Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE

 
Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
SOUTH AFRICAN SUGARCANE
   RESEARCH INSTITUTE

                          Progress Report
                                     2014/2015

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Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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

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Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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

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Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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-

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Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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.

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Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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

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Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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.

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Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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

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Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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:
  ƒ Crop Nutrition (7 projects)            ƒ Production Sustainability (3 projects)
  ƒ Soil Health (3 projects)               ƒ Water Management (3 projects)
  ƒ Crop Ripening (2 projects)             ƒ Technology Development (5 projects)
  ƒ Crop Physiology (4 projects)
  ƒ Crop Residue Management
    (2 projects)                           VARIETY IMPROVEMENT
  ƒ Water Management (1 project)           Key Research Areas:
  ƒ Climate Change (2 projects)            ƒ Breeding and Selection (7 projects)
                                           ƒ Variety Characterisation (3 projects)
  CROP PROTECTION                          ƒ Novel and Improved Traits (9 projects)
  Key Research Areas:                      ƒ Genomics and Bioinformatics
  ƒ Biosecurity (5 projects)                 (1 project)
  ƒ Crop Resistance (3 projects)           ƒ Sucrose Metabolism (1 project)
  ƒ Agro-ecology of Pathogens                                                             Derek Watt
    and Pests (4 projects)                                                            (Research Manager)
  ƒ Biological Control, Cultural and
    Environmental Practices                  CROP
    (3 projects)                         PERFORMANCE
  ƒ Agrochemicals (6 projects)                                       SYSTEMS
                                             AND
                                                                    DESIGN AND
                                         MANAGEMENT
                                                                   OPTIMISATION

                                          CROP
                                       PROTECTION                VARIETY
                                                              IMPROVEMENT

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Progress Report 2014/2015 - SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE
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
                                         ƒ 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
                    ƒ 18 projects          Cyperaceae).                            ƒ Eldana eradication from sugarcane
                                         ƒ 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
           ƒ 56 projects                   scavenge externally on the stalk          other locales.
                                           protected by the leaf sheaths; (c)      ƒ 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      ƒ Continous reproduction makes
                    PRINCIPAL
                   LONG-TERM               stalk or when externally, frequently      targeted      eldana     management
                    PROJECTS               behind a leaf sheath.                     through biocontrol agent releases
                    ƒ 11
                   projects              ƒ Eldana reproduction is continuous,        or agrochemical applications only
                                           apart from two peaks in moth              partially effective.
                                           numbers around April and October.       ƒ The complexity of the eldana mating
                                         ƒ 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
           ƒ 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.

                                                          10
Eldana 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.

                                                          11
VARIETY 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
    ƒ 1 project
  SUCROSE
                                             NOVEL AND
METABOLISM
                                          IMPROVED TRAITS
 ƒ 1 project
                                             ƒ 9 projects

                                                                                               Dr Sandy Snyman
                          BREEDING
                                                                                             (Programme Manager)
                             AND
                         SELECTION               VARIETY
                         ƒ 7 projects       CHARACTERISATION
                                               ƒ 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
ƒ 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
ƒ 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
ƒ 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.

                                                            12
STRATEGIC OBJECTIVES                                      PROJECT PORTFOLIO OVERVIEW
ƒ 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
ƒ To provide comprehensive variety                              ƒ 6 projects                               ƒ 5
                                                                                                          projects
  information to assist the industry in
  making optimal variety choices.
ƒ To diversify breeding strategies to
  exploit the full genetic potential of         ONGOING PROJECTS                            FIXED TERM PROJECTS
                                                  ƒ 15 projects                                 ƒ 16 projects
  sugarcane.
ƒ To implement molecular breeding
  and crop modelling strategies to
  improve variety delivery.
ƒ 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:       ƒ 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.

                       ƒ 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.

                       ƒ 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.

                       ƒ Among established pests and diseases, eldana and sugarcane smut are likely to become more
                         prominent, as both are favoured by warmer and dryer winters.

                       ƒ 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.

                       ƒ To address these challenges, greater genetic diversity will be needed and introgression
                         breeding has been identified as a way to achieve this.

                       ƒ 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               ƒ 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.

                                                           13
Project           ƒ 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.

                   ƒ 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).

                   ƒ To generate knowledge about the breeding systems of wild and related sugarcane species.

                   ƒ 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:   ƒ 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       ƒ Comprehensively characterised performance of planting material derived from the NovaCane®
 Outcomes:           technology, facilitating better advice to bulking co-operators and growers.

                   ƒ 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.

                                                       14
Agronomic 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.

                                                        15
Anticipated       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.

                                                        16
Development 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.

                                                       17
OUTCOMES FROM ONGING RESEARCH
                      Advances Made:                                                      Value Derived:
                                       Breeding of new and improved varieties
Genotypes 01G1662 and 02K0663 were approved                           ƒƒ 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.
                                                                      ƒƒ 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.

                                                                 18
Advances 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
ƒƒ The rate of sucrose production by sugarcane leaves                ƒƒ 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
ƒƒ This research sought to characterise the negative                    stalk has been described.
   feedback system which modulates the rate of leaf                  ƒƒ 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         ƒƒ This work is not being pursued further at this time
   photosynthesis.                                                      due to shifts in resource allocations and research
ƒƒ The investigations were undertaken with a view to                    priorities.
   identifying targets for the future genetic engineering of
   higher stalk sucrose content.
ƒƒ 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.
ƒƒ 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
ƒƒ The hypothesis underlying this research is that the               ƒƒ 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
ƒƒ Methylation is one of the processes occurring in                     silencing.
   plants (and animals) through which gene expression is             ƒƒ 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?).
ƒƒ Observations made in this study indicate that silenced            ƒƒ 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
ƒƒ 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
ƒƒ Strains of the fungus, Fusarium, occur naturally within           ƒƒ 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.                                    ƒƒ Selected lines are currently undergoing field
ƒƒ 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).
ƒƒ The hypothesis tested in this research was that                   ƒƒ 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.
ƒƒ 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
ƒƒ Breeding for sugarcane disease resistance is difficult,           ƒƒ 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
ƒƒ 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                 ƒƒ 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
ƒƒ 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.

                                                                20
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