Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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SOUTH AFRICAN SUGARCANE
RESEARCH INSTITUTE
Progress Report
2014/2015
1
Contents
SASRI Committee and Management Page 2
Chairman’s Report Page 3
Director’s Report Page 5
Overview of SASRI Research Page 8
Variety Improvement Research Page 11
Crop Protection Research Page 21
Crop Performance and Management Research Page 31
Systems Design and Optimisation Research Page 38
Research Contracts Page 45
Achievements and Awards Page 47
Extension Page 49
Technology Transfer and Knowledge Exchange Page 55
Publications and Presentations Page 60
2
SASRI Committee &
Management
SASRI COMMITTEE 2014 - 15 MANAGEMENT TEAM 2014 - 15
(as at 31 March 2015) (as at 31 March 2015)
Chairman PW Russell Executive Committee
Vice-Chairman ST Naidoo Director: CM Baker
GROWERS Representatives Research Manager: DA Watt
KM Hurly, TJ Murray, F Potgieter, S Sharma, Operations Manager: KA Redshaw
GD Stainbank, R Talmage, GD Nelson, Finance and Admin Manager: AJ Van Der Nest
TB Funke (alternative), D Littley (alternative),
Human Resources Manager: C Botes
A Russell (alternative)
Programme Managers
MILLERS Representatives
Variety Improvement: SJ Snyman
EA Bruggemann, J Dewar,
JPM de Robillard (alternative), Crop Protection: RS Rutherford
SJ Saunders (alternative), D Sutherland (alternative), Crop Performance and Management: R van Heerden
TB Ngeleza (alternative), D van Rooy, DP Rossler,
Systems Design and Optimisation: R van Antwerpen
PM Schorn
Resource Managers
SASA Representatives
Crop Biology Resource Centre: S Buthelezi
MK Trikam, CM Baker, DA Watt,
AJ van der Nest (Secretary) Plant and Environment Resource Centre: B Naidoo
Diagnostic and Analytical Resource Unit: KA Collings
Breeding and Field Resource Unit: S Ramgareeb
Extension: GW Maher
Knowledge Management: ML Binedell
Biorisk Management: RA Stranack
3
Chairman’s
Report
A
“A world class sugarcane research changing needs of the industry and to
institute delivering relevant tech- adapt its research approach to meet
nology and facilitating implemen- these challenges.
tation of innovative solutions for a
sustainable industry” is the proposed SASRI is a world class establishment,
new vision for the South African well placed to meet the challenges
Sugarcane Research Institute as it ahead. Its influence throughout
strives to meet the requirements of its the African continent is notable
customers in the face of challenging with technology and variety sales
times. This vision, developed by the making up a significant revenue
SASRI committee members working source. Varieties propagated at the
together with SASRI management and institute are in high demand and
scientists, reflects on the recent past SASRI has variety licence agreements
and describes the role of the institute and variety evaluation agreements
as it celebrates its ninetieth year of with the SADC and further afield to
existence. countries such as Cameroon, Congo, Paul Russell
Sudan, Senegal and Nigeria. SASRI’s (Chairman - SASRI Committee)
The year under review has come scientists are highly regarded with
‘
with its challenges, specifically the Drs Rutherford, Zhou and Ramburan
dry conditions which have been being awarded National Research
experienced across the bulk of the Foundation ratings over the past 12
sugarcane growing regions. The months, joining a long list of SASRI
industry mean annual rainfall was scientists who received this award
64% of the long-term mean measured in previous years. Dr Sandy Snyman SASRI is a world class
from May 2014 to April 2015 with and Dr Ruth Rhodes also received establishment, well placed to
some regions, notably Zululand, recognition for their respective
being particularly negatively industry leading contributions meet the challenges ahead.
impacted. Here, rainfall measured as to the Public Understanding of Its influence throughout the
little as 439 mm, down from a long- Biotechnology and Crop and Soil
term mean of 920 mm. These climatic
African Continent is notable.
Science.
conditions, together with external
pressures on the industry, certainly In an effort to improve plant breeding
challenge SASRI to respond to the and promote the planting of disease-
4
SASRI Progress Report 2014/15
free seedcane, the industry has As the sugar industry expands in Sustainable agriculture within the
embraced NovaCane® technology. Africa, the risk of pest and disease sugar industry remains a key focus area
This has resulted in plans being incursions increase, requiring the with all SASRI programmes supporting
approved to construct a NovaCane® South African sugar industry to the SUSFARMS® management system.
facility that significantly enhances the maintain and build on its defence The system is designed to reduce
existing plant breeding facility and capabilities. Since 2000, the various the negative impacts of sugarcane
its capability to produce true to type growing regions within South Africa farming on the environment whilst
seedcane. Maintaining varietal purity have experienced outbreaks of new ensuring economic sustainability
in the plant breeding function through pests and diseases including brown and social upliftment through
tissue culture and the control of plant rust, maize streak virus, thrips, yellow the implementation of better
germplasm are key components of sugarcane aphid and tawny rust. Chilo management practices. All growers
the NovaCane® process and are best borer, not yet encountered within should be encouraged to adopt the
managed “in house” by experienced South African borders remains a system, and in partnership with their
SASRI scientists and programme significant threat to the industry and milling colleagues, work towards an
managers. The strategic objective to will require extensive collaboration integrated industry outcome where
develop and release varieties with with our SADC partners if the pest is best practice becomes the new norm.
improved genetic traits acceptable to be controlled. With this in mind, it
to both growers and millers in order has been encouraging to witness the I would like to acknowledge the
to enhance sucrose yield, increase support that the South African Sugar commitment and expertise of
resistance to pest and diseases Association at large has given to SASRI the SASRI Director, the functional
and improve milling characteristics in its successful drive to incorporate managers and the resource and
remains the primary focus of this the entire pest, disease and variety research programme managers as
programme. Its ultimate success will control programme into the SASRI well as the efforts of the extension
be dependent on the rate of adoption function. Adherence to industry rules specialists. I would also like to thank
of these varieties by the industry. and regulations, and improved hazard all the SASRI, Grower and Miller
This objective is supported by a identification and risk assessment representatives on the committee for
number of research areas including will better position the industry their considerable input and support.
integrated pest management, crop to respond to pest and disease The next twelve months will pose
protection and systems design and incursions in an integrated fashion, a number of challenges I am sure....
optimisation. The integration of these limiting the potential negative impact bring it on!
initiatives has established a sound of incursions.
launching pad for accelerated, albeit
long-term, research into genetically
modified sugarcane that could well
result in a step change in sugarcane
yield with improved traits such as
pest resistance, enhanced nitrogen
utilisation and herbicide resistance.
