1

ANNUAL PROGRESS REPORT 2012/13

ISCM PROJECT ON

“MODELLING WORLD-WIDE GXE INTERACTION”

A. Eksteen, S. Chinorumbe, M. Singh, D. Zhao, K. Polacik, J. Shine, J. Martine

and A. Singels

11 June 2014

1. General

The goal of the project is to gain a better understanding of the physiological mechanisms

underlying the genetic variation in crop response to environmental factors by monitoring key

plant processes contributing to yield and quality in a common set of diverse cultivars grown in

diverse environments from around the world. Specific objectives are to:

measure canopy development, radiation interception, water use, water stress

sensitivity and, biomass accumulation and partitioning for a number of diverse cultivars

(from different countries) in diverse environments (in different countries),

determine model trait parameters (genetic coefficients) for each cultivar, derived from

development, growth and water use measurements,

identify and formulate underlying mechanisms of genotype response to environmental

factors, and

evaluate models’ ability to simulate genotypic differences in crop performance.

The following organizations are participating in the project: SASRI, ZSAES, SIRC, and CIRAD

and the following cultivars will be used in the trials: N41, R570, CP88-1762, HoCP96-540 and

ZN7. In some cases NCo376 and Q183 will also be planted. The main activities in the project

so far have been to generate and distribute genetically-true, disease-free seed material of the

relevant cultivars to each of the participating countries, to propagate for the experiments, and

to plant experiments. Crop measurements have started in three experiments.

A standardised field sampling sheet, including detailed information on sampling protocols, was

created for experiment measurements in July 2013 by SASRI staff. The sampling sheet and

sampling protocols formed part of a G x E data capture template (MS Excel), which was

emailed to all project participants in August 2013. The template is to be completed by all

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project participants to standardise and collate information regarding experiment details,

treatments per plot, soil characteristics, trial management, field operations, weather data, as

well as soil and leaf observations. The template also includes a data capture tab, and will

automatically summarise data captured for the different sampling measurements.

2. Progress in South Africa

Soil description and analysis

The soil of the fields at the Pongola Research station that will be used for the trial is of a Hutton

form and of the Shorrocks series (SA soil classification system as shown in SASRI, 1999),

otherwise correlated with a Rhodic and Helvic Ferrasol (FAO) or Oxisols/Ultisols (USDA Soil

Classification).

The chemical and physical analysis of soil layers in Field 322 (plant crop experiment) at

Pongola is shown in Table 1.1 and 1.2, respectively. Soil samples at four sampling points were

taken with an auger on Field 322 at the following depths: 0 – 20cm, 20 – 40cm, 40 – 60cm,

60 – 80cm and soil from each layer was mixed together to form four composite depth samples

for analysis. Soil chemical analysis was performed by FAS (Fertiliser Advisory Service) at

SASRI and the soil physical analysis was performed by the Soil Physics Lab at SASRI, Mount

Edgecombe.

All soil layers have a pH of approximately 5.0. The acid saturation was very low (0.6% in each

layer) and therefore the existence of subsoil acidity is very unlikely. Soil phosphorous and

potassium were found to be adequate and FAS advised that 100 kg /ha of MAP fertiliser should

be applied in furrow at planting.

Results from the soil physical analysis showed that all soil layers have a relatively high clay

content (29 – 38%) and the bulk density of the soil ranged from 1.27 – 1.30 g soil cm-3. The

available soil water content in each of the layers ranged from 129 – 137 mm. Soil depth

exceeds 2.5 m.

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Table 1.1: Chemical Analysis of different soil layers at Field 322 at SASRI Research Farm in

Pongola, South Africa

* P > 16.4 mg/L (adequate); ** K > 155 mg/L (adequate)

Table 1.2: Physical Analysis of different soil layers at Field 322 at SASRI Research Farm in

Pongola, South Africa

Trial Planting

Seedcane from the bulking plots from five varieties (N41, R570, ZN7, HOCP96-540, CP88-

1762) was planted into plant crop and ratoon crop fields at the SASRI Research station in

Pongola (on 25 March 2014). Seedcane from each variety was planted into four replicate plots

