I'm sorry, I thought everyone got the RosCAP reviews. Bert's e-mail is below:
USDA, ARS Appalachian Fruit Research Station
2217 Wiltshire Road
Kearneysville, WV 25430
phone: 304-725-3451 ext. 387
Folks, here are the reviews of the CAP proposal. It personally think that this did not
review well and if we are going to submit it elsewhere or in the next call, it will need
extensive revisions, mainly details. I am sorry that we did not do better, I hope this can
be turned around and improved. Please digest and think about these reviews for our
upcoming conference call. Bert
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Date: Thu, 19 Jun 2008 08:36:27 -0400 (EDT)
Subject: Review Package for Proposal 2008-02264 Submitted to USDA\CSREES
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June 19, 2008
Area: National Research Initiative Competitive Grants Program
Program: Plant Genome
Proposal Number: 2008-02264
Proposal Title: RosCAP: An Integrated Educational, Extension, and Research Program for
Building Translational Breeding Infrastructure in Rosaceae Specialty
Albert Glenn Abbott
Genetics and Biochemistry
100 Jordan Hall
Clemson, SC 29634-5702
Dear Albert Abbott,
Thank you for submitting your proposal to the Applied Plant Genomics Coordinated
Agricutural Project (CAP) part of the Plant Genome Program of the National Research
Initiative (NRI). We regret that the program is not able to provide funding for your
proposal this year. The CAP part of the Plant Genome Program is able to fund 25% of the
proposals received this year. Although the costs of integrated projects are constantly on
the rise, the availability of funds for agricultural research, education and extension has
not matched these increases. We are continuing our efforts to make awards that are
meaningful in terms of duration and funds awarded. However, the overall quality of
proposals has also increased, and thus the competition is extremely keen for the limited
The panel rating report, panel summary, and individual reviews of your proposal are
below. The panel members carefully evaluated your proposal. These panel members are
fellow scientists selected for their competence in research, education and extension, and
knowledge of your field. Your proposal was evaluated on scientific merit, qualifications
of project personnel, adequacy of facilities, project management, and relevance to
long-range improvements in and sustainability of U.S. Agriculture. We hope this
information will be helpful to you.
If you have any questions, please contact Dr. Ed Kaleikau at 202-401-1931 or
Thank you for your interest in the NRI.
USDA/CSREES NRI Plant Genome Program
Ed Kaleikau Ph.D., National Program Leader
Gera Jochum, Program Specialist
Plant Genome - PANEL SUMMARY
The panel decision regarding your proposal is based on the input provided by the reviews
and the collected expertise and judgment of the individual panel members. This panel
summary reflects the consensus opinion of the panel regarding your proposal.
Proposal Number: 2008-02264 Project Director: Abbott
Proposal Title: RosCAP: An Integrated Educational, Extension, and Research Program for
Building Translational Breeding Infrastructure in Rosaceae Specialty
Research: Positive Aspects of the Proposal
This CAP proposal by Abbott and colleagues is seeking to enhance undergraduate and
graduate education, to integrate extension service with academic programs, and to
coordinate a mapping project of relevant traits of species in the Rosaceae family. The
fruit crops are of great economic value and could benefit from enhanced academic programs
in plant genomics. The team includes a large diversity of Rosaceous crops, numerous
breeders, and important traits. The group has strengths in breeding, specifically
Attempting QTL discovery directly in breeding populations is very desirable, and the use
of FlexQTL to increase the robustness of QTL detection vs. simple biparental populations
is a strength of the proposal. Because FlexQTL is still being developed and will be new
to many of the breeders, the PD wisely included one of the developers of FlexQTL as a
Research: Negative Aspects of the Proposal
Although the general concept of developing a breeder's toolbox of markers for each
crop and for designated traits sounds good, the proposal is quite superficial regarding
the details. Overall, the proposal conflates QTL mapping with marker-assisted breeding;
essentially this project will map QTL, not develop markers tightly linked to economically
important traits that are validated and used directly in breeding. In other words, the
leap from QTL mapping to nailing down a marker-trait association and verifying that the
linked markers are indeed linked in target populations and easy for breeders to use is
completely absent from the proposal.