5
Director’s
Report
‘F
The prevailing conditions highlighted the relevance
of resilient varieties and the urgent need for a secure
and robust biosecurity system.
Founded in 1925, SASRI celebrates its importance of adhering to good
90th year in 2015. Throughout this time management principles based on
the primary mandate of the institution sound research.
associated with research and extension
has remained unaltered. What has
Sugarcane varieties
changed, however, is the specific focus
of these two main functions, which are Two new varieties were released:
influenced by the prevailing industry N58, with its superior RV and cane
conditions and its requirements for yields and good general disease and
sustainability - and hence the specific eldana resistance was geared for the
focus constantly shifts. Regardless, coastal long-cycle conditions; while
the unique challenges associated with N59 with similar characteristics was
growing sugarcane in South Africa targeted for the hinterland. Further
have successfully stimulated the efforts to improve the plant breeding
development of innovative research programme culminated in approval Carolyn Baker
and resulted in delivery of valuable for the development of a tissue (Director)
outcomes that are tailor-made for the culture facility at SASRI that is directed
sugar industry. towards production of NovaCane® for
the final stages of the programme.
Work in this past year was conducted This facility, with a targeted capacity
within the context of a looming for development of 300 000 plants,
drought that influenced the approach will be built during the course of
adopted in developing the programme 2015 for use in the 2016 season.
of work. The prevailing conditions
highlighted the relevance of resilient Significant debate on the value of
Biosecurity
varieties and the urgent need for a developing and deploying a GM Recognising the considerable yield
secure and robust biosecurity system. variety was held, following delivery of losses that eldana continues to incur
The importance and value of engaging a business case for insect resistance. in the industry, an effort to refocus
with growers to share knowledge on The specific approaches that should the work conducted on this pest
practices geared towards ensuring be adopted in embarking on such a was initiated within the context of
sustainability was highlighted and programme in conjunction with their an integrated pest management
through this process the ‘lived’ associated risks will form the basis approach. This resulted in the
experiences of growers enabled of further discussions in the coming development of an eldana research
others to more fully appreciate the year. framework to enable a more directed
6
SASRI Progress Report 2014/15
approach towards achievement of the Closely associated with pest and of progeny from crosses. Further
outstanding work that is required to disease research at SASRI, are the understanding of the performance
provide the additional tools required surveys conducted by the industry’s of released varieties was achieved
to complete the ‘tool-kit’. Of the six local pest and disease structures in an investigation into the genetic
focal areas that included crop stress to monitor the industry pest and traits that are associated with
management, plant resistance, habitat disease status. Arguably, one of the good ratooning ability as well as
management, chemical control, most significant changes to the SASRI the emergence, growth and yield
monitoring, and implementation, gaps complement took effect at the end responses of varieties grown and
were identified in several key areas of March 2015, when the pest and cut under either burnt or green-cane
associated with habitat management disease (P&D) operations (and 164 harvested conditions.
and chemical ecology that relate to new employees) were assumed into Emphasis continues to be placed on
biological control of the pest. The SASRI. In preparation for the new determining efficiencies associated
effective implementation of sterile function, some re-arrangements were with nitrogen fertiliser usage. At the
insect technology (SIT) to control made to the Extension structure to molecular level early results from
false coddling moth in the citrus accommodate the new function in genetically engineered NCo376 to
industry encouraged an investigation recognition of their close alignment. enhance nitrogen use efficiency
into the suitability of this method This culminated in the development enabled a 36% reduction in nitrogen
of population control for the eldana of a combined Extension/ Biosecurity applications, while in the field specific
moth. Following a fascinating visit function. placement of fertilisers and also crop
to the Western Cape to view the rotation research have generated
facilities and infrastructure required The research programme some good results. The importance
to successfully mount a sterile moth of soil health and its impact on
The extent and scope of SASRI’s
release programme, details regarding the sugarcane plant root system
research programme forms the
the pilot project to establish proof prompted investigations into top- and
bulk of this progress report, and
of concept for the technique were sub-soil acidity studies, and the focus
reflects on the range of innovations
finalised and presented to the SASRI on soils was further highlighted by
and achievements accomplished
Committee. Fundamental to the the distribution of the new soils book,
by our team. The drive to improve
success of the project is construction Understanding and Managing Soils in
the genetic base of South African
of an irradiator for sterilisation of the South African Sugar Industry.
sugarcane varieties through intro-
moths, and support for fully scoping
gression breeding continued, Good progress was made in the
this facility was granted.
with some progress being made development of a range of diagnostic
Following the incursion of yellow in understanding the relationship and predictive tools: the molecular
sugarcane aphid, a LINK article alert- between DNA content and
ing the industry to the new pest chromosome number,
appeared in May 2014. While designed to enable
considerable information regarding prediction in the
this pest was available in the chromosome
literature, evidence for its role in numbers
transmitting SCMV was lacking,
leading to the initiation of a research
project in this regard. Further work
on establishing the response of
commercial varieties to the pest as
well as the likely yield loss from
this pest was also initiated,
but hampered by the
ephemeral nature of
the pest.
