TIP-MAG VOL2 NO1 - Forestry South Africa
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TIP-MAG
2021
Vol.2 No.1
Timber Industry Presents Magazine
A new
Genetic perspective
breakthrough? on pesticides
A new DNA marker resource for The revised FSC® Pesticide Policy
genome-assisted breeding of pine trees. means new rules for foresters to follow,
but will it change the way they think?
The enemy of my enemy is my friend!
Using natural enemies of insect pests for their management is an old and
generally well-known approach. But is this approach still valuable within the
current and future plantation forestry landscape?
THIS ISSUE: CAN WILD POPULATIONS HELP OUR EUCALPYTS ADAPT TO CLIMATE CHANGE? | ADDRESSING COMMON
CHALLENGES ON SOUTH AFRICAN SOIL: AN INTERNATIONAL COLLABORATIVE EFFORT | PERFORMANCE-BASED STANDARDS:
REVOLUTIONISING THE WAY LUMBER IS TRANSPORTED BY ROAD | GENOMIC SELECTION, A REVOLUTION IN TREE BREEDING
1 • TIP-MAG • VOL 2 NO 1
TABLE OF CONTENTS
3 Carrying on in the face of adversity
TIP-MAG
2021
Message by Dr Ronald Heath
Vol.2 No.1
Timber Industry Presents Magazine
OPINION PIECES
4 The enemy of my enemy is my friend
Using natural enemies of insect pests for their management is an old and
generally well-known approach. But is this approach still valuable within
the current and future plantation forestry landscape?
7 Addressing common challenges on South African
A new soil: an international collaborative effort
Genetic perspective International collaboration provides an opportunity to address common
breakthrough? on pesticides problems using an array of divergent mindsets, differing experiences,
A new DNA marker resource for The revised FSC® Pesticide Policy
genome-assisted breeding of pine trees. means new rules for foresters to follow, backgrounds and approaches.
but will it change the way they think?
The enemy of my enemy is my friend!
Using natural enemies of insect pests for their management is an old and
generally well-known approach. But is this approach still valuable within the
9 A New Perspective on Pesticides
current and future plantation forestry landscape? The revised FSC® Pesticide Policy means new rules for foresters to follow,
THIS ISSUE: CAN WILD POPULATIONS HELP OUR EUCALPYTS ADAPT TO CLIMATE CHANGE? | ADDRESSING COMMON but will it change the way we think?
CHALLENGES ON SOUTH AFRICAN SOIL: AN INTERNATIONAL COLLABORATIVE EFFORT | PERFORMANCE-BASED STANDARDS:
REVOLUTIONISING THE WAY LUMBER IS TRANSPORTED BY ROAD | GENOMIC SELECTION, A REVOLUTION IN TREE BREEDING
INTEREST PIECES
“
11 Can wild populations help our eucalypts adapt
to climate change?
While the pandemic has An assessment of wild Eucalyptus grandis populations in search of adaptive
brought a multitude of genetic variation
additional challenges, the Sector 14 Genomic selection, a revolution in tree breeding
still needed to continue to adapt, A comparison of traditional and genomic breeding strategies in Eucalyptus
grandis
evolve and grow in response
to the existing abiotic challenges
that clearly did not TECHNICAL NOTES
get the memo about going 17 Breakthrough for pine tree genetics
”
into isolation. A new DNA marker resource for genome-assisted breeding of pine trees
22 Revolutionising the way lumber is
transported by Road
Performance-Based Standard: Moving from pilot project to practical solution
2 • TIP-MAG • VOL 2 NO 1
CARRYING ON IN THE FACE OF ADVERSITY
THE FORESTRY SECTOR ONCE AGAIN SHOWCASING ITS DETERMINATION, ADAPTABILITY AND RESILIENCE
“ ...across the globe, Forestry is a challenging sector
to be in. On a daily basis we need to deal with
economic, social, biotic and abiotic challenges.
I BEGAN the introduction to the last
issue of TIP-Mag, stating how, “across
the globe, Forestry is a challenging sector
management, utilising new
technology and embracing the
”
implementation of innovation. As I
and students involved in forest research
to publish work that might not fit the
criteria for peer-reviewed scientific
to be in. On a daily basis we need to previously mentioned, “none of this journals but is still of exceptional
deal with economic, social, biotic and would be possible without the Sector’s quality and valuable to the Industry”.
abiotic challenges.” At the time of strong knowledgebase, generated by Reading through the pre-published
writing this, I could not have world class research and supported by version of this issue, after receiving so
imagined the challenges 2020 and the financial investment into Research and much positive feedback from the first,
COVID-19 pandemic had in store for Development.” This investment is still I feel TIP-Mag not only has provided
the Industry, the Sector, South Africa, more than double the country average this platform it has also made
and the World. despite the increasingly challenging innovative and complex science
Yet, while the pandemic has economic situation the Sector available to a far wider audience. This
brought a multitude of additional currently faces. is something that everyone involved
COVID-19-related health, financial, The Industry’s strong research-base in both publications should be
logistical, and social challenges, the will be critical in moving the Sector immensely proud of.
Sector still needed to continue to forward as it negates the challenges After reading through this issue, I
adapt, evolve and grow in response to currently faced and, if the Sector’s role am excited about the next two that
the existing abiotic challenges that in the globally identified green are scheduled for publication in 2021
clearly did not get the memo about economic response to the COVID-19 and urge everyone who is conducting
going into isolation. crisis is realised, it will also play a role research in the Sector to consider
If anything, 2020 has placed even in South Africa’s economic recovery. contributing. For those not actively
more emphasis on the Sector’s ability As FSA Director of Research and involved in forestry research, I urge
to adapt, its need to be both proactive Protection, 2020 has made me even you to find a few minutes to thumb
and progressive and applying a more proud of the world class through this second issue of TIP-Mag
holistic approach to forest research being conducted by the and to get acquainted with some of
Sector, both in house and by our the incredible work that will no doubt
research partners, especially when we shape our Sector in the future.
consider the 2020 restrictions that May you enjoy reading and
have had to be put in place. interrogating this second issue of
As mentioned in the opening TIP-Mag.