The proposal gives far too few details on some significant areas. The number of markers
available and approaches to develop more markers to get close to traits were not
specified. In order for FlexQTL to work, pedigrees need to be known, but whether they
actually are known for the germplasm to be evaluated in each of the crops is not stated.
Also, how all the phenotypic and genotypic data will be assembled and analyzed is not
mentioned. This will not be trivial. While involving many labs is commendable, rather
than presenting a diffuse set of goals for many different species, an opportunity has been
missed to focus on fewer traits, really trying to identify markers for them using the
power of comparative mapping among these species.
Freedom to operate across programs, particularly if markers are very tightly associated,
could be a problem, yet this issue was not addressed.
Lastly, the proposal mentions the value of vertical integration, but unfortunately, this
synergy is not apparent. Little coordination exists among the different research groups,
and since traits are already identified, the growers and extension personnel seem to have
had little input into the proposed research directions.
Research: Synthesis Comments
The proposal has some conceptually interesting ideas, but the discussion of actual
details was simply too vague, with too many loose ends. The research plan lacks
originality and presents no clear timeline to reach the milestones desired. The panel
appreciates the complexity of trying to pull a number of diverse crops with divergent
needs together into a single proposal. However, the proposal was not written clearly. It
appears that different members wrote their specific sections with little coordination, and
integration among the groups was not evident. The proposal needs a tighter focus and
critical details on methodology must be presented.
Education/Extension: Positive Aspects of the Proposal
The Education program targets undergraduate life science majors who are not aware of
translational plant breeding (modern plant breeding) as a life science career. A small
scale, but intensive, program to excite and direct undergraduates to be the next
generation of plant breeders is proposed. The program would also support graduate
students that are a part of the CAP program PIS and integrate both levels of students into
working groups of geneticists, breeders, extension specialists and producers.
The program describes many of the priority items for the CAP grant program. The team
integration proposed would establish the professional relationships and understanding that
are key to modern plant breeding. Facilitating a mentoring role for graduate students is
an excellent decision, as was early stakeholder involvement. The RoseCAP team has
identified the correct target population for the desired impact of educating the next
generation of plant breeders. In addition, they propose alluring hooks to attract
students such as opportunities to travel and the chance to work with interesting crop
species. The workshops on plant breeding could be of interest, especially in field tours
that provide visual highlights of the plant breeding process.
Education/Extension: Negative Aspects of the Proposal
The methods and approach are high risk and not likely to produce successful outputs and
outcomes for several reasons. It is not likely that students who are at this stage of
decision making and self discovery are prepared to make this degree of commitment or can
determine their interest from preliminary or promotional exposure. The process described
would benefit from a process that provides more opportunity for more students in the early
stages or that can accommodate students later in their degree programs.
The weakness of an implementation plan for education and extension was emphasized in our
discussion. For education, detail should be provided about the nature of course modules
that introduce and excite freshman and sophomore life science students about translational
plant breeding. Panelists expected these modules would start with clear learning outcomes
that would be a part of first and second year undergraduate biology courses. For example,
the role of genotype and environment on the expression of a trait, or the desire to make
better predictions by using DNA sequence or linkage analysis are applications of concepts
taught in introductory genetics. These are also the kinds of problems solved and
decisions made by a translational plant breeder. Undergraduate teaching modules that use
translational plant breeding of apples or peaches as the case study to hook students into
the possibilities of this work as a career would be the kinds of specific education
outputs that should be described. There are examples of peer reviewed scholarly outputs
of this work in The Journal of Life Sciences and Natural Resources. Partnering with
curriculum development experts at the CAP institutions would facilitate the learning
impact of these modules. Generally, the extension proposed to growers and extension
specialists is traditional.