7
SASRI Progress Report 2014/15
tool for detecting sugarcane mosaic served as a valuable aid that enabled and is associated with completion of
virus and sugarcane yellow leaf virus growers to discuss their own practices degrees usually over two or three years.
will be used in the Quarantine facility with their Extension Specialist in In the past period six MSc students and
to assist in mitigating the biosecurity order to monitor their management one PhD student graduated.
risk posed by the pathogens; the new improvement. Notably in two mill
As a way of determining the extent
assay for RSD detection enables near- areas, 100% submission of Progress
to which the research programmes
field analysis of sugarcane; the stalk Trackers was achieved. Benchmarking
meet industry requirements and
juice purity calculator that relies on SUSFARMS® against an international
also compare with international
simple in-field brix measurements will standard facilitated identification of
standards, a review of one of the four
assist in decision-making associated any gaps in the system and provided
research programmes by an expert
with ripening; and a model to assess valuable guidance in developing the
panel is conducted annually. In 2014,
costs associated with crop residue updated version.
the Systems Design and Optimisation
recovery for electricity co-generation
SASRI’s reputation for delivery of programme was the subject of review
demonstrated economic viability.
high quality education was evident by three specialists: one from the
Continued investigations into suitable in the demand for enrolment in the USA; the second from Australia; and
chemistries for combating pathogens certificate courses in sugarcane the third from South Africa. In their
and pests resulted in identification agriculture. A total of 326 students report, the reviewers articulated their
of two new products suitable for attended the Junior and Senior “commendations”, “affirmations” and
eldana control, and one other for courses, 70% of which emanate from “recommendations”, providing clear
thrips control. Further work on the South Africa. comment on where, in their collective
efficacy of a range of products aimed view, SASRI was making excellent
Ensuring that all new research
towards yellow sugarcane aphid headway, and those areas where
outcomes are made available in
control was initiated. In an effort to some attention was required. The
an appropriate format for our
achieve environmentally sensitive value in conducting such reviews is
stakeholders remains a key purpose
ways to control pests, investigations patent.
for the Knowledge Management
into appropriate bio-pesticides for
Unit at SASRI, and production of Benchmarking SASRI scientists’
the control of white grubs and stalk
technical publications to meet performance against national and
borers were ongoing.
the requirements of a range of international standards is another
stakeholders is required. Apart from important gauge of scientific
Service delivery the Link, the Ingede, Information excellence, and during the past year
Strides in delivering a cost Sheets and Mechanisation Reports, a three researchers were awarded
effective, consistent and reliable host of more specialised guides were National Research Foundation
Fertiliser Advisory Service (FAS) produced including the pocket-sized scientific ratings, bringing the SASRI
were evident in its achievement of Pest and Disease Guide, the Manual for total to nine rated scientists. Such
SABS accreditation and also its ISO Successful Implementation of Small- ratings not only signal the stature of
9001:2008 quality management scale Grower Projects, the updated our scientists but also enables access
system certification. Further, Sugarcane Diseases in South Africa to external incentive funds designed
refinements in recommendations booklet, and the P&D Operations to augment research activities and
emanating from analysis of soils Manual. facilitate research delivery.
and leaves were realised through
development of improved methods Developing new expertise In a year filled with a number
of significant advancements and
and also acquisition of several and assuring quality achievements it is with sadness that
new instruments including the
To develop future scientific expertise, we remember the loss of several of
mid-infrared spectroscope (MIR)
SASRI remains committed to our staff members including one of
that has enabled faster sample-
developing young scientists and our senior Plant Breeders in a tragic
throughput and an expanded range of
accomplishes this through their road accident. Our commitment to
determinations.
research internship programme the industry and delivery against
Promoting the adoption of and also through postgraduate stated objectives remains unabated
SUSFARMS®, a sustainable sugarcane development. While the intern group however, and it is a tribute to the
farm management system, remained remains fluid, since their employability collective effort of all SASRI staff that
a key focus in Extension, with several and prospects are greatly enhanced we are able to meet our mandate and
study groups and grower events through their association with SASRI conduct our research, development
structured to elaborate on the specific and during the course of the year and knowledge exchange activities
value that the management tool would several replacements are made, the within budget.
deliver. The Progress Tracker tool postgraduate group is more stable
8
Overview of SASRI
Research
Goals
To develop and deliver new sugarcane varieties providing increased economic
returns for all sectors of the industry.
To undertake research and provide services that advance nutritional, agronomic
and engineering practices and pest and disease control measures.
To generate new ideas with the potential to enlarge the scope of sugarcane
agriculture and sustain the industry into the future.
RESEARCH PROGRAMMES AND KEY RESEARCH AREAS
CROP PERFORMANCE AND MANAGEMENT SYSTEMS DESIGN AND OPTIMISATION
Key Research Areas: Key Research Areas:
Crop Nutrition (7 projects) Production Sustainability (3 projects)
Soil Health (3 projects) Water Management (3 projects)
Crop Ripening (2 projects) Technology Development (5 projects)
Crop Physiology (4 projects)
Crop Residue Management
(2 projects) VARIETY IMPROVEMENT
Water Management (1 project) Key Research Areas:
Climate Change (2 projects) Breeding and Selection (7 projects)
Variety Characterisation (3 projects)
CROP PROTECTION Novel and Improved Traits (9 projects)
Key Research Areas: Genomics and Bioinformatics
Biosecurity (5 projects) (1 project)
Crop Resistance (3 projects) Sucrose Metabolism (1 project)
Agro-ecology of Pathogens Derek Watt
and Pests (4 projects) (Research Manager)
Biological Control, Cultural and
Environmental Practices CROP
(3 projects) PERFORMANCE
Agrochemicals (6 projects) SYSTEMS
AND
DESIGN AND
MANAGEMENT
OPTIMISATION
CROP
PROTECTION VARIETY
IMPROVEMENT
9
RESEARCH OBJECTIVES RESEARCH FOR SUSTAINABLILITY: ELDANA MANAGEMENT
Variety improvement
Nature of Eldana
To conduct research and implement
The African sugarcane stalk Borer,
strategies for the continual release
Eldana saccharina, remains an ongoing
of new varieties that add value and
and severe constraining factor on
enhance productivity.
industry production. After being first
Crop protection observed on the Umfolozi flats in
To minimise the effects of disease, 1939, this highly damaging insect
weeds, nematodes and insect pests pest is now ubiquitous throughout
on crop production in a sustainable the South African sugar belt, from the Eldana saccharina larva
manner. lower South Coast of KwaZulu-Natal complex cocktail of pheromones
through to the Mpumalanga Lowveld. from both wing and abdominal
Crop performance and
The impact of this pest on the industry glands that is thought to attract
Management
is estimated to be in the region of females over long distances; (c)
To develop new and fine-tune
R 0.9 billion of lost revenue per three to six males aggregate during
existing crop management practices
annum, both as direct sucrose yield calling to amplify the pheromone
to enhance the economic and
loss due to infestation damage, as signal; and (d) eldana is a ‘hearing’
environmental sustainability of sugar-
well as the cost incurred by growers moth, emitting acoustic cues that
cane production.
to implement the agronomic and pest are believed to orientate females at
Optimisation management practices required to close range.