statement, the dissemination of the
research being produced by the Sector
is still one area that needs to be
worked upon. This is critical in
enabling its implantation and increase
our return on investment. Back then,
I suggested that this is where the
TIP-Mag may constructively Dr Ronald Heath
contribute to the Sector as a whole, FSA Director:
“providing a platform for researchers Research and Protection
3 • TIP-MAG • VOL 2 NO 1
OPINION INTEREST TECHNICAL NOTE
THE ENEMY OF MY ENEMY
IS MY FRIEND
Professor Brett Hurley – FABI, University of Pretoria – Associate Professor
“ Using natural enemies of insect pests for
their management is an old and generally
well-known approach. But is this
approach still valuable within the current
An ichneumonid wasp parasitises a larva of
Sirex noctilio, a global pest of pine trees
”
The opinion shared in this article are the views of
and future plantation forestry landscape? the author and not necessarily those
of the University of Pretoria
THE PROVERB ‘the enemy of my This approach is nearly as old as the
enemy is my friend’ is known from as proverb itself, being first reported
early as the 4th century BC, where it is around the 3rd century AD.
mentioned in the ancient Indian But is this approach still valuable as
Sanskrit treatise, the Arthaśāstra. The a pest management approach?
doctrine underpinning this proverb Especially within today’s plantation
has subsequently been referred to and forestry environment, where new pests
followed in numerous major historic are being reported at an exponential
events, perhaps most notably the rate and budgets to manage these pest
cooperation between the Allies (US incursions are tight.
and Britain) and the Soviet Union
against the common Nazi enemy in
World War II. THE VALUE: CURRENT
This proverb is also useful in
explaining the pest management
AND POTENTIAL
approach known as biological control. Interestingly, biological control is
Simply put, this involves the use of a particularly suited for use in
pest’s natural enemies to reduce the plantation forests, due to the longer
population of that pest in the rotations in forestry, as compared to
environment where it is not wanted. most agricultural crops, which offers Prof Brett Hurley
4 • TIP-MAG • VOL 2 NO 1
OPINION INTEREST TECHNICAL NOTE
“
associated with the nematode
The action of these unsung, and largely production and in-field releases. That
said, evaluations of the South African
unknown, heroes likely saves the forestry
”
Sirex Control Programme showed
that the reduction in losses associated
sector millions every year. with the use of biological control
exceeded the costs by approximately
R350 million over ten years.
more stability in the environment for Limited releases of hundreds of these
Besides the economic value of
the natural enemies to establish. Thus, parasitic wasps have resulted in their
biological control, this approach also
establishment rates and successes of establishment (of likely millions or
offers an alternative to the use of
natural enemies are higher on pests of trillions) across eucalypt growing areas
insecticides when the use of the latter
woody plants than on pests of of the country – at very little initial
is not feasible due to environmental,
herbaceous plants. cost.
regulatory or cost considerations. In
Most of the biological control Perhaps the best-known biological
some cases, biological control is the
used in South African plantation control programme in South African
only effective management option
forests has been classical biological plantation forests is that of the Sirex
available.
control (CBC) which involves the woodwasp. Here, a form of
What is generally not considered
intentional introduction of biological augmentative biological control has
is the massive value provided by
control agents, usually non-native, been used, involving the mass
natural biological control. This refers
with no further intervention. This production and annual inoculations
to the effect of indigenous biological
approach is generally used as a tactic of thousands of Sirex-infested trees
control agents already present in the
against non-native pests. A recent with a parasitic nematode (Deladenus
environment. For example, naturally
example is the release of a parasitic siricidicola). Contrary to a CBC
occurring small tetraviruses that are
wasp (Selitrichodes neseri) of the programme, this augmentative
thought to regulate populations of the
Eucalypt gall wasp (Leptocybe invasa). approach involves continual expenses
pine emperor moth, causing muscular
flaccidity and internal liquefication of
the larvae. The action of these
unsung, and largely unknown, heroes
likely saves the forestry sector millions
every year.
But perhaps of greater relevance is
the potential to improve the role of
these agents in regulating the pest
populations. A conservation biological
control approach involves modifying
the environment or existing practices
to protect and enhance the
populations of existing natural
enemies. This could be by providing a
food source or shelter for the natural
enemies. Such approaches are used
very successfully for forestry pests in
countries such as Colombia but
remain largely unexplored in South
Africa.
THE CHALLENGE… AND
PROPOSED SOLUTIONS
Of course, if biological control was
the ‘silver bullet’ for pest
management, we would have no pest
problems – and that is certainly not
the case.
One of the benefits of biological
Inoculations of a parasitic nematode to control populations of the Sirex woodwasp control is also one of its challenges
5 • TIP-MAG • VOL 2 NO 1
OPINION INTEREST TECHNICAL NOTE
– biological control agents, at least in
a CBC approach, are host-specific.
That’s great news in terms of not
having non-target effects, an attribute
that often makes biocontrol preferable
over insecticides. But it means that a
biological control programme needs
to be developed for each insect pest.
This can be a costly and lengthy
process; and, of course, not
guaranteed to result in successful
control of the pest.
A commonly acknowledged
strategy within the biological control
field to reduce this challenge is
collaboration. The growing movement
and establishment of many of the
major insect pests is in a sense a saving
grace, as it means there are many
institutes and countries around the
world with the same problem. Sharing
of information and even the biological
control agents themselves is
commonplace between research
programmes working on insect pests of
plantation trees, thanks to initiatives
such as BiCEP (Biological Control of
Eucalypt Pests, bicep.net.au).
Changes in climate, new pest Release of minute parasitic wasps imported from Australia for the control of an invasive
introductions and further eucalypt pest
introductions of new diversity of
current pests complicate biological
control approaches. Broader associated with pest management
collections of biological control agents options. Here, internationally relevant
LOOKING AHEAD
need to be considered and tested, to guidelines can be helpful, such as the
better match the agent with the pest recent publication of “Guide to the Despite its long history, I believe the
population and climate. Collaborative classical biological control of insect potential of biological control as a pest
networks can help to offset these pests in planted and natural forests” management strategy remains largely
challenges. by the Food and Agricultural untapped. There have been many
As with insecticides, the use of Organization (FAO) of the United success stories of biological control to
biological control needs to be Nations (http://www.fao.org/ manage forest insect pests, in South
regulated. Introduction of non-native documents/card/en/c/CA3677EN/). Africa and abroad. But for this approach
species need to be tested for potential But perhaps the biggest to remain a viable tool in a rapidly
non-target effects on native or challenge with biological control is changing environment, we will need to
beneficial species, and new biological this – sometimes it just doesn’t adapt. Increased collaborations,
control products, such as work. The reality is that although including with relevant government
entomopathogens, need to be biological control is often a key tool departments; improved monitoring and
registered. This can be a timely and for the management of forestry optimizing of biological programmes to
very costly process. pests, this is not always the case. address potential drops in efficacy from
In my experience, engaging with And even for insects where new pest strains or a changing climate;
the government and other relevant biological control has been used and better use of natural enemies that
bodies to provide input for the successfully, the addition of other are already present.
development of responsible and approaches could be very valuable. We will certainly face an
efficient regulatory and Thus, an integrated approach, increasing number of pest ‘enemies’ in
implementation policy is critical. Not considering other viable control the future. Some of these could
many governments have the capacity options such as host resistance, threaten the sustainability of the
to develop policy in response to the silvicultural control and chemical forestry sector. It will be important
growing and changing needs control is a must. not to forget our friends.