Assessment of education/extension outcomes is not described. The education outcomes that
would be measurable from this project would be the number of students that start and stay
with this project. However, this is not likely to be a measure of success.
Education/Extension: Synthesis Comments
The education and extension components meet program expectations but are high risk and
lack the detail necessary to evaluate implementation.
Overall Synthesis Comments
The panel felt that this proposal not only lacked a convincing workable research plan,
but also failed to demonstrate the synergy of contributors. Integration of education and
extension lacks originality and details to achieve desirable goals.
The following reviews were submitted for your proposal, the names of the reviewers have
been removed to maintain confidentiality.
The RosCAP project proposes to develop an integrated research, education, and extension
program that focuses on Rosaceous crops. The project is based on a strategic plan that has
come out of workshops that had input from the broader Rosaceae community.
In reviewing this proposal it was clear to this reviewer that there were strengths in
this project across all three areas. However, the organization and structure of the
proposal, in particular the degree of parsing the components, made review of the proposal
difficult. This structure seemed to result in some components being described with
well-written prose but too few details (e.g., student outputs) or components being
detailed with lists that suffer from too little description and context (e.g., subfamily
The undergraduate education model focuses on 18 students across participating
institutions that will engage in new curricular elements, research, and (potentially)
international internships. The approach of recruiting and educating students within the
allied disciplines, developing plant breeding courses, and offering international
opportunities are meritorious. However, critical details are missing: How many students
per institution? Are they enrolled together in online courses or separately, and if so are
these small lab classes? Who develops the courses and what is their expertise? The
evaluation component is weak and there is no dissemination plan. And, importantly, what
part of the vertical integration does the undergraduate education piece aim to address:
are these students being educated to enter careers in plant breeding or into graduate
careers to be researchers.
The graduate education component is strong, particularly with regard to mentoring
undergrads and interacting with stakeholders early on. It is unclear who will develop the
specialty workshops and what their expertise is in this area. There is no evaluation
Similarly the extension component is weak in describing who the experts are, how
evaluation will be done, and how this effort will be sustained.
The genomics research sections tend to take the form of lists of activities. There is
little or no detail or discussion in these sections. It is unclear to this reviewer what
the breeder's "toolkits" are exactly, or why they would be referred to as
toolkits as opposed to resources.
The novel statistical approach is an exciting new opportunity in this area of research.
This CAP proposal by Abbot and colleagues is seeking to enhance undergraduate and
graduate education, to integrate extension service with academic programs, and to
coordinate a mapping project of relevant traits of species in the Rosaceae family. This is
a very superficial proposal that is seeking to please the program requirements but has
very little substance. Clearly, the synergy is not apparent. Two to three regular proposal
could have achieved the scientific components of this proposal. Many of its objectives are
rather regular institutional duties and subject to regular academic planning and
priorities. If not done so, their institutions would not meet regular accreditation
requirements. For instance, the PI proposes to attract students to plant breeding.
However, the actual recruitment of freshmen is not well laid out. Experience abroad is an
excellent although not original concept. To bring undergraduates to the San Diego meeting
is questionable. There will be no way to measure the success of this objective at the end
of the grant. Integration of extension service into academic programs is one of the main
challenges to Ag Experiment Station Directors, but should be anyway an institutional goal.
If these initiatives would have been already in place and would now benefit from
innovative research projects, one could have considered this as a serious proposal, but
that is not the case. In respect to the research projects there was no underlying theory
for any of the traits, but rather a request for a fishing expedition.
The principal investigator (PI) is Albert Glenn Abbott, who rose through the ranks at
Clemson since 1984 and became an internal appointment of the Coker Chair of Plant
Molecular Biology after Rod Wing left for Arizona. The PI has also submitted a similar
size grant to NSF on Rosaceae Genomics. There are numerous CVs attached to this proposal,
but there is no integration of how talents are applied in a synergistic manner.