To design and improve farming constrain the population size of the Managment implications
systems that account for the econo- pest.
The original eldana host switch from
mic, social and environmental issues Several characteristics of eldana
sedges to sugarcane in Umfolozi
that impact on the sustainability of make the design and implementation
was likely due to widespread
sugarcane production. of effective and sustainable
habitat disturbance. However, the
management practices particularly
maintenance of wetland habitats
PROJECT PORFOLIO OVERVIEW challenging.
under intensive sugarcane mono-
Pest characteristic culture is an important component
Project Disposition
Eldana is an indigenous of eldana IPM. These wetland areas
lepidopteran insect that is native serve as an important sink for eldana,
to African wetlands and resident in which populations are maintained
NEW at low levels by natural enemies.
primarily in sedges (members of the
PROJECTS
18 projects Cyperaceae). Eldana eradication from sugarcane
Eldana displays cryptic behaviours: is not attainable due to the
(a) female moths lay most eggs widespread ocurrence of natural
in concealed locations (e.g. in dry host plant species and continuous
leaf material); (b) larvae initially population replenishment from
ONGOING PROJECTS
56 projects scavenge externally on the stalk other locales.
protected by the leaf sheaths; (c) The cryptic nature of eldana in
surviving larvae bore into the stalk sugarcane renders the insect largely
where they spend the remainder inaccessible to biocontrol agents
Project Type of the larval stage feeding on the and agrochemicals during the
internal tissues; and (d) pupation majority of the life cycle.
occurs internally in the excavated Continous reproduction makes
PRINCIPAL
LONG-TERM stalk or when externally, frequently targeted eldana management
PROJECTS behind a leaf sheath. through biocontrol agent releases
11
projects Eldana reproduction is continuous, or agrochemical applications only
apart from two peaks in moth partially effective.
numbers around April and October. The complexity of the eldana mating
When compared to the vast majority process requires the development
FIXED-TERM PROJECTS of moth species, eldana has a highly of a fully customised management
63 projects unusual reproductive biology: (a) it strategy, as those applied
is the male eldana moth that calls successfully to other lepidoteran
female moths for mating; (b) after pests are not effective against this
dusk, eldana male moths emit a unique pest.
10Eldana IPM principles
Knowledge gained from years of provide growers and other industry
research into the biology and agro- stakeholders and roleplayers with
ecology of eldana has formed the insights into the requirements for
foundation of an area-wide Integrated effective eldana management. The
Pest Management (IPM) approach book is available from the SASRI
that will ultimately facilitate the Knowledge Management Unit and
sustainable management of the pest. interested parties are invited to
contact the SASRI library for further
In 2014, SASRI published a book details (library@sasa.org.za).
describing the precepts of Eldana
IPM and which is intended to SASRI Eldana IPM Book
Eldana IPM research
Research and technology develop-
ment to provide growers with the Entomology
Pathology
necessary repertoire of tools for Nematology
effective Eldana IPM is multi-disci-
plinary and is conducted across the CROP
Bio
PROTECTION
op cie y
Bre chno
tri e
Cr il S om
n
four research programmes (Variety
Nu nc
tio
te
ed log
So ron
Improvement, Crop Protection, Crop
EM E
ing y
IM
T
AG NC
Ag
EN
VA VEM
PR
Performance and Management and
& M FO OP
AN RMA
RIE EN
O
PER CR
Systems Design and Optimisation)
TY T
and encompasses the activities of SASRI
the Knowledge Management Unit and ELDANA
Extension Services. IPM
RESEARCH
De gric al Da
SASRI Eldana IPM Research occurs in
SY IGN ION
OP
DE ISA
cis ult ta
lde ge
A ati
Fa Sup l En nag
ION
ST &
TIM
six Focus Areas corresponding to the
S
Sp
ho an
ion ura Ma
Sta e Ex of
rm
rs
EM
NS
ke ch
n
required technology components of
ing port inee ent
wi led tio
TE
T
EX
a
Sy
the Eldana IPM toolkit (right). ow di
g
ste ode ng
Kn Me
KNOWLEDGE
M
ms llin
g
MANAGEMENT
th
r
m
i
Media, Resources and
g
Processes to facilitate and
mediate Knowledge Exchange
with Stakeholders
1. Crop stress management 3. Habitat managment 5. Spatial planning and
To develop technologies that To develop cost-effective technologies monitoring
enable the reduction, avoidance or that permit the establishment of agro- To implement digital spatial mapping
priming of plant stress such that ecological environments in which (GIS) that facilitates the collation
plant innate resistance to eldana is eldana populations are suppressed and interpretation of environmental
not compromised or is potentially to low levels by benign biological and biological data that are central
enhanced. means. to effective and proactive eldana
management.
4. Chemical control
2. Plant resistance To develop a suite of effective
6. Implementation
To harness native and foreign genetic insecticidal eldana control agents and To enhance adoption of eldana IPM
sources of resistance to eldana and responsible application tactics that through practical demonstration of
implement technologies to increase are agriculturally, environmentally, efficacy and promote the approach as
the efficiency of eldana resistance ecologically and economically an integral component of sustainable
breeding. sustainable. sugarcane farming practice.
11VARIETY IMPROVEMENT PROGRAMME
Goal
Conduct research and implement strategies for the continual release of
high sugar yielding (biomass and sugar content), adaptable, pest and
disease resistant varieties that add value and enhance Industry productivity.