6 • TIP-MAG • VOL 2 NO 1
OPINION INTEREST TECHNICAL NOTE
ADDRESSING COMMON CHALLENGES ON
SOUTH AFRICAN SOIL: AN INTERNATIONAL
COLLABORATION EFFORT
Noxolo Ndlovu – Nelson Mandela University – PhD student
“ and though a man might prevail against one who is alone, two
will withstand him – a threefold cord is not quickly broken
”
– Ecclesiastes 4v12
Although this verse was addressed to man, the principle holds for the global forestry sector –
together, we are stronger!
GLOBALLY, forest plantations face studies conducted in climates and/or short-term risk to aquatic and terrestrial
common challenges: from uncertainties use patterns which are not relevant to environments. This led to the
associated with climate change; to the forest plantation conditions. As a reinstatement of these two herbicides in
growing negative impacts of pests and result, pesticides that might pose little New Zealand, almost eight years after
diseases; and pesticide use restrictions or no risk when used within the the restriction (Rolando et al. 2015).
posed by certification bodies. The list is plantation landscape, in adherence to This was a great relief to the industry
extensive. legislation and best practice, have especially since alternative methods
International collaboration been banned. proved less economically viable and
provides an opportunity to address Following the restriction or using herbicides under derogation
common problems using a diverse prohibition of hexazinone and meant applying herbicides as a spot-
array of divergent mindsets, differing terbuthylazine, two of the most spay (instead of the normal practice of
experiences, backgrounds, and important herbicides for use within broadcast). Spot spray applications
approaches. This inevitably results in New Zealand (NZ) forest plantations, posed challenges in that they were
richer ideas and fast tracks progress New Zealand forestry stakeholders took limited by labour availability and
towards finding solutions, especially if the initiative to implement a series of suitability of the area (Rolando et al.
resources beyond intellect are pooled. trials. These trials not only aimed to 2011b).
find alternative ‘environmentally
acceptable’ vegetation management
NEW ZEALAND: LEADING SOUTH AFRICA: FOLLOWING IN
methods (Rolando, Gous & Watt
THE WAY WHEN IT COMES TO 2011a) but also aimed to determine the NEW ZEALAND’S FOOTSTEPS AND
ENVIRONMENTAL PESTICIDE FATE actual environmental fate and risk posed TAKING THE RESEARCH FORWARD
In the past two decades, increased by these two herbicides when used The South African forestry industry is
emphasis has been placed upon under NZ environmental conditions already limited in terms of the
reducing reliance on pesticides. For and industry-use patterns (Baillie,
certified plantations and those seeking Neary, Gous & Rolando 2015; Baillie
certification, this has meant 2016; Garrett, Watt, Rolando & Pearce
sometimes discontinuing the use of 2015; Garrett, Watt & Pearce 2016).
pesticides that provide the only viable When compared to vegetation
(cost-effective and efficient) option for management with terbuthylazine and
the management of an economically hexazinone, alternative methods were
important pest or disease, because of associated with growth losses of up to
their hazard classification by 30% (Rolando, Todoroki & Watt 2015)
certification bodies. Needless to say, and reduced internal rate of return
these prohibitions pose challenges to ranging from 0.5 to 1.7% (Rolando,
forest managers and the sustainability Watt & Zabkiewicz 2011b). In
of the global forestry sector. addition, and perhaps more
The hazard classification criteria of importantly, environmental fate trial
pesticides, used by certification results showed that, under NZ forestry
bodies, is often founded on use patterns and conditions, hexazinone
laboratory-based studies and/or field and terbuthylazine pose a low and Noxolo Ndlovu
7 • TIP-MAG • VOL 2 NO 1
OPINION INTEREST TECHNICAL NOTE
providing funding for this crucial
work.
In 2019, PhD student Noxolo
Ndlovu visited New Zealand to
interact with numerous pesticide
environmental fate experts, including
Dr Brenda Ballie and Dr Carol
Rolando. Noxolo drew knowledge
from guided experience in trial
implementation, data collection
procedures, tools required, mistakes to
avoid and tips for project success from
an established team of experts who
had designed, developed,
implemented and improved many of
the methodologies that would be
employed during the South African
study. Trials in South Africa began in
January 2020, with data collection
still ongoing. The first output of the
project will be submitted for
publication in December 2020. The
project is due for completion in
December 2021. Despite challenges
relating to COVID-19 restrictions,
the study looks set to yield several
Conducting stream flow measurements
interesting results that have the
number of pesticides registered for use potential to alter the way pesticide use
within the forestry landscape. This has is governed in South African certified
been further reduced in certified plantations.
plantations as a result of the International collaboration,
restrictions and prohibition put in between scientists, working ultimately
place by certification bodies to protect towards the same goals just in different
human health and reduce continents, has been key to the success
environmental impact. Yet, with no of this project. The guidance, support,
pesticide environmental fate studies patience, and expertise of supervisors
related to South African silvicultural working in separate times zones and
regimes and environmental yet equally invested in the success of
conditions, it is difficult to know the the project is illustrative of the
impact of pesticides on aquatic and potential international collaborations
terrestrial environments. can produce. The question now is,
Consequently, without this Water and sediment sampling where to next?
information, it is impossible for
national legislation and certification REFERENCES
bodies to make informed decisions Baillie B. 2016. Herbicide concentrations in waterways following aerial application in a steepland planted forest in New
regarding the actual impact certain Zealand. New Zealand Journal of Forestry Science 46:16.
pesticides will have in South African Baillie BR, Neary DG, Gous S, Rolando CA. 2015. Aquatic fate of aerially applied hexazinone and terbuthylazine in a New
forestry conditions. Zealand planted forest. Journal of Sustainable Watershed Science & Management 2: 118–129.
To address this gap, a partly Garrett LG, Watt MS, Pearce SH. 2016. Environmental fate of terbuthylazine and hexazinone in a planted forest steepland
Forestry South Africa (FSA) funded Recent Soil, New Zealand. New Zealand Journal of Forestry Science 46:17.
study investigating the fate of key, Garrett LG, Watt MS, Rolando CA, Pearce SH. 2015. Environmental fate of terbuthylazine and hexazinone in a New Zealand
operationally used pesticides was planted forest Pumice soil. Forest Ecology and Management 337: 67–76.
initiated as a collaboration between Rolando C, Todoroki C, Watt M. 2015. Minimising the environmental impact of forest weed management in New Zealand:
Nelson Mandela University (South final report on field trials. Scion Publication No. S0015. Rotorua: New Zealand Forest Research Institute Limited.