The fruit crops are of great economic value and could benefit from enhanced academic
programs in plant genomics. There is also a need to attract young researchers to the
breeding profession to implement new strategies resulting from genomics research.
Problem - lack of breeding infrastructure for specialty crops
1. Improve education of future specialty crops breeders
2. Promote value of translational breeding
3. Build Rosaceae breeding infrastructure
4. Promote and support translational breeding in Rosaceae
1. Strengthen fruit industry
2. Strengthen breeding programs
3. Attract and educate new breeders
4. Build effective breeding pipeline
5. Partner with international breeders
6. Vertically integrate research education extension and stakeholders
7. Create an effective pipeline to market
8. Create a platform for the Rose community to exchange ideas
As seen above project objectives and outcomes are clearly described. However each has
not been adequately justified in the current grant. The current short fall of plant
breeders is unclear as is how much the training proposed will impact that short fall.
Also, it seems that the primary extension focus is to promote translational breeding.
While this seems appropriate to improve plant breeder efficiency I wonder how this effort
will help industry and other stakeholders. So in this proposal it is unclear how
stakeholders benefit from extension efforts, although they will benefit from the
production of new varieties and varieties might better suit their needs if communication
is improved. The proposal does not clearly address how the outputs will achieve all the
listed objectives, although the reader can see how several would be positively impacted by
the current proposal. In particular Outcomes 4 and 7 above are not clearly addressed.
Research education and extension are all addressed in the objectives.
(b) Proposed approach, procedures, or methodologies are innovative, original, clearly
described, suitable, and feasible;
Proposes to attract and educate new breeders by first initiating RosCap Creative
Inquiry Program for 18 undergraduates. This project will be implemented in 6 US
institutions. It will include two new courses and a summer research internship. It might
include study abroad depending on the student. Problems: Recruitment is not well
defined. A specific recruitment plan is necessary that will describe how new students
will be attracted and what steps will be taken if no students are attracted. Involvement
of a recruitment officer might be helpful. I wonder if it would not be better to attract
students through a scholarship that is given to High School Seniors that would support
their education as long as they remained in the program. It is unclear if or how the two
new classes will be different from existing courses. It is unclear how these new courses
will be created and how they will be integrated between the participating universities.
It is unclear who will be responsible for the creation of these courses. It is unclear
how the content will meet the objectives and outcomes. There is no documentation that the
participating Universities will accept the new courses and no plan to make them a
permanent part of the curriculum.
This objective also involves the support of nine graduate students. It is unclear how
these students will be recruited. The graduate training does not seem to go beyond the
normal training of students in the applicant's laboratory. Although joint workshops
for graduate students are planned, they are undefined as to who will be responsible for
design and implementation, as well as the objectives, and outcomes. They also seem to
include such a broad audience (stakeholders) making specific objectives unclear. Again
it is unclear how the training of these students is different and how it will provide a
long term change.
Objective 2 - Extension
The focus of the extension plan seems two-fold. 1) To build relationship amongst the
Rosaceae community 2) and to convince stakeholders of the value of MAB. To build
community strategic planning sessions will be implemented. The plan for these sessions is
undefined other than they will meet in year 1 and 4. Will the group meet as a whole or as
commodity groups? What will be the structure of these meetings? Who will organize? Who
will attend? How will stakeholders be encouraged to attend? Is there financial support
for attendance? I could identify travel money to support PIs attendance, but am unclear
about what other support is planned. To build community it seems important to meet more
often than is planned. Informing stakeholders of the importance of MAB is critical to
garner support for breeders, but does not seem to directly benefit the stakeholders. They
will benefit from improved varieties however they are created. There is money for an
extension coordinator whose duties include creating outputs and assessments. In all, this
objective would benefit from identifying specific outcomes for each audience so that
outputs could be designed to meet those outcomes. Extension personnel are part of this
program, but I wonder if extension agents need/want to be trained in MAB. How will they
be encouraged to attend training? What is the learning outcome here? Another objective
is to encourage breeders to initiate MAB. It is unclear from the proposal how many
breeders would be impacted by this effort. How many breeders are in the Rosaceae
community? How many currently use MAB? How many will be part of this project?