Key research areas
GENOMICS AND
BIOINFORMATICS
1 project
SUCROSE
NOVEL AND
METABOLISM
IMPROVED TRAITS
1 project
9 projects
Dr Sandy Snyman
BREEDING
(Programme Manager)
AND
SELECTION VARIETY
7 projects CHARACTERISATION
3 projects
Breeding and selection development of resources to Novel and Improved Traits
facilitate the use of genetic
The principal, long-term Plant This Key Research Area is strongly
markers for the selection of
Breeding Project lies at the core of focused on the development of
parents for crossing.
the Variety Improvement Programme. innovations of strategic importance to
This research is strongly comple- the future delivery to, and sustainable
The project consists of five primary mented by investigations conducted maintenance of, varieties with novel
areas of research and operations, in the Resistance Key Research Area traits (characteristics) to the industry,
viz. crossing, selection, genotype of the Crop Protection Research for example enhanced nitrogen-use
testing, bulking and release. Programme. efficiency and herbicide tolerance.
Research projects in this area develop
The project facilitates the develop- Variety Characterisation technologies and resources required
ment and release of varieties with for genetic engineering, mutagenic
Running in parallel to the Plant
high sugar yield (both sucrose breeding and preservation of valuable
Breeding Project is the principal,
and cane yield), pest and disease germplasm, as well as demonstrate
long-term Variety Evaluation Project,
resistance, adaptability, ratooning proof-of-concept regarding the
which aims to provide comprehensive
ability and agronomic and milling performance of the novel lines
information on the performance
characteristics that are desirable to produced.
of new varieties under different
both millers and growers.
management practices and agro- Genomics and Bioinformatics
The Plant Breeding Project is climatic zones upon, or soon after,
their release to the industry. Projects in this Key Research Area
complemented by a cluster of focus on unravelling the extremely
research projects that aim to As for the Plant Breeding Project, complex sugarcane genome with
improve the efficiency of sugarcane the Variety Evaluation Project is a view to the development of
breeding for the industry through complemented by a series of research genetic markers linked to important
innovation, including: projects that are instituted to address sugarcane traits, for example pest and
expansion of the genetic base of specific issues, for example variety disease resistance. Knowledge and
germplasm used as parents for ratoon longevity and the performance resources generated in this area feed
crossing through introgression of varieties derived from the into the Breeding and Selection Key
breeding; and NovaCane® technology. Research Area.
12STRATEGIC OBJECTIVES PROJECT PORTFOLIO OVERVIEW
To develop and release varieties Project Disposition Project Type
with sucrose, yield, pest and
disease, agronomic and milling
characteristics desirable to both PRINCIPAL
millers and growers. NEW LONG-TERM
PROJECTS PROJECTS
To provide comprehensive variety 6 projects 5
projects
information to assist the industry in
making optimal variety choices.
To diversify breeding strategies to
exploit the full genetic potential of ONGOING PROJECTS FIXED TERM PROJECTS
15 projects 16 projects
sugarcane.
To implement molecular breeding
and crop modelling strategies to
improve variety delivery.
To conduct basic research to develop
new genetic resources for variety
improvement through commercial
breeding, genetic engineering and
mutagenic breeding.
New Projects
Introgression Breeding
Need Statement: The international sugarcane breeding community is in general agreement that the intensive
selection for high sucrose over the past several decades has resulted in a narrowing of the
sugarcane genetic base, which is arguably the primary factor responsible for the apparent
lack of significant gains in sugarcane breeding.
Evidence suggests that chromosome loss with each successive generation, particularly of the
Saccharum spontaneum component of the sugarcane inter-specific genome, has eroded this
genetic diversity.
Effects of the postulated erosion of genetic diversity has become noticeable at a time when
new challenges for sugarcane agriculture are emerging: in biosecurity (more pest and disease
incursions); in climate change (longer dry periods, higher temperatures) and from increasing
input costs.
Among established pests and diseases, eldana and sugarcane smut are likely to become more
prominent, as both are favoured by warmer and dryer winters.
Within the current breeding material at SASRI, there is an inverse relationship between
resistance to the stalk borer and resistance to smut, making breeding for resistance to both
problematic.
To address these challenges, greater genetic diversity will be needed and introgression
breeding has been identified as a way to achieve this.
The goal of the introgression research is to provide the Plant Breeding Project with superior
parental material from which to develop commercial sugarcane varieties with an expanded
genetic base.
Project To increase genetic diversity of parental populations through introduction of new traits, viz.
Objectives: high cane yield and high levels of eldana and smut resistance, from wild ancestral and closely
related species.
13Project To characterise wild and related germplasm and assess levels of genetic diversity in the
Objectives: Saccharum germplasm collection at SASRI to aid selection of a core set of clones for
introgression.
To optimise all parameters relevant to the success of creating intergeneric hybrids, viz.
synchronised flowering, pollen fertility and molecular techniques (flow cytometry and
genomic in situ hybridisation).
To generate knowledge about the breeding systems of wild and related sugarcane species.
To generate breeding values for identification of superior parents to include in mating designs.
Anticipated An expanded set of genotypes, with novel sources of pest and disease resistance, for use as
Outcomes: parents in breeding superior sugarcane varieties into the future.
Technology and/ (a) Hybrids obtained from introgression breeding will revert to commercial breeding for use
or Knowledge in the crossing programme; (b) results from the studies will be communicated in The Link,
Exchange Plan: Proceedings of the South African Sugar Technologists’ Association and articles in science
journals.
Value to The sustainability of the South African sugar industry is linked to the ongoing release of
Industry: superior and adaptable varieties that can withstand prevailing climatic conditions and pests
and disease pressures.
Agronomic performance under rainfed conditions of NovaCane® plantlets compared with plantlets
derived from conventional seedcane
Need Statement: New varieties are to be routinely released to the industry as NovaCane® plantlets for bulking
and subsequent distribution for planting in regional seedcane programmes. Consequently, the
performance of NovaCane®-derived seedcane requires thorough characterisation.