Africa) and New Zealand forestry Rolando CA, Gous SF, Watt MS. 2011a. Preliminary screening of herbicide mixes for the control of five major weed
pesticide fate experts. With NCT species on certified Pinus radiata plantations in New Zealand. New Zealand Journal of Forestry Science 41: 165–175.
Forestry, Nelson Mandela Rolando CA, Watt MS, Zabkiewicz JA. 2011b. The potential cost of environmental certification to vegetation management
University and FP&M SETA also in plantation forests: a New Zealand case study. Canadian Journal Forest Research 41: 986–993.
8 • TIP-MAG • VOL 2 NO 1
OPINION INTEREST TECHNICAL NOTE
A NEW PERSPECTIVE ON PESTICIDES
Manushka Moodley – FSC Global Development GmbH – Southern African Manager
“ A revised FSC Pesticides Policy means new
rules for foresters to follow. But more
importantly, it should change the way we
Pesticides are a feature of many parts
of our lives, and as time goes by, we
are learning more about less obvious,
chronic, cumulative and interacting
effects of their use. Sadly, global
average pesticide use per area of
think.
”
integrated pest management and
silviculture which avoids, or aims at
eliminating, the use of chemical
pesticides. They forbid the use of any
chemical pesticides prohibited by FSC
policy, and when pesticides are used,
were subject to the same controls. The
revised policy recognises three
different categories of Highly
Hazardous Pesticides i.e.: restricted,
highly restricted, and prohibited.
Prohibited HHPs are the worst of
cropland is much higher now than it they require forest managers to the worst – chemical pesticides so
was in the 1990s. Agriculture may be prevent, mitigate, and/or repair dangerous that the risks associated
the major player in pesticide usage, damage to environmental values and with them cannot be realistically
but how can we in the forestry sector human health. There is a clear role for managed. Using international
contribute to turning the tide? How the FSC pesticides policy here, but conventions regulating global
can we ensure that our forests remain what else does it bring to the mix? pesticide use, they have been
full of life, and that they support An important emphasis of the identified on the basis of their
livelihoods without invisible threats to policy was, and remains, on the inherent properties: if they are acutely
the health of forest workers? control of the use of Highly toxic and can induce cancer, if they
Surely very few forest managers Hazardous Pesticides (HHPs). It is contain dioxins, or if they contain
use pesticides uncritically – even if worth noting that this is not a heavy metals. FSC permits their use
our motivations were purely financial, concept unique to FSC – both the only in emergency situations or if
pesticides might be cheaper than Food and Agriculture Organization mandated by a government order.
some other control options, but they (FAO) of the United Nations and the Restricted and highly restricted
still cost money. Maybe there are a World Health Organization (WHO) HHPs can be used in FSC-certified
few people out there who apply refer to HHPs – but, through the forests if the requirements of the
pesticides just because that’s what pesticides policy, FSC aims to ensure Policy are met. Restricted HHPs fall
they’ve always done, but on the most that the concept is applied into one of the hazard groups acute
part, those applying chemical control consistently and robustly in FSC- toxicity, chronic toxicity, or
agents are going through some sort of certified forests across the world. The environmental toxicity – highly
thought process beforehand, even if aims of the policy go further, the restricted HHPs fall into two or three
only to decide whether it is worth stated short-term objectives are to: of these groups.
incurring the cost. With responsible • Promote best practices to minimise
forest managers already thinking far associated risks to human health
more broadly about environmental and the environment when using
and social costs. The challenge is how chemical pesticides.
we take that thinking to the next
• Reduce the overall volume and
level, and make sure that all foresters
number of chemical pesticides in
are thinking along the same lines?
use.
The revised FSC pesticides policy
is intended to facilitate this, by • Eliminate the use of the most
changing the way we think about hazardous chemical pesticides.
pesticides.
NOT ALL PESTICIDES ARE EQUAL…
PRINCIPLES AND POLICIES –
In the previous iteration of FSC’s
WHAT ARE THEY FOR? policy and procedures, a HHP was a
The FSC Principles and Criteria HHP was a HHP – there was no
already require forest managers to use distinction between them, and all Manushka Moodley
9 • TIP-MAG • VOL 2 NO 1
OPINION INTEREST TECHNICAL NOTE
This categorisation recognises that Broad rules are set by FSC HHPs over highly restricted HHPs.
there is considerable variation among International, including what factors Before foresters apply any chemical
Highly Hazardous Pesticides, and should be considered, and how. The pesticide, they must incorporate the
allows us to take a more nuanced South African Standard Development results of the ESRA into operational
approach to manage the risks they Group, with support from TIPWG, plans, identifying site-specific risks
present – this should steer us towards will adapt the finalised international and adapting generic mitigation and
the least hazardous options, and to generic indicators for HHPs and assist monitoring measures accordingly.
the most effective management of with the development and roll-out of Risk assessments might sound
risk. the ESRAs. bland, but this is powerful stuff,
The Policy requires the bringing new and consistent thinking
identification and assessment of key to integrated pest management. Every
NO MORE DEROGATIONS? THANK
environmental and social risks one of us will have to think in terms
GOODNESS! associated with each restricted or of hazard levels, and in terms of a
The revised policy does away with the highly restricted HHP used or likely broad range of environmental and
previous system of derogations, to be used in the country. Thankfully, social risks. We’ll even have to discuss
whereby anyone who wanted to use a the bulk of this work has already been those issues at a national level, making
Highly Hazardous Pesticide had to completed by TIPWG for South informed decisions about what
apply to FSC International for Africa. Once the approved Highly Hazardous Pesticides we think
temporary permission to deviate from international generic indicators are it is acceptable to use in our country.
FSC’s rules – a derogation. It is fair to released by FSC, standard developers The revised policy might not bring
say that this system was pretty will undergo an assessment of each about wholesale change overnight,
unpopular. There was a charge for the HHP utilised in South Africa and will but it will at least ensure that we are
processing of derogation applications, engage with stakeholders in this all thinking the right thoughts and
and decisions were made by a central process, which represents the key shift moving in the right direction.
committee which realistically could from international to national
not be aware of all the subtleties of deliberation. BUT WILL IT REALLY CHANGE THE
every national situation. New policy Individual certificate holders will WAY WE THINK IN SOUTH AFRICA?
requirements remove the need for eventually have to comply with these
In short, yes, I hope so. We are already
charges and shift a lot of decision national indicators and thresholds,
seeing change within the sector with
making to the national level. alongside the policy ESRA
greater levels of risk-based thinking
requirements. TIPWG has developed
being integrated into Certificate
A CONSISTENT APPROACH TO RISK environmental and social risk
holder’s integrated pest management
To replace the centralised derogation assessments for South Africa to
strategies and operational activities.
system, the revised policy introduced identify the lowest risk option to
This accompanied with the research
a framework of environmental and control a given pest, weed or disease,
into alternatives for restricted
social risk assessment (ESRA), with giving preference to non-chemical
chemicals and other HHPs will
elements operating at international, methods over chemical pesticides,
hopefully yield long term positive
national and management unit levels. non-HHPs over HHPs, and restricted
results for the foresters, workers and
the environment.