Objective 3 - will primarily build translational breeding infrastructure. It will
provide phenotyping, software and statistical support, a web based portal and database,
and a DNA Reference bank. These all seem necessary and important to the project and
Objective 4 - involves implementing MAB in three sub-family groups Maloideae,
Amygdaloideae, and Rosoidae. Traits for MAB have been selected with stakeholder input.
Different levels of information are currently available for each of the sub-families. For
Maloideae, QTLs have been identified for acidity sugar content and fire blight resistance
by European researchers. It is the plan to identify closer markers, although it is
unclear from the proposal what makers will be pursued or how new markers will be created.
It is unclear the level of polymorphism within the populations, the number of potential
markers and the likelihood of developing other markers. Information for Amygdaloideae is
more complete. For this sub-family they have SSR markers that have been mapped at a
resolution of 10cM in peach. As well as sequence information from peach that can be used
to created new markers. They also have indications that the other members of the
sub-family show enough co-linearity to be able to use the peach markers and sequence.
They plan to identify 2 QTLs for each of 4 traits for fine mapping and further marker
development. The success of the peach mapping seems sure, but success for almond and
cherry depend on the ability to use peach to provide the necessary tools. In the Rose
sub-family it is planned to focus on flowering. It is stated that this trait is highly
effected by environment and I wonder if 2 to 3 environments is enough. It is helpful that
the populations will be propagated asexually for the different environments. There is a
SSR AFLP map for Fragaria, although it is not stated the level of marker resolution. I
wonder if polyploidy will pose a problem. It is a stated goal to develop more markers for
raspberry and rose, but not clear what markers will be pursued.
(c) Expected results or outcomes are clearly stated, measurable, and achievable within
the allotted time frame;
Although outcomes are stated, it is difficult to estimate the likelihood of success
without more information.
(e) Proposed extension leads to measurable, documented changes in learning, actions, or
conditions in an identified audience or stakeholder group; and
There is no clear measurable change in learning actions or conditions for stakeholders.
One measurable change could be increased use by breeders of MAB, but no indication of how
prevalent its use is currently.
(f) Proposed education (teaching) has an impact upon and advances the quality of food and
agricultural sciences by strengthening institutional capacities and curricula to meet
clearly delineated needs and train the next generation of scientists and educators.
No letters of support from Universities that curriculum changes are welcome or will be
permanently instituted. No clear change in the recruitment or mentoring of students.
2. Qualifications of Project Personnel, Adequacy of Facilities, and Project Management
(a) Roles of key personnel are clearly defined;
Role of extension coordinator not clearly defined. Who will create new curriculum and/or
workshops is not clearly defined. Who will measure outcomes not clearly defined.
(b) Key personnel have sufficient expertise to complete the proposed project, and where
appropriate, partnerships with other disciplines (e.g., social science or economics) and
institutions are established;
As mentioned above, someone to give advice on recruitment might be helpful.
(e) A clear plan is articulated for project management, including time allocated for
attainment of objectives and delivery of products, maintenance of partnerships and
collaborations, and a strategy to enhance communication, data sharing, and reporting among
members of the project team; and
There is no clear plan for the distribution of the "Future National Interest"
money which is proposed to be subcontracted to several groups including almost 300,00 to
the Appalachian Fruit Research
(f) The budget clearly allocates sufficient resources to carry out a set of research,
education (teaching), and/or extension activities that will lead to desired outcomes, with
no more than two-thirds of the budget focused on a single project component.
There appears to be appropriate funding of research, education and extension, although it
is very hard to determine the distribution of funds amongst the three priorities. Most of
the money for education is for the support of students that will work on the project. The
primary extension expense is for an Extension Coordinator and to establish three workshops
and the travel to those workshops. It is not clear if any money is set aside for the
vertical integration of extension education and research. For example, cannot find money
for the train the trainer workshop or the strategic planning sessions.