Project (a) To compare the yield and agronomic performance of crops derived from NovaCane® plants
Objectives: with those from conventional seedcane sources in the first, second, and third propagation stages
across several ratoons under rainfed conditions; and (b) to evaluate plant spacing and planting
density to optimise performance of NovaCane® plantlets and NovaCane®-derived seedcane.
Approach to be The investigation, which is to be conducted on the SASRI Mount Edgecombe Research Station,
Adopted: will be based on fully replicated field trials specifically designed to compare the performance
of crops derived from the NovaCane® technology with those derived from transplants (plantlets
derived from single-bud setts). The trial will be continued over three crop cycles to further
examine the performance of NovaCane®-derived crops across ratoons. In addition, the stalks
from NovaCane®-derived crops will be used as planting material for subsequent trials to examine
subsequent crop performance over several ratoons.
Anticipated Comprehensively characterised performance of planting material derived from the NovaCane®
Outcomes: technology, facilitating better advice to bulking co-operators and growers.
Evaluation of whether plant spacing and planting density influence the performance of
NovaCane®-derived crops.
Technology and/ The results of the study are to be communicated through the publication of articles in The Link
or Knowledge and the hosting of grower events.
Exchange Plan:
Value to The information generated will allow SASRI to provide recommendations to bulking co-operators
Industry: and growers regarding the agronomic performance of NovaCane® plantlets and NovaCane®-
derived commercial sugarcane crops. The information generated on the effects of plant
spacing and planting density will assist both seedcane producers and growers in optimising the
performance of NovaCane®-derived crops.
14Agronomic evaluation of several imazapyr tolerant lines and characterisation of resistance
Need Statement: Previous research (Projects 07VI03 and 11VI01) resulted in the development of three mutant lines
of N12 that show increased tolerance of the herbicide, imazapyr (active ingredient of Arsenal®).
When compared to non-mutant N12 controls, improved herbicide tolerance of the mutants may
be ascribed to either: (a) greater expression of the gene encoding the enzyme acetolactate
synthase (ALS); (b) alteration of the DNA sequence of the ALS gene which prevents the inhibitory
binding of imazapyr to the ALS enzyme; or (b) higher capacity for imazapyr detoxification.
Project (a) To evaluate and compare the agronomic characteristics of three imazapyr-tolerant mutant
Objectives: N12 lines to a standard N12 control; (b) to determine the mode of tolerance of the mutant lines
to imazapyr; and (c) to sequence the ALS genes of the three mutant lines to determine whether
any of the mutated ALS genes might be useful in the development of a selectable marker system
for the genetic engineering of sugarcane.
Approach to be The three lines with enhanced imazapyr tolerance will be subjected to field screening to confirm
Adopted: their tolerance under standard weed control regimes. A concurrent phenotypic assessment
(stalk height, stalk diameter, number of tillers, sucrose and fibre content) of the lines relative
to standard N12 will be conducted in replicated field trials to assess whether unintended
somaclonal variation effects have occurred during the mutation breeding process. In addition,
the mechanism leading to the enhanced tolerance to imazapyr will be investigated through the
genotypic characterisation of the mutant lines, which will include the analysis of ALS activity,
examination of ALS gene copy number and determination of the ALS gene sequence.
Anticipated (a) Agronomic performance assessments for three mutant lines of N12 displaying improved
Outcomes: tolerance to imazapyr; (b) comprehensive information regarding the mechanisms underlying the
increased imazapyr tolerance of the three mutant lines; and (c) ALS gene sequence data that
will enable the development of a selection marker technology for future genetic engineering of
sugarcane.
Value to Upon the introduction of a herbicide tolerant N12-based variety, it is envisaged that the cost of
Industry: Cynodon control (per ha) under certain circumstances could potentially be reduced by almost
50%. Early spraying would reduce the Cynodon population thus also reducing the total number
of herbicide applications required to control this weed. Similar cost reductions are envisaged for
the control of other problematic weeds.
Protocol optimisation for genetic modification of sugarcane
Need Statement: For commercial release in South Africa, genetically modified (GM) crops must satisfy the regulatory
requirements established by the Department of Agriculture, Forestry and Fisheries (GMO Act
17 of 1997). One of the features of a GM crop considered by the regulators is the number of
copies of the transgene and associated selectable marker gene inserted into the genome of the
host plant, with single copies of each being viewed most favourably. Furthermore, a practical
requirement in the production of the GM plants is that the genetic transformation protocol must
generate a sufficient number of plants to enable the selection of the best candidates to satisfy
potential commercialisation requirements.
Project (a) To develop a sugarcane transformation protocol that yields high numbers of GM plants
Objectives: containing single copies of both the gene of interest and selection marker gene; and (b) to
evaluate the size of the genetic construct that can be successfully delivered into sugarcane
plants using micro-projectile bombardment (biolistics).
Approach to be Varying concentrations and sizes of linearised genetic constructs containing a transgene
Adopted: of interest and associated selection marker genes will be introduced into sugarcane callus
(undifferentiated cell masses produced through tissue culture) by biolistics. The targeted plant
callus will be subjected to various post-bombardment and selection treatments, after which
the cells surviving selection will be regenerated to form plantlets. The resulting plants will be
subjected to a series of DNA analytical tests that will enable the determination of the number of
copies of the transgene and selection marker gene inserted into the genome of each GM plant.
15Anticipated A sustainable, high-throughput genetic engineering protocol optimised to produce high
Outcomes: numbers of GM plants containing single copies of both the gene of interest and the selectable
marker gene.
Technology and/ The optimised protocol will be included in the SASRI Biotechnology Laboratory Protocol Manual
or Knowledge and become standard laboratory practice. The results will also be presented for peer evaluation
Exchange Plan: and scrutiny at a science congress.
Value to The protocol will reduce the manpower requirements and costs associated with transgenic
Industry: plant production and ease aspects of the regulatory approval process.
Tissue-specific transgene expression in the SA sugarcane germplasm: Do we have functional promoters?