WE ALL NEED TO SEE PESTICIDES
FROM A NEW PERSPECTIVE
If 2020 has taught us anything, it is
that nothing can be taken for granted.
A pandemic is just one symptom of
the profound influence we have on
the natural environment. Pesticides
have revolutionised the way we
interact with that environment, and
while we have gained from their use,
we also now face problems entirely of
our own making, including threats to
our own health. It is likely that some
of the damage we have caused cannot
now be undone. Are you ready to
change your perspective on pesticides
before things get worse?
10 • TIP-MAG • VOL 2 NO 1OPINION INTEREST TECHNICAL NOTE
CAN WILD POPULATIONS HELP
OUR EUCALYPTS ADAPT TO
CLIMATE CHANGE?
AN ASSESSMENT OF WILD EUCALYPTUS GRANDIS POPULATIONS IN SEARCH OF ADAPTIVE GENETIC VARIATION
Marja Mostert-O’Neill and Professor Zander Myburg – Forest Molecular Genetics (FMG) Programme, Forestry and Agricultural
Biotechnology Institute (FABI), University of Pretoria
Any opinions shared in this article are the views of the authors and not necessarily those of the University of Pretoria
FOR A CENTURY since the first navigate the expected change in
import of Eucalyptus grandis seed in abiotic and biotic threats, readily
1896 (then still incorrectly identified available genetic diversity is required.
as E. saligna), the species and its The natural species range of
hybrids have been the darlings of E. grandis, along the east coast of
eucalypt forestry in South Africa. Australia, spans several climate zones
Throughout its cultivation history, from subtropical provenances in the
foresters and breeders had to navigate north to temperate areas in the south
several challenges and, in some cases, (Fig. 1). Only a fraction of this
resorted to hybrid breeding to genetic diversity has been imported
overcome them. For instance, in and advanced in South African
response to stem canker disease, the breeding programmes. Despite its
species was hybridized with disease- commercial importance, not only in
tolerant E. urophylla, and in order to South Africa but also globally in
cultivate E. grandis in cooler regions, subtropical and temperate regions,
E. grandis x E. nitens hybrids were little is known about the untapped,
“
Marja Mostert-O’Neill
These “hybrid provenances” may
represent valuable variation for future provenances spanning the species
distribution (Fig. 1). The seedlings
genetic infusion into South African
”
were later established by Mondi Ltd
in a Gene Conservation Park in the
breeding programmes. KwaZulu-Natal Midlands (Fig.3).
We combined population
genomics (genetic profiling of
developed. An even greater challenge potentially adaptive, genetic diversity hundreds of individuals using
faces us today in the form of rapid harboured in the natural species approximately 20 000 molecular
climate change. Weather conditions range. To this end, we set out to markers that cover the entire length of
are forecast to become more extreme profile wild E. grandis populations in the 11 chromosomes of E. grandis)
and the already erratic distribution of terms of genomic diversity and with environment association analysis
pests and diseases will become harder adaptation to geographic, climatic, to uncover genes that may underlie
to predict. As such, varieties – be it and soil-related variables in a study adaptive differences between
improved families or hybrid clones – published in Molecular Ecology provenances. As would be expected,
that have been favoured in the past (Mostert-O’Neill et al., 2020). We the genes identified were enriched for
may no longer perform as anticipated imported and germinated 193 abiotic and biotic stress response
under future climate conditions. To individual tree seed families from 33 functions. We also identified
11 • TIP-MAG • VOL 2 NO 1OPINION INTEREST TECHNICAL NOTE
Sample locations
Northern
subpopulation
Windsor Tablelands 1
Mackay
subpopulation
Windsor Tablelands 2
Brooweena
Tinaroo Creek provenance
Copperlode
Southern
Wild River subpopulation
Mt. Spec, Paluma
Paluma Species
Eungella distribution
Finch Hatton Gorge
Driest period
average precipitation
(mm; Bio14)
Woondum Brooweena 3
Yabba Kin Kin 4
6
Mapleton 8
Conondale
Beerwah 10
Mt. Mee 11
Mt. Tamborine
Mt. Lindsay
Cherry Tree
Bagawa
Newfoundland
Orara West (71)
Wedding Bells
Tuckers Nob Lower Bucca
Orara West (72)
Gladstone
Köppen climate classification
Subtropical - no dry season Newry
Orara East
Subtropical - moderately dry winter
Temperate - no dry season Bulahdelah Pine Creek
(warm summer)
Temperate - no dry season
(hot summer)
Fig.1. Sampling locations of wild E. grandis populations along the east coast of Australia. Three provenances (green circles), Eungella and Finch
Hatton Gorge in the Mackay subpopulation, and Brooweena at the northern edge of the Southern subpopulation, had extensive introgression
from one or more unknown, non-E. grandis sources. Circle circumferences indicate average precipitation during the driest period. Map shading
indicates Köppen climate classification with the four main climate zones sampled given in the colour legend.
provenances that carry genetic genome originated from E. grandis This study revealed that wild
footprints of natural introgression from and which originated from the hybrid E. grandis populations contain
other (non-E. grandis) species, thought partner/s in natural populations adaptive genetic variation that may
to be in response to increased aridity (Fig.2). This method can also be used assist us in navigating future climate
(Fig. 1). These “hybrid provenances” in hybrid breeding programmes to conditions in South Africa. It also
may represent valuable variation for trace the inheritance of genomic showed that hybridization remains an
future genetic infusion into South segments, harbouring genes with important means of introducing
African breeding programmes. adaptive or economically important adaptive genetic variation, which may
To investigate adaptive functions, originating from allow a species to prevail beyond its
hybridization further, we modified a hybridizing partner species such as predicted niche. Lastly, advances in
method to map the genetic ancestry E. urophylla. Furthermore, it allows us eucalypt genomics and genetically
(species origin) of blocks of DNA to identify cryptic or unintended profiled reference populations enable
throughout the genome. This method, hybrids within pure species us to trace the genetic origin of
called ancestry mapping, allowed us populations, even if the identity of individual genome segments. In
to trace which segments of the the introgressing species is unknown. collaboration with Sappi Forests and
12 • TIP-MAG • VOL 2 NO 1OPINION INTEREST TECHNICAL NOTE
Chromosome
Mondi Ltd, 190 families used in this
1 2 3 4 5 6 7 8 9 10 11
study are being established in two
2
large common garden trials in
E. grandis
0
Zululand and the KwaZulu-Natal
-2
2
Midlands, with ~3400 individuals
each. In addition, other genotype-by-
GU
0
-2 environment (GxE) interaction trials
2 are being established in various
GUxU
0
locations around the world by
-2
Camcore using 108 of these seed
2
E. urophylla
0
families. These trials will be used for
-2 landscape genomics studies whereby
2 genetic profiles, phenotypes and
environmental variables are combined
GN
0
-2
to model genotype-by-site
2
compatibility.
