
Oropeza
Gates Foundation: Gary Atlin
UAAAN-UL: Armando Espinoza Banda
Bidasem: María E. Rivas-Dávila
ICAMEX: Francisco Javier Manjarrez
Productores de Semilla de Copandaro: Humberto Vallejo
Seeds of Discovery
Genome Wide Association Study
(GWAS) in Maize
● Breeder’s Core Collection from the CIMMYT Maize
Germplasm Bank (4471 accessions).
● One plant per accession crossed with a CIMMYT hybrid to
make a series of modified topcrosses.

The same plant was sampled for DNA extraction/GBS
● Accessions were crossed hybrids of their same
environmental adaptation (where possible).
Tropical Accessions X Tropical Hybrid
Subtropical Accessions X Subtropical Hybrids
Highland Accessions X Highland Hybrid
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Trial Sites in Mexico: GWAS
115o
110o
105o
100o
95o
90o
85o
30o
30o
Obregon, Sonora
Drought; Heat
Heat &25Drought
San Pedro
Lagunillas, Nay
El Batán,
Celaya, GTO
Mex
Cortazar, GTO
Agua Fría,
Numaran, MI
Pueb
Tarimbaro , Almoloya, Mex
Tlaltizapán, Mor
Michoacan
Iguala, GRO
Cercospora
20
o
Stalk Rot
15o
Ocotito, Guerrero
115o
Phenotypic Trials
● 36 trials planted - 34 harvested (34,606
rows and over 687,000 unique data points)
● 19 Trials for abiotic Stresses (Drought, Heat,
Low Nitrogen)
● 11 Trials for diseases (Tar Spot Complex,
Grey Leaf Spot, Turcicum Leaf Blight,
Fusarium Ear Rot, Fusarium and
Acremonium Stalk Rot)
● 3 Trials hand pollinated to produce grain
for Quality Component Analysis.
Experimental Design
Unreplicated augmented row-column
design
For each trial location accessions are
selected for adaptation zone and maturity.
Overlapping sets of topcross entries
Two widely adapted commercial checks
and resistant and susceptible checks
where appropriate
Stalk Rot; Quality
Torreon, Coahila
o
110o
105o
25o
Low Nitrogen, Ear Rot,
Quality, Turcicum
20o
Low Nitrogen
Guadalupe-Victoria, Chiapas
15o
Tar Spot Complex
Drought
95o
90o
85o
Yield and Agronomic Data Taken :
All Locations
● Yield (field weight, grain and cob weight,
moisture, number of ears)
● Plant Height and Ear Height
● Male and Female Flowering (50% of row)
● Stalk and Root Lodging
Faja
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Surco
1
40
41
80
81
120
121
160
161
200
201
240
241
280
281
320
321
360
361
400
1
2
39
42
79
82
119
122
159
162
199
202
239
242
279
282
319
322
359
362
399
2
3
38
43
78
83
118
123
158
163
198
203
238
243
278
283
318
323
358
363
398
3
4
37
44
77
84
117
124
157
164
197
204
237
244
277
284
317
324
357
364
397
4
5
36
45
76
85
116
125
156
165
196
205
236
245
276
285
316
325
356
365
396
5
6
35
46
75
86
115
126
155
166
195
206
235
246
275
286
315
326
355
366
395
6
7
34
47
74
87
114
127
154
167
194
207
234
247
274
287
314
327
354
367
394
7
8
33
48
73
88
113
128
153
168
193
208
233
248
273
288
313
328
353
368
393
8
9
32
49
72
89
112
129
152
169
192
209
232
249
272
289
312
329
352
369
392
9
10
31
50
71
90
111
130
151
170
191
210
231
250
271
290
311
330
351
370
391
10
11
30
51
70
91
110
131
150
171
190
211
230
251
270
291
310
331
350
371
390
11
12
29
52
69
92
109
132
149
172
189
212
229
252
269
292
309
332
349
372
389
12
13
28
53
68
93
108
133
148
173
188
213
228
253
268
293
308
333
348
373
388
13
14
27
54
67
94
107
134
147
174
187
214
227
254
267
294
307
334
347
374
387
14
15
26
55
66
95
106
135
146
175
186
215
226
255
266
295
306
335
346
375
386
15
16
25
56
65
96
105
136
145
176
185
216
225
256
265
296
305
336
345
376
385
16
17
24
57
64
97
104
137
144
177
184
217
224
257
264
297
304
337
344
377
384
17
18
23
58
63
98
103
138
143
178
183
218
223
258
263
298
303
338
343
378
383
18
19
22
59
62
99
102
139
142
179
182
219
222
259
262
299
302
339
342
379
382
19
20
21
60
61
100
101
140
141
180
181
220
221
260
261
300
301
340
341
380
381
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Example of Trial Design
Standard commercial checks (
and
) to adjust for spatial variance
and link trials from multiple locations and trait specific, resistant (
) and
susceptible (
) checks, to adjust for spatial variation for specific traits
within the trial.