Need Statement: Foreign genes introduced into sugarcane for the purposes of genetic engineering are frequently
silenced, which is an unwelcome phenomenon experienced by sugarcane biotechnology
laboratories across the globe. For several years, SASRI has worked towards the development of
gene promoters to enable targeted transgene expression in specific regions of the sugarcane
plant (e.g. insect resistance gene expression in the mature regions of the stalk) but these too
have been silenced. Evidence now suggests that: (a) the characteristics of the reporter gene
encoding the enzyme b-glucuronidase, which SASRI uses routinely to test the expression level
and specificity of gene promoters, may trigger silencing; and (b) the specific complex, polyploid
genetic background of the N series of varieties may somehow render tissue-specific promoters
particularly susceptible to silencing.
Project To determine whether: (a) specific characteristics of the foreign genes (e.g. b-glucuronidase
Objectives: reporter gene) used in the genetic engineering of sugarcane trigger the silencing phenomenon;
and (b) the genetic environment of the N varieties triggers endogenous gene silencing
mechanisms.
Approach to be Propensity for silencing will be tested through the genetic engineering of: (a) an N variety with
Adopted: genetic constructs in which a root-specific promoter has been fused to a reporter gene other
than b-glucuronidase (e.g. bovine lysozyme); and (b) the genetic engineering of varieties from
Australia (e.g. Q117) and the United States (e.g. CP72-1210) with a root-specific promoter
developed by SASRI.
Anticipated Confirmation of the root-specificity of a gene promoter previously isolated by SASRI and an
Outcomes: indication of whether promoter silencing is particularly problematic in the N varieties, which will
enable the design and testing of appropriate strategies to overcome this limitation. If successful,
the approach will be used to validate the specificity of other tissue-specific promoters (e.g. stem
specific) previously isolated by SASRI.
Technology and/ The information will be communicated through the publication of an article in a science journal.
or Knowledge
Exchange Plan:
Value to The knowledge will strengthen the SASRI GM technology platform and the capacity of the institute
Industry: to support the production of GM varieties for potential commercialisation into the future.
16Development of a semi-automated AFLP technique (one-year project)
Need Statement: At SASRI, the analysis of genetic relationships amongst sugarcane varieties for certain breeding,
genetic engineering and mutagenic breeding applications relies on an expensive, complex and
labour-intensive laboratory technique that uses a radioactive isotope of phosphorus (33P). Due
to the potentially hazardous nature of the isotope and the development of alternative non-
radioactive technologies internationally, 33P has become difficult and costly to source (many
nuclear facilities throughout the world have ceased or down-scaled production).
Project To develop a semi-automated method for certain types of genetic analysis that increases
Objectives: analytical throughput, improves efficiency and removes the reliance on costly and increasingly
difficult to source radioactive P-isotopes.
Approach to be Several duplicate blind analyses will be conducted to compare the results obtained using the
Adopted: currently established protocol with those generated by means of semi-automated capillary
electrophoresis optimised for the SASRI ABI3500 Genetic Analyser.
Anticipated A semi-automated method for certain types of genetic analysis that permits increased sample
Outcomes: throughput and improved efficiency and which does not depend upon costly and difficult to
source radioactive P-isotopes.
Technology and/ The optimised protocol will be included in the SASRI Biotechnology Laboratory Protocol Manual
or Knowledge and become part of standard laboratory practice.
Exchange Plan:
Value to The semi-automated technology for the determination of sugarcane genetic relationships will
Industry: enable improved research and operational efficiencies.
17OUTCOMES FROM ONGING RESEARCH
Advances Made: Value Derived:
Breeding of new and improved varieties
Genotypes 01G1662 and 02K0663 were approved N58 has superior RV and cane yields with good
for release to the Industry as varieties N58 and N59, general disease and eldana resistance under Coastal
respectively. long-cycle (18-month cycle) conditions, relative to
varieties established in the region.
N59 has superior RV and cane yields with good general
disease and eldana resistance under Hinterland
conditions, relative to varieties established in the
region.
Breeding and selection
Selection tactics have been revised to improve pest Enhanced pest and disease resistance breeding
and disease resistance breeding efficiencies: (a) pest efficiencies, particularly with regard to eldana
and disease screening trials are to be conducted resistance.
simultaneously to advanced variety trials to enable
enhanced statistical analysis of pest and disease
resistance data for decision-making; and (b) resistance
traits are to be screened in the early stage of breeding,
particularly at the first stage of selection in which families
of plantlets from specific parental crosses are evaluated.
Introgression (Diversification) Breeding
Analysis of the genetics of ancestral noble canes Application of the technologies developed
(Saccharum officinarum), ancestral wild canes in 2014/2015 provides a foundation for the
(S. spontaneum), modern cultivars (inter-specific S. spp implementation and analysis of introgression breeding
hybrids) and the complex hybrid progenies produced by strategies that aim to enhance sugarcane vigour and
crossing noble and wild canes with the modern hybrid stress tolerance.
cultivars, revealed that: (a) increases in genome size in
the progenies were generally accompanied by increases
in chromosome numbers; (b) chromosome transmission
from the parents was n+n for all the progeny; and (c) some
progeny experienced chromosomal loss or gain.
Variety evaluation
In instances where the direct assessment of damage A feasible harvesting strategy to maximise ERC
caused by frost events are not feasible, a general rule-of- yields in frost-prone areas, in instances where actual
thumb has been developed which indicates that growers assessments of frost damage are not possible.
should target the mid-May to mid-June period for the
harvesting of cane cultivated in frost-prone areas.
NUE genetic modification
The nitrogen-use efficiencies (NUE) of two genetically- GM technology enables the improvement of sugarcane
modified NCo376 lines were significantly higher than NUE.
the untransformed controls in a four month pot trial
assessment.
Overcoming transgene silencing in GM sugarcane
Gene promoters (the on-off switches) in which key Overcoming transgene silencing removes a significant
sequences have been mutated to prevent transgene impediment to GM technology deployment.
silencing were identified, synthesised and re-introduced
into sugarcane for functional testing.