E. nitens
0
-2
2 ACKNOWLEDGEMENTS:
GUxGN
0 This study was made possible through financial support
-2 from the National Research Foundation (NRF) of South
Africa - Bioinformatics and Functional Genomics
Fig.2. Ancestry maps of DNA segments for pure species and hybrid Eucalyptus individuals of Programme (BFG Grant UID 97911), the Technology and
known ancestry. Ancestry assignments along the 11 chromosomes are given for seven Human Resources for Industry Programme (THRIP Grant
individuals; pure E. grandis, E. grandis x E. urophylla F1 hybrid (GU), E. grandis x E. urophylla UID 96413), the Department of Science and Innovation and
backcrossed to E. urophylla hybrid (GUxU), pure E. urophylla, E. grandis x E. nitens F1 hybrid Technology Innovation Agency (DSI/TIA, Strategic Grant for
(GN), pure E. nitens, and a three way hybrid (GUxGN). Each colour dot represents a single DNA the Eucalyptus Genomics Platform), the Forestry Sector
marker (7736 markers across 11 chromosomes). Grey shade indicates that both alleles Innovation Fund (FSIF Eucalyptus Genome Diversity Atlas
originate from E. grandis (value of 0); while blue (value of 2) and purple (value of -2) shades grant) and by the Forest Molecular Genetics (FMG) Industry
indicate that both alleles have non-E. grandis Latoangulatae and Maidenaria ancestry, Consortium at the University of Pretoria. We would also like
respectively. Intermediate values indicate mixed ancestry (one allele originates from to thank Sappi Forests and Mondi Forests South Africa for
E. grandis and the other allele originates from another species). A value of -2.5 indicates that support towards seed acquisition and establishment of the
one allele assigned to non-E. grandis Latoangulatae and the other allele to Maidenaria Gene Conservation Park, respectively. Lastly, we would like
ancestry. The non-E. grandis Latoangulatae ancestral reference population used in this analysis to acknowledge Camcore (North Carolina State University)
included E. urophylla and E. saligna individuals. The Maidenaria ancestral reference population and the Department of Agriculture and Fisheries
included E. dunnii, E. nitens and E. viminalis. (Queensland, Australia) for assistance with seed imports.
Fig.3. Mondi Ltd personnel establishing wild
E. grandis germplasm in a Gene Conservation Park
in the KwaZulu-Natal Midlands
13 • TIP-MAG • VOL 2 NO 1 (photo credit: Mr Mmoledi Mphahlele)OPINION INTEREST TECHNICAL NOTE
GENOMIC SELECTION,
A REVOLUTION IN TREE BREEDING
A COMPARISON OF TRADITIONAL AND GENOMIC BREEDING STRATEGIES IN EUCALYPTUS GRANDIS
Mmoledi Mphahlele – Mondi South Africa – Research and Development Department
Professor Zander Myburg – Forestry and Agriculture Biotechnology Institute (FABI) – Director of Forest Molecular Genetics (FMG)
Programme
Any opinions shared in this article are the views of the authors and not necessarily those of the University of Pretoria
Mphahlele, M.M., Isik, F., Mostert-O’neill, M. M., Raynolds, S. M., Hodge, G. R., and Myburg, A. A. (2020). Expected
A lay-summary of
benefits of genomic selection for growth and wood quality traits in Eucalyptus grandis. Tree Genetics & Genome 16, 49.
research recently published.
https://doi.org/10.1007/s11295-020-01443-1
AS CLIMATE change and global
trade accelerate, associated biotic and
abiotic challenges are increasingly
affecting commercial forestry
plantation areas in South Africa. In
“ A complete reconfiguration of the
breeding steps of the traditional
breeding approach is
”
particular, the commercial
deployment of Eucalyptus grandis, warranted.
formerly a premier species for pulp
and paper production, has
dramatically declined due to pest and demand for sustainable wood genetic variation throughout all of the
pathogens. Similar threats are products, means faster and more agile chromosomes of the tree (the
imminent for many of South Africa’s breeding approaches are needed to genome). Genomic estimated
other commercial forestry species. mitigate risk factors while ensuring breeding values can be obtained for
This, together with the increasing gains to sustain the growth in the trees while they are still seedlings, i.e.
wood-derived bioenergy, biomaterials without having to wait many years to
(including pulp, paper and timber) determine the tree’s genetic merit
and biochemical (biorefinery) based on field trial measurements.
industries. Traditional tree breeding Genomic prediction of tree breeding
approaches face many challenges, values is based on statistical modelling
including long rotation cycles of genomic (DNA marker) and
associated with late reproductive phenotypic (trait) data of individuals
maturity, delayed expression of in a training population. Adopting
commercially important traits GS as an alternative or a
(rotation age volume, density, pulp complementary tree breeding strategy
yield and timber quality) and the cost for growth and wood quality traits
of land for long-term field trials. requires a practical demonstration of
There is a need to fast track tree its benefits compared to traditional
breeding to accelerate gains in growth, breeding approaches.
wood quality and tolerance to biotic E. grandis is one of the “Big Nine”
and abiotic stressors. eucalypt species (together with
Genomic selection (GS) is a E. urophylla, E. tereticornis,
breeding approach that predicts the E. camaldulensis, E. saligna, E. dunnii,
genetic merit of individuals, based on E. pellita, E. nitens, E. globulus, and
their genetic make-up as determined their hybrids) planted around the
Mmoledi Mphahlele using DNA markers that detect globe. The availability of a reference
14 • TIP-MAG • VOL 2 NO 1OPINION INTEREST TECHNICAL NOTE
genome sequence (Myburg et al. 0.47 (for diameter growth) to 0.67 18-year period including three GS
2014) and development of a (for wood fibre width), which are cycles and two traditional breeding
Eucalyptus single nucleotide achieved at the seedling age and cycles ranged from 1.53 (for diameter)
polymorphism (SNP) marker chip equivalent to what breeders would to 3.35 (for wood density). Together
(used to simultaneously genotype achieve at rotation age. these results suggest that GS breeding
hundreds of individuals using 10,000s Using potted orchards and flower approaches can significantly improve
of DNA markers) have created new induction using chemical treatments genetic gains per unit time in
opportunities for genetic analysis of (such as paclobutrazol), tree breeders E. grandis.