(5 varities x 4 replicates = 20 plots) that consisted of 5 rows per plot (with 1.5m row spacing)

and each plot was 21m in length, with a 1m break between plots (see Figure 2.1). The single

plot detail is shown in Figure 2.2, which includes the destructive sampling areas at 3, 6, 9 and

12 months crop age. Each row was fertilised with 100 kg / ha of MAP fertiliser on 25 March

2014 (as per SASRI Fertiliser Advisory Service (FAS) recommendations) and sprayed with

fungicide (26 March 2014). Plant emergence is currently being monitored every two weeks in

two 4m sections of each plot in the 4th destructive sample area. Further plant measurements

will commence in May 2014. Planting operations are shown in Figure 2.3 and 2.4.

Soil layer #

Depth of bottom of soil layer (cm)

pH P (Truog) (mg/L)*

K (mg/L)**

Soil Organic Matter (%)

Cation Exchange Capacity (cmol / kg)

Acid saturation (%)

Extractible Aluminium (cmol / kg)

1 20 5.04 21.6 192 2.1 9.06 0.6 0.05

2 40 5.14 12.1 77 1.3 8.96 0.6 0.05 3 60 4.95 5.4 70 1.0 8.69 0.6 0.05

4 80 5.02 10.5 66 0.9 8.16 0.6 0.05

Soil layer #

Depth of bottom of soil layer (cm)

Clay (%) Silt (%)

Sand (%)

Bulk density (g soil / cm3)

Drained upper limit (Field capacity) (mm)

Lower limit (PWP) (mm)

Available soil water (mm)

1 20 29 10 61 1.30 279 150 129 2 40 36 7 57 1.28 335 201 134 3 60 37 8 55 1.27 338 203 135 4 80 38 9 53 1.27 349 212 137

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Figure 2.1: Trial plan of the plant crop (Field 322) and ratoon crop (Field 323) at the SASRI

Research Station in Pongola. Plot detail is not drawn to scale.

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Figure 2.2: Single plot detail of each plot in Field 322 showing four destructive sample areas,

row spacing and breaks between each sample area.

Figure 2.3: Bulked seedcane (variety ZN7) before cutting.

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Figure 2.4: Planting operation of Field 322 at Pongola (plant crop sampling).

3. Progress in Reunion

Because of heavy rains at the end of 2012 and at the beginning of 2013, the first planting

of N41 failed (see May 2013 report). With a few sets of N41 from eRcane we planted

this variety again in November 2013 (Figure 3.1) for rapid multiplication, but this caused

a great delay in previously planned operations. Three weeks ago, the other five varieties

(R570, Q183, CP88-1762, NCo376 and N41) were planted in the nursery (Figure 3.2)

with success using the one-eye method, and will then be transplanted at the beginning

of May in a last bulking plot. So, the seedcane of five varieties will have exactly the

same age and will be planted, in January 2015, into plant crop and ratoon crop field

trials. Unfortunately, HoCP96 were not available from Montpellier Quarantine.

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Figure 3.1 Bulking plot (November 2013)

Figure 3.2 One-eye sets nursery

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4. Progress in Zimbabwe

Hardened tissue cultured plants from six varieties (ZN7, N41, Q183, CP88-1762,

HoCP96-540, and R570) were planted into the field on 15 December 2011 at the ZSAES.

The varieties were harvested and planted out on 2 November 2012 for further bulking to

produce the amount of seedcane required for planting out the trials.

Sites

The trials were planted out on 30 October 2013 and on 11 December 2013 in Fields L3,

Sable Block (plant crop) and B1-5, Impala Block, ZSAES (ratoon). Other sites details

include 21º 02’ S, 31º 36’ E, and 21º 02’ S, 31º 37’ E, Alt 430 m.

A B

Figure 4.1. Crop growth stage [A] and re-growth following the first destructive sampling

[B] of variety R570 at three months of age in Field L3, Sable block.

Fertiliser application:

Soil samples will be collected at a depth of 0 – 30 cm using Dutch Augers after the fields

were ploughed and disced but before opening up the planting furrows [ridging]. ZSAES

recommended application [banding in the furrows] of phosphorus at 100 kg•ha-1 P2O5 [Single

Super Phosphate was the source of P]. Nitrogen was applied as a top dressing of

Ammonium Nitrate (34.5% N) in three splits of 47 kg ha-1 each at four, seven and ten weeks

after the average day of emergence of cane varieties. Potassium, as muriate of potash

[MOP, 60% K2O] was applied in two equal splits at 30 kg ha-1 K2O each split together with

the first two nitrogen applications (at four and seven weeks).