18Advances Made: Value Derived:
Preserving valuable germplasm
Progress was made towards the development of a method Cryo-preservation of valuable sugarcane germplasm re-
for the storage of encapsulated sugarcane meristems duces the costs and risks associated with maintenance
(excised growth points) at ultra-low temperatures. of collections under natural field (ex-vitro) conditions.
Genomics and bioinformatics
Further significant progress was made in fulfilling Availability of a partial sequence of the sugarcane
the South African sugar industry contribution to the monoploid genome will provide significant impetus to
international effort to sequence the gene-rich portions of development of sugarcane marker-assisted breeding,
the sugarcane genome. as has occurred with other important crop species (e.g.
rice, wheat).
OUTCOMES FROM CLOSED PROJECTS
Specific observations: Essential outcomes:
Sugar sensing and signalling-mediated regulation of photosynthesis in sugarcane
The rate of sucrose production by sugarcane leaves A potential molecular mechanism mediating the
(via photosynthesis) declines as the leaves age and the relationship between the rate of sucrose biosynthesis
plant (stool) matures. in the leaf and the sucrose storage demand of the
This research sought to characterise the negative stalk has been described.
feedback system which modulates the rate of leaf Uncoupling of this mechanism may serve as a viable
photosynthesis according to the amount of sucrose in means to increase sucrose content per unit biomass
the stalk, particularly the molecule which transmits the through genetic engineering.
message from stalk to leaf and its site of action on leaf This work is not being pursued further at this time
photosynthesis. due to shifts in resource allocations and research
The investigations were undertaken with a view to priorities.
identifying targets for the future genetic engineering of
higher stalk sucrose content.
Glucose was identified as a candidate molecule for
signalling the stalk sucrose status (sucrose demand) to
the leaf photosynthetic machinery and two potential
signalling cascades in the leaf were identified as
recipients and amplifiers of the signal.
In the leaf, the amplified signal was observed to modulate
the expression of numerous genes associated with
several important functions, including photosynthesis,
starch metabolism and cell wall biosynthesis.
Overcoming transgene silencing in sugarcane
The hypothesis underlying this research is that the Specific regions of genetic constructs used in genetic
silencing in sugarcane of foreign genes (transgenes) engineering that appear to trigger the silencing of
inserted during genetic engineering is a result of a foreign genes have been identified and mutated
process called ‘methylation’. experimentally to reduce their propensity for
Methylation is one of the processes occurring in silencing.
plants (and animals) through which gene expression is Examination of the expression in GM sugarcane of the
naturally regulated and involves the addition, at multiple mutated foreign gene sequences is currently under
locations in a gene, of a chemical group (methyl group; way in a related project (13VI01: Tissue-specific
— CH3) to a particular type of DNA molecule, which transgene expression in the SA sugarcane germplasm:
stops expression. do we have functional promoters?).
Observations made in this study indicate that silenced Should the mutation approach developed in this study
transgenes in GM sugarcane are heavily methylated, proof successful, new avenues for the targeted, tissue-
although the genetic complexity of sugarcane does not specific expression of transgenes in SA sugarcane
permit unequivocal interpretation of the data. varieties will become available.
19 The regions of transgenes that were identified as being
heavily methylated have been mutated to reduce their
propensity for methylation and reintroduced into
sugarcane by genetic engineering for testing.
Specific observations: Essential outcomes:
Unlocking genetic variation in sugarcane for disease resistance
Strains of the fungus, Fusarium, occur naturally within Fusarium-tolerant lines of N41 and NCo376 were:
sugarcane (endophytically) without causing negative (a) produced by targeted mutation breeding and
effects but, when the plant is damaged or stressed, they selection; and (b) demonstrated to be resistant to
frequently secrete chemicals that are toxic to the plant stem rot and have improved eldana resistance.
(phytotoxic) causing stem rot. Selected lines are currently undergoing field
In addition to causing stem rot, some of these phytotoxins experimentation and analysis of mode of resistance
(e.g. beauvericin) are also harmful to insects that infest in a follow-on project (14VI03: Mutation breeding for
sugarcane (e.g. eldana). eldana resistance).
The hypothesis tested in this research was that Project 14VI03 also explores whether the mutation
overcoming the negative effects of beauvericin on breeding approach could be applied to produce other
the sugarcane plant would increase eldana resistance types of eldana resistance.
without any compromise to plant health.
Through targeted mutation breeding and selection,
Fusarium-tolerant lines of N41 and NCo376 were
produced that were resistant to stem rot and which had
improved eldana resistance.
Genomics of quantitative disease resistance in sugarcane
Breeding for sugarcane disease resistance is difficult, The project has demonstrated that the potential
frequently leading to high-yielding genotypes not being exists for: (a) the development of DNA markers for
released due to susceptibility to a particular pathogen. brown rust resistance that are complementary to
This project sought to: (a) develop a deeper the current marker of the major rust resistance gene,
understanding of the genetic basis of sugarcane disease Bru1; and (b) the use of rapid screening methods to
resistance, using brown rust resistance as a model; and establish variety resistance or susceptibility to brown
(b) assess the potential of rapid screening methods rust resistance.
(e.g. chlorophyll fluorescence and near infra-red Both (a) and (b) above are being pursued and applied
spectroscopy [NIRS]) as means to detect resistance or to additional pathogens and pests in a current project
susceptibility to brown rust. (14CP07: Prediction of quantitative resistance to
Results obtained indicated that: (a) the major brown eldana, smut, rusts, YSA and thrips using NIRS).
rust resistance gene, Bru1, contributes to the resistance
of SA varieties to brown rust; (b) the occurrence of the
Bru1 gene has increased in the N varieties from 46%
(1975-1985) to 68% (2001-2005), with 75% of all
recent releases containing the gene; (c) this prevalence
exceeds that observed in USA-bred varieties: 15%
(1975-1985) to 47% (in the current decade); (d) in
some instances, other sources of resistance to brown
rust appear to underlie the effect of the Bru1 gene
in the N varieties; and (e) rapid screening methods
show potential for detecting a resistant reaction of
sugarcane to rust infection and distinguishing between
constitutive resistance and the physiological response
of the sugarcane plant to infection.
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