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Model for Analysis
Trial
Mean
Check 1
Acc.
Topcrosses
Check t
Range of Female Flowering
(mínimum, mean and máximum)
BLUPs (Best Linear Unbiased predictors)
calculated for male accession
parent by removing the average
effect of the hybrid tester and
using check entries to adjust for
spatial variation.
Hybrid 1
Hybrid p
Accession 11
Accession p1
Accesión 1a1
Accesión pap
Challenges
● Range of maturities (flowering extends for
5 weeks)
● Lodging
● Segregation
● Diversity of environments (both origin of
accessions and evaluation sites).
Tar Spot Complex
100
95
90
85
80
75
70
75
80
85
90
95
100
Average Female Flowering (days post planting)
Comparison of average female flowering date with range
of female flowering for 191 accession topcrosses (per
plant data)
Tar Spot Complex
Tar Spot Trials
● 2011B Guadalupe-Victoria, Chiapas – 600
Accession/Topcross entries
● 2012B Guadalupe-Victoria, Chiapas – 810
accession/topcross entries (including
accessions per se)
Photo: Rosemary Shrestha
● 2 foliar ratings 0-5 scale (Ceballos and
Deutsch) two weeks apart.
● Data taken both by row and as average
of 6 plants per row
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Oaxa280
(CML269/CML264)/Oaxa280
Guat153
Root Lodging %
Yield(g/plot)
(CML495/CML494)/Guat153
Guat153
(CML269/CML264)/Oaxa280
(CML495/CML494)/Guat153
Oaxa280
Tar Spot Foliar Rating (0-5)
Tar Spot Foliar Rating (0-5)
Relationship between Tar Spot rating and Yield (2nd foliar rating: scale 05; average of 6 plantas)
=Accessions; = Topcrosses; = Commercial Checks
Relationship between Root Lodging and Tar Spot Rating (2nd foliar
rating)
=Accessions; = Topcrosses;
= Commercial Checks
Characterization for Stalk Rot
Fusarium Stalk Rot: Artificial Inoculation
Yield (t/ha 12% hum)
Evaluation of Accessions PerSe for
Acremonium Stalk Rot
Entry
Commercial (resistant check)
PUEB45
MORE85
GUER125
NAYAGP6
CHIS128
MICH21
TC X URUG39 (susceptible)
Accession Perse (2013)
Accession Topcross (2012)
Stalk Rot Scale Average
0.43
1.16
1.53
1.59
2.13
2.56
3.21
4.5
Stalk Rot Scale Average
0.5
1.7
2.3
2.4
2.5
2.9
2.9
5.97
Stalk Rot Scale (proportion of stalks with Acremonium strictum
times intensity 1-5)
Relationship between Yield and Stalk Rot Scale (percentage of
stalks with disease x intensity of disease)
=Topcrosses ; = Commercial Checks
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Lots of data still to analyze…
Thank You
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