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Table 4.1. Field plans of the plant crop (L3, Sable Block) and ratoon crop (B1-5,

Block, Impala) at the ZSAES.

Plant crop

1

R570

2

Q183

3

ZN7

4

CP88-1762

5

HoCP96-540

6

N41

12

ZN7

11

Q183

10

R570

9

CP88-1762

8

HoCP96-540

7

N41

13

CP88-1762

14

ZN7

15

HoCP96-540

16

Q183

17

N41

18

R570

24

Q183

23

R570

22

HoCP96-540

21

N41

20

CP88-1762

19

ZN7

Ratoon Crop

1

N41

2

ZN7

3

R540

4

CP88-1762

5

HoCP96-540

6

Q183

12

HoCP96-540

11

CP88-1762

10

R570

9

N41

8

ZN7

7

Q183

13

R540

14

ZN7

15

CP88-1762

16

N41

17

HoCP96-540

18

Q183

24

ZN7

23

R540

22

HoCP96-540

21

CP88-1762

20

N41

19

Q183

Weed control

The herbicides [a tank-mix of Acetochlor and Metribuzin as pre-emergence] were

applied a day after irrigation when soil was still moist.

Irrigation

The plant crop trial [L3, Sable Block] is irrigated using furrows at 50 % moisture

depletion and the ratoon is irrigated using floppy sprinkler system.

Progress on data collection

Weather data

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All other necessary data is collected routinely at the nearest meteorology station

[about 600m away] except for the solar radiation.

Soil data

Soil sampling.

Pits (measuring 1 m by 0.7 m) were dug manually, up to gravel level and shaped before

soil sampling (Figure 4.2). The sides of the pits were smoothened using a spade to

clearly expose the different layers with different characteristics e.g. colour and particle

size. The vertical distances (0-5; 6-10; 11-15; 16-20; 21-25; 26-30; 30-40; 41-55; 56-

70; 71-85; 86-100; 101-120 etc); were measured and samples collected at centre of

the layers as indicated (Figure 4.2.). Mechanical analysis was done to determine clay

and silt percentages. The information was used to calculate within DSSAT; Bulk

density, Upper and lower drained limits. Other soil information collected included slope

and color. Permeability and drainage were estimated.

Figure 4.2. Layout of the cross section of soil profile showing layers numbered from 1

upwards. The central marked positions (holes) show where the soil samples were

collected.

Data Collection:

Non – Destructive Measurements

Number of shoots: The counting of shoots (tillers and stalks) continue routinely for 8m row length at bi-monthly intervals from planting and now at one month until harvest. Stalk (TVD) height and canopy height are also measured every two weeks with stalk height being measured from ground level [fixed] to the TVD leaf. Also being measured is the light interception at bi-monthly from 11am to 2pm with SunScan (10 readings per plot). Leaf counts and measurements Total number of leaves up to the spindle is being counted. The length of leaves [from the stalk to the tip of the leaf] and width [maximum width] of the TVD leaves

Layer 1 a

Layer 2

Soil depth Holes

Layer 3

Layer 4

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is also measured. Complete TVD leaf analysis [N, P, K, Ca, Mn, Fe, Cu] of actively growing crop at 4 months of age was done however Si was not done due to lack of capacity. The Minolta SPAD is being used to collect data on TVD leaf chlorophyll at time of destructive sampling and when leaf sampling for nutrient analysis is done. Destructive sampling

Two destructive samplings at 3 and 6 months of age have been done. The following were measured in a sub sample of 2 m of cane that was collected in each destructive sampling: number of millable stalks, total fresh mass, total millable stalk fresh mass, total green leaf fresh mass, average stalk length from ground level to the apex, total millable stalk dry mass [samples are oven dried at 60oC until constant weight], total green leaf dry mass, leaf sheath dry mass, tops dry mass and trash dry mass.