3. Project Relevance
(a) The project addresses a stated program priority;
(b) Project components (research, education, and/or extension)-at least two are
required-are fully integrated and necessary to address the problem or issue;
To a certain extent the three components are integrated in that the research is
stakeholder driven and students trained will do the research and in the future be involved
in sustaining breeding efforts. The extension part is not as well integrated in that the
research does not seem to be interdependent with the extension. Not clear how industry
will benefit from extension efforts.
(f) For extension or education (teaching) activities, curricula and related products will
sustain education or extension functions beyond the life of the project; and
Although it is hoped that education and extension will continue, there is no plan for
sustained education and extension after the life of the project. There is no supporting
documentation supporting this continuation.
(g) For extension or education (teaching) activities, the resulting curricula or products
share information and recommendations based on knowledge and conclusions from a broad
range of research initiatives.
The curriculum for education and extension activities is not well defined or described.
Merit - This project is intended to strengthen Rosaceae specialty crop breeding,
coordinate research efforts and improve the state of plant breeding education and training
in the US. However, the proposal lacks necessary detail in all of its components.
While the 'pedigree genotyping' approach to QTL detection might no longer be
considered innovative, it is well-aligned with the current trend to detect marker-trait
associations in relevant breeding populations. Still, there is not even brief mention of
methods for detecting QTL, computing IBD probabilities, estimating and incorporating
polygenic effects, or combining unbalanced phenotypic data, nor how RosCAP will extend
methods and software already available. Do the PIs expect difficulty in combining
gel-based SSR data across programs, and if so how will they address that? Training U.S.
staff and students in data analysis by WUR scientists is mentioned without providing a
specific plan for implementation or evaluation, though this component of
knowledge/technology transfer has proven to be a frequent challenge in deploying molecular
breeding to the field. What specific marker platform will be used in the
'breeders' toolkit' and what infrastructure will be needed or is available?
In describing projects for each sub-family, there is inconsistency in information
provided on experimental design; in some cases important detail on sample size, marker
density, number of reps and germplasm sampling strategy is absent. Organization by
sub-family may run the risk of groups operating in silos where there may be critical
advantage in maximizing discussion of strategies (e.g. most efficient pedigree structure,
sample size, field design), logistics (e.g. standardization and collation of phenotypic
data, common checks, timelines) and lessons learned.
The authors propose a RosCAP Creative Inquiry Program to attract undergraduates to plant
breeding, but its coursework is not distinct from standard curricula, and it is unclear
why such courses ('Molecular Techniques in Plant Breeding' or 'Plant
Breeding Techniques') need to be developed here. There is no clear connection
between this program and its stated outcome 'to encourage development of graduate
programs directed at translational breeding'. Similarly, the authors propose
developing graduate workshop courses also apparently of generic content (basic molecular
marker technologies, translational breeding theory and practice, bioinformatics in
translational breeding). One distinction might be exposure to 'breeders, growers,
industry representatives and research scientists', but this piece needs to be
emphasized much more and formalized to ensure concrete outcomes. Letters of support are
provided, but neither the Education nor Extension team (Management Plan) enlist an
Qualifications - Statistical analysis will be a major component and should be covered
well by van de Weg (% time?) and PRI collaborators. I could not find a timeline to track
project milestones (except for administrative activities), and it is unclear if some
sub-projects can be completed in four years as described (SSR marker development,
population development, phenotyping, QTL detection and/or fine-mapping).
Relevance - Target crop species and traits are relevant and prioritized by the community.