Eucalyptus breeding populations. can reasonably achieve a four-year GS Expanding the traditional and
In a study recently published in breeding cycle compared to the genomic breeding approaches to
Tree Genetics and Genomes (Mphahlele eight-year traditional breeding cycle include commercial deployment
et al., 2020), the authors interrogate for E. grandis, thereby greatly opportunities, we show that over an
the benefits of adopting a GS improving gains per unit time. The 18-year period the traditional
breeding approach for growth and relative efficiency which is the ratio of breeding approach should result in
wood quality traits (fibre length, fibre the four-year GS breeding cycle three clonal trials and clonal seed
width, cellulose, SG ratio, density, compared to the eight-year traditional orchards (CSO) as demonstrated in
diameter and height) in an E. grandis breeding cycle ranged from 1.20 Figure 1. Clonal seed orchards will
breeding programme. The training (20%, for wood density) to 1.62 allow the deployment of commercial
population consisted of 1,575 (62%, for fibre length). The efficiency seedlings, whereas the clonal trials will
individuals, phenotyped for growth increases with even shorter GS result in improved clonal varieties.
and wood quality traits, and breeding cycle times, pointing to the Over the same period, the GS
genotyped for 15,000 genome-wide importance of early flower induction approach should result in four clonal
SNP markers. This resulted in approaches. The benefit ratio in terms trials and CSOs, as demonstrated in
prediction accuracies ranging from of accumulated genetic gains over an Figure 2. In the GS approach, the
Figure 1 | Illustration of the traditional breeding cycle of E. grandis and associated commercial
Figure 1. Illustration of the traditional breeding cycle of E. grandis and associated commercial deployment opportunities over 18 years. The
cycle includes two eight-year full rotation open-pollinated progeny trials (red) with corresponding nursery activities to turn over the generations
deployment opportunities over 18 years. The cycle includes two eight-year full rotation open-
(green). Over 18 years, the tree breeder can establish three clonal seed orchards (CSO, yellow) for commercial seed deployment and three
pollinated
clonal progeny
trials to identify trials
improved clonal(red)
varietieswith corresponding nursery activities to turn over the generations
(yellow).
(green). Over 18 years, the tree breeder can establish three clonal seed orchards (CSO, yellow)
for commercial seed deployment and three clonal trials to identify improved clonal varieties
15 • TIP-MAG • VOL 2 NO 1
(yellow).OPINION INTEREST TECHNICAL NOTE
Figure 2. Plausible genomic selection breeding cycles for E. grandis over an 18 year period. The breeding approach starts with an open-
Figure
pollinated 2 |population
training Plausible (blue) genomic selection
to train the initial breeding
GS model (A). cyclesthree
The cycle includes forfour-year
E. grandis over the
periods involving anestablishment
18 year period.
of
potted orchards (red) for control pollination (CP) crosses. The nursery activities (green) to turn over the generation includes the genomic
Theofbreeding
selection approach
CP seedlings using GS model A. starts with
The four an open-pollinated
established clonal seed orchards willtraining population
provide commercial (blue) to
seed for deployment, train the
whereas
the four clonal trials (yellow) will serve to identify improved clonal varieties and to update the GS model (A+B) leading to further increases in
initial
accuracy GS model
and efficiency (A). The cycle includes three four-year periods involving the establishment
of selection.
of potted orchards (red) for control pollination (CP) crosses. The nursery activities (green) to
turn
clonal over
trials the begeneration
can also used to includes
such asthe genomic
maintaining selection
genetic diversityof CP
withseedlings using GS
critical information model A.
to achieve
validate the current GS model (A) and accelerating genetic gains, breeding goals and produce elite
andTheimprovefourthe established
model (A+B). clonal respectively.
seed orchards
Lookingwill provide
forward, GS commercial
clonal varietiesseed forsources
and seed deployment,
for
For tree breeders to realise the approaches will provide breeders commercial deployment.
whereas the four clonal trials (yellow) will serve to identify improved clonal varieties and to
benefits of implementing genomic
selection
update approaches
the GSofmodel
selection
(A+B) leading to further increases in accuracy and efficiency of selection.
accuracy, selection efficiency, as well
as improved genetic gains per unit
time in E. grandis. A complete
reconfiguration of the breeding steps
of the traditional breeding approach is
warranted.
It is important to note that this
reconfiguration of breeding strategies
is associated with additional
operational and genotyping (DNA
marker analysis) costs. Although
these investments will lead to
improved genetic gains, they may
increase the cost per unit genetic
gain in the short-term. Long-term, as
genotyping costs continue to decline,
the cost per unit genetic gain will
also decline. Traditional and genomic
breeding strategies can advance as
two separate but complementary
breeding activities with objectives
16 • TIP-MAG • VOL 2 NO 1INTEREST OPINION TECHNICAL NOTE
A NEW DNA MARKER RESOURCE
FOR GENOME-ASSISTED BREEDING
OF PINE TREES
Nanette Christie1, Colin Jackson2, Gary Hodge2, Juan Jose Acosta2, Alexander A. Myburg1
1
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural
Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
2
Department of Forestry & Environmental Resources, North Carolina State University, Raleigh,
NC, USA.
Any opinions shared in this article are the views of the authors and not necessarily those of the University of Pretoria
SUMMARY wide range of applications in tree breeding. These include
DNA fingerprinting for identification of individuals and
Pine tree breeders have for many years been searching for clonal varieties, and parentage analysis for pedigree
ways to speed up breeding cycles and make it cheaper and reconstruction, e.g. identifying the seed and pollen parents
more efficient to improve specific traits. Besides selecting of superior individuals. The SNP chip can also be used for
for desirable traits such as growth and wood quality, species and hybrid identification, genetic resource
breeders have to deal with the fact that plantations have management and genome-assisted breeding.