Cane Quality analysis The following were measured at the second destructive sampling; stalk brix, fibre, pol, non-pol and moisture content [DAC analysis method]. At three months, no such stalks were available for processing.

Data entry Data capture into electronic format is being affected by shortage of staff [more graphs could have been presented in the report]

Figure 4.3. Sugarcane shoot population up to 126 days after planting for all the sugarcane varieties represented in the trial. Challenges faced:

Leaf scald

During the planting out of the trial, symptoms associated with leaf scald [chlorosis,

excessive side-shooting, ‘pencil lines’ and general necrosis] were observed in variety

Q183 but serological diagnoses was not done due to lack of capacity. Stalks showing

no signs were used as source of seed. There were fears however that plants not

0

50

100

150

200

250

21 31 47 84 112 126

No

. of

sho

ots

/ 8

m

Days after planting

R570

Q183

ZN7

CP88-1762

HoCP96-540

N41

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showing any visible symptoms could have been latently infected and symptoms would

develop during the plant crop or in the ratoon crops.

A B

Figure 4.4. Photos of variety Q183 in the seed bulking stage infected with a disease

suspected to be Leaf scald. Symptomless stalks were selected and planted in the

trials.

Yellow aphids;

There was also an outbreak of yellow aphids in both the plant and ratoon trials. The

attacked varieties exhibited yellowing and reddening of leaves, premature senescence

of leaves as in the grass species shown [A, Figure 4.5]. Also identified were natural

enemies that ensured the densities of Sipha flava remained low so no insecticide was

sprayed and the cane has grown out of the infestation (no aphids were observed at

the time of compiling this report).

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Yellow aphids

A B

Figure 4.5. Yellow aphids [Sipha flava (Forbes)] on the underside of a leaf [A] of a

weed [Echinocloa crus-galli] close to the experiment site [L3, Sable Block, ZSAES].

Variety N41 [B] at the same site after recovering from aphid attack. The aphids were

also observed on all sugarcane varieties in the trial except on ZN7.

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5. Progress in U.S.A

General:

Varieties N41, NCo376, CP 88-1762, R 570, Q183, and HoCP 96-540 were planted

manually on Dec 12, 2013 at the Everglades Research and Education Center (EREC)

of the University of Florida at Belle Glade, FL. Seed cane was harvested from the plots

planted for seed bulking in the fall of 2012. The test was planted in a randomized

complete block design (RCBD) with four replications, each for data collection from

plant-cane crop and from first-ratoon crop (Figure 5.1).

As shown in Figure 5.1, plot # 1-24 will be used for data collection from plant-cane crop

in 2014 and plot # 25-48 will be used for data collection from first-ratoon crop in 2015.

Each plot consisted of 9 rows spaced 1.5m with row length of 11m. Four sections were

marked in each plot (3 rows with row length of 4m; Figure 5.1, bottom panel), to perform

destructive harvest at around 3, 6, 9, and 12 months period. Non-destructive

measurements will be conducted in the section reserved for final destructive harvest.

Emergence in all varieties started around early January (Figure 5.2). Early growth was

delayed due to cold weather conditions in south Florida in mid-late January. Variety

Q183 showed earliest emergence and fast early growth compared to other varieties.

By early April, all varieties have shown good early growth (Figure 5.3).

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Figure 5.1: Layout of the trial for plant-cane crop (top panel), first-ratoon crop (middle panel),

and individual plot (bottom panel).

NCo376 HoCP96-540 Q183 CP88-1762 N41 R570

Q183 NCo376 R570 N41 CP88-1762 HoCP96-540

CP88-1762 R570 N41 Q183 HoCP96-540 NCo376

HoCP96-540 Q183 R570 CP88-1762 NCo376 N41

Rep 4

Rep 3

Rep 2

Rep 1

3m

5m

96m

123456

789101112

131415161718

192021222324

Rep 4

Rep 3

Rep 2

Rep 1

HoCP96-540 R570 Q183 CP88-1762 N41 NCo376

N41 CP88-1762 NCo376 Q183 HoCP96-540 R570

NCo376 CP88-1762 N41 HoCP96-540 R570 Q183

R570 HoCP96-540 Q183 N41 NCo376 CP88-1762

3m

5m

252627282930

313233343536

373839404142

434445464748

1m

4m

1m

4m

1m

2 3 4 5 61 7 8 9

11m

13.5m

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Figure 5.2: Planting (leaf panel) and emergence (right panel) for all verities in the trial.

Figure 5.3: Varieties planted in the trial: (A) N41, (B) NCo376, (C) CP 88-1762, (D) R 570,

(E) Q183, and (F) HoCP 96-540. Pictures were taken on April 10, 2014.

A B

C D

E F

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Challenges faced

Variety Q183 has shown brown spotting symptoms that could not be identified after

consultation with various scientists at EREC and USDA-ARS (Figure 5.4). No disease spores

or insect damage was seen on the leaves showing these symptoms. These spots were present

both in the plant-cane crop in the current trial and in the first-ratoon crop in the plots used for

seed cane. These spots are present in all plots in the main study and are severe on lower

canopy. Some symptoms were also present on varieties N41 and NCo376 but absent in other

varieties.

Figure 5.4: Brown spotting observed on Q183 during March 2014, in the main trial planted in

fall of 2013 (plant-cane crop; top panels) and in the plots planted for seed bulking in the fall

of 2012 (first-ratoon crop; bottom panels).

Due to mild winters, this year has seen early initiation of brown and orange rust symptoms in

sugarcane in south Florida. In this trial, variety HoCP 96-540 has shown most severe

symptoms of brown rust (Figure 5.5, left panel). Minimal to no symptoms were seen in other

varieties until now. Manganese nutrient deficiency symptoms were observed in only one

variety (Q183; Figure 5.5, right panel) in this trial.

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Figure 5.5: Brown rust on HoCP 96-540 (leaf panel) and Manganese deficiency in Q183

along with some brown spotting (right panel).

The study is kept weed-free by in-row cultivation and herbicide spray. Various narrow and

broad leaf weeds, particularly fall panicum (Panicum dichotomiflorum), infested the study

plots. Herbicide Asulam was sprayed to control fall panicum in the plots.

Progress on data collection

Data were collected on sugarcane emergence and tiller count in all the varieties (Figures 5.6

and 5.7). Variety Q183 showed earliest emergence and time to reach to 90% emergence

compared to all other varieties. Variety R570 showed the slowest emergence rate (Figure 5.6).

Tiller count data was collected in the section marked for final destructive harvest. Again,

varieties Q183 and R570 have showed highest and lowest tiller count in the early phase of

growth. Eight plants were tagged in each plot (in the section marked for final harvest) and data

will be collected on green leaf count and plant height. Some data have already been collected

on these parameters. Also, first destructive harvest was conducted on April 10, 2014. We also

conducted destructive harvest on three CP varieties during 2013 (CP 89-2143, CP 88-1762,

and CP 00-1101) in one of our trials during August and December of 2013 to acquaint

ourselves with the sampling protocol.

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Figure 5.6: Sugarcane emergence (%) for all six varieties planted on December 12, 2013.

Figure 5.7: Tiller count per hectare for all six sugarcane varieties planted on December 12,

2013.

0

20

40

60

80

100

20 40 60 80 100 120

Eme

rge

nce

(%

)

Days After Planting (DAP)

N41 NCo376

CP 88-1762 R 570

Q183 HoCP 96-540

0

20000

40000

60000

80000

100000

120000

40 60 80 100 120

Tille

r co

un

t p

er

he

ctar

e

Days After Planting (DAP)

N41 NCo376

CP 88-1762 R 570

Q183 HoCP 96-540

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6. Conclusion

The project is well on track. Trials have been planted in the USA and South Africa and data

have been collected in these two trials as well as the trial planted earlier in Zimbabwe. It is

estimated that the Reunion trial will be planted in January 2015.

The focus is now on managing the trials and collecting the data according to the agreed trial

and data collection protocols. To this end a data recording and storage sheet was developed.

The suggestion is that project participants send the first batch of data (collected up to an

including the first destructive sampling) in the data storage sheet to the project manager so

that potential discrepancies can be addressed as soon as possible. A technical report is also

due after the completion of the first season.

7. Reference

South African Sugar Research Institute (1999). Identification and management of the soils of

the South African sugar industry (3rd Edition).

.