become more vulnerable to biotic and abiotic stresses
linked to rapid climate change. Another problem is that In the future, the SNP chip can aid in fast-tracking the
commercially important traits such as wood quality are pine breeding cycle. Large numbers of informative SNPs
only fully expressed at maturity and can typically only be can be incorporated into models for genomic prediction of
selected after 8-10 years in field trials. The significant time breeding values at seedling stage. The use of inter-species
and cost associated with traditional tree improvement hybrids to improve growth, wood properties, adaptability,
methods, and recent successful application of DNA-based or disease tolerance is imminent. An example in South
(genomic) technologies in animal and crop plant breeding, Africa is the P. patula x P. tecunumanii hybrid, which has
have stimulated the international tree breeding community shown excellent growth and significantly better tolerance
to explore the implementation of these genomic breeding to pitch canker disease (caused by Fusarium circinatum)
approaches. Using tens of thousands of DNA markers relative to the widely-planted pure species P. patula. The
spread out across all of the chromosomes of the plant, the SNP chip will be invaluable for species and hybrid
genetic merit or breeding value of trees can be predicted discrimination, and tracking of growth, wood property
when they are still seedlings. This can potentially shorten and disease resistance loci, thereby increasing the accuracy
the breeding/selection cycle by a decade for pine trees. of pine hybrid breeding. The SNP chip and future genome
However, until recently, there has been a lack of resources sequencing efforts may also enable the analysis and
to analyze large numbers of DNA markers for genomic prediction of genotype by environment (GxE) interactions,
breeding of pine trees, partly due to the enormous size of allowing us to potentially make climate-specific selections
pine tree genomes (over 20 billion base pairs – seven times and breed for future environments. The development of
larger than human genomes). suitable experimental populations for genomic mapping
and modelling is a high priority that will be the focus of
Single nucleotide polymorphisms (SNPs) are the most research in the next five to ten years.
common type of natural genetic variation which leads to
biological variation among individual trees. These
differences in DNA building blocks can ultimately
INTRODUCTION
influence a variety of traits including growth, wood Pine tree species are economically important primarily
properties and disease resistance. We used targeted genome because their wood is used for timber products, including
and gene sequencing to identify a set of 50,000 furniture, window frames, paneling, floors and roofing.
informative SNP markers for the development of a Tropical pine species play an important role in plantation
commercial DNA marker chip for tropical pine trees forestry in South Africa. Eight tropical and subtropical
(Pitro50K). Used as a genome-wide genotyping pine species were included in this study due to their
technology, the chip can uncover genetic differences for a commercial and ecological importance: P. oocarpa,
17 • TIP-MAG • VOL 2 NO 1INTEREST OPINION TECHNICAL NOTE
include sufficient unique markers for species and hybrid
identification and ancestry reconstruction. This array
provides at least 10,000 usable markers for each of the
commercially grown tropical pine species and their F1
hybrids, and large numbers of these markers should be
transferable to other closely related species in the Pinus
section Trifoliae, subsections Australes and Ponderosae
enabling wider genetic investigations.
MATERIALS AND METHODS
An automated bioinformatics pipeline for SNP discovery
was established using (i) RNA sequencing (RNA-seq) data
from five tropical pine tree species (Pinus patula, P.
tecunumanii, P. oocarpa, P. greggii and P. maximinoi) and
(ii) targeted capture sequencing (capture-seq) data across
85 provenances from the natural range in Mexico and
Central America representing six species (the five species
mentioned above plus P. caribaea) (Figure 1a). An
P. patula, P. tecunumanii, P. greggii, P. caribaea, P. elliottii, aggregate of 200 million paired-end RNA-seq reads were
P. maximinoi and P. pseudostrobus. These species can be aligned back to the five respective transcriptome (expressed
deployed in a variety of commercial settings and can gene) assemblies (Visser et al., 2018). A total of
readily hybridize and produce viable offspring (Gwaze 5.3 million RNA-based SNPs were detected and identified
1999; Hongwane et al. 2018). As a result, pine breeders 1.3 million that could be targeted for SNP genotyping. In
can develop hybrid breeding populations for specific niche parallel, 30 million paired-end capture-seq reads were
environments and for disease resistance. aligned back to the P. taeda (loblolly pine) reference
Traditional pine tree improvement is a slow, laborious genome assembly. Out of the 3.3 million capture-seq SNPs
and expensive process. Therefore, the tree breeding identified, 1.02 million were detected in at least two of the
community is exploring the possibility of implementing provenances and 415K SNPs were shared among two or
genome-assisted breeding technologies that can speed up more species. From these two sets, a total of 563K could
breeding cycles. Next-generation DNA sequencing be targeted for genotyping. After in silico scoring for SNP
methods have revolutionized the field of genetics by assay design criteria, we selected a final set of 300K
facilitating the identification of natural genetic variation RNA-seq derived SNPs and 120K capture-seq derived
(DNA markers) and the development of high-throughput, SNPs for tiling on a 420K screening array (ThermoFisher
low-cost marker genotyping assays. Single nucleotide Scientific, Figure 1b).
polymorphisms (SNPs) have become the DNA marker of The screening array was used for genotyping of 576
choice due to their abundance in plant and animal individual trees from the 85 provenances and from
genomes, amenability to automation, low cost of commercial breeding material representing eight species,
genotyping and being co-dominant in nature. P. taeda is including P. elliotti and P. pseudostrobus. Samples that
the best characterized pine reference genome, but the passed quality control filtering (98.3% of the samples)
current assembly of the 22 Gb megagenome still consists were subjected to genotype calling by Thermo Fisher’s
of over 2.8 million sequence fragments (“contigs”) with Axiom Analysis Suite software. Besides evaluating assay
>80% repetitive content (Wegrzyn et al. 2014). Whole performance for each SNP probe set, the main aim with
genome sequencing of many pine trees required for SNP the screening array was to estimate the allele frequency and
discovery efforts therefore remain both costly and pattern of sharing of each marker across species. This
computationally intractable. Instead, methodologies based information was crucial for selecting a set of 50K SNP
on reduced representation sequencing, for example markers that maximized the representation of each species
transcriptome and targeted genome capture sequencing are on the final commercial Pitro50K array (Figure 1c). We
being used for DNA marker discovery in pines (Telfer et prioritized SNPs that were informative (with allele
al. 2019). frequencies greater than 5%) in three or more species.
The lack of high-throughput, low-cost genome-wide Since P. greggii and P. maximinoi were under-represented in
genotyping resources has created a bottleneck in pine tree this set, we also included markers unique to P. greggii and
genetics research. To advance both commercial breeding P. maximinoi (but still with allele frequencies greater than
programs and academic research, we have successfully 5%). Finally, a set of 966 diagnostic SNPs (that vary
designed the Pitro50K SNP array (DNA marker chip) greatly in allele frequency among species) were included to
with 49,674 markers carefully selected to optimize the aid in future discrimination of species, sub-species and
number of polymorphic markers within each species and their F1 hybrids.
18 • TIP-MAG • VOL 2 NO 1You can also read