Pedigree genotyping is increasingly used for detection in elite breeding populations both
in public and private sectors. Indeed, there is a critical gap in plant breeding
recruitment, education and training of the nature stated here, but the approaches to
address this problem are not clearly distinct from current (and mostly unsuccessful)
programs, or their description lacks the detail to recognize key differences and assess
All my reviews focus on a subset of Integrated proposal criteria.
a. Education and Outreach Objectives/Outcomes
-Focus audience is the undergraduate in the life science who would be potentially excited
by a career in modern plant breeding (translational plant breeding). These students will
be recruited from existing student pools at the CAP team institutions.
-Also budget for graduate students in translational plant breeding programs.
-The extension audience is the breeder , extension educator and business people who
support the end user of Rosacae crops
- Create a four year program to attract science oriented undergraduates into plant
breeding, build summer work experience , two unique courses and one workshop into their
- Support graduate students (9 per year)
- International experience for participants (not sure)
Extension approach is traditional (fact sheets)
c. Outcomes and e. Impact Measurables
- student participation in program
- institutional changes in programming in the life sciences
- student choice of career path
f. Capacities and Curricula for next generation of Scientists and Educators
The target audience is ideal for this goal, but a challenging audience to impact. The
CAP group has the expertise at the various institutions and the meetings thus far in
preparing this proposal have started the process of connecting 'broken
pipelines' in the Rosacea research, breeding and production system.
Connect with CDPC should be goodŠ. Start to build an expert network.
GDR existsŠ. Is research orientedŠ not yet a venue for the nonexpert.
If students who are 16/17 years old now buy into the plan and stay with the plan, the
infrastructure will start to be built.
Curricula are not likely to impact a large audience than the recruited students.
2. Qualification & Management
a/b/c. Roles, Expertise, Capacity.
The academic and breeding expertice is clear. The track record on working with and
motivating young people is not. Therefore, management needs to be explicit in order to
stay with time line goals.
e. Clear plan
I believe the plan has some attractive hooks with interesting work that uses science and
the opportunity for travel. The CAP team is broad and diverse and likely has individuals
with track records in working with undergraduates. However, it is difficult for 18 year
olds to buy into a four year program that has this level of commitment. Therefore, the
plan is high risk.
The same is true of graduate students and the program here is really focused on the
success in recruiting undergrads.
The plan for sub group teams (Researcher, Breeder, Educator, Extension Specials
Industry Rep.) for the students to join is attractive and should result in the CAP
infrastructure developing as a user/learner friendly resource. The tool kit approach
provide a good context for learning and thinking about how the combine contributions of
specialists works together to the common goal.
Support for education and extension seems to be dispersed among CAP team members.
f/g. Sustainable and Broad
Breath from institutions, crop diversity and contributions of diverse professionals.
Sustainability relies on changes in institutions or changes in teaching motivated by the
effort to translate teaching into problem solving stories. The proposal provides little
evidence that their valid goal of igniting an interest in modern plant breeding among our
science oriented undergrad students will cause sustainable change in how the CAP team does
There is no evidence of this CAP leveraging the efforts and success of other CAPS or
other places that successfully impact and motivate translational science.
The research will be conducted within three groups corresponding to three sets of species
within the Rosaceae that have economic value.
The plan is basically to genotype a large number of individuals-either core germplasm
sets or biparental mapping populations-and apply the genotypes to phenotypic data that
will be generated based on common protocols. Data analysis will be done using FlexQTL to
enable pedigree data to be incorporated into the mapping process. The goal is to develop
"breeders' toolkits" for selected traits.
Conceptually, I like the general idea, but the devil's in the details. The most
obvious potential problem is that the number of markers available for some species is not
particularly large. Actually, the numbers of markers that are currently available is not
specified for any of the species, so it is somewhat difficult to know how large a problem
this will be.
The QTL analysis method sounds very good, and certainly using pedigree information will
help identify QTL. What isn't clear to me is to what extent the pedigrees are known
for the genotypes to be evaluated in the different species. Are the pedigrees clearly
known? Also, what happens if a very broad array of starting germplasm is entered into the
program-won't there be problems of many alleles/haplotypes and small class sizes? I
have reservations about the QTL analysis in the absence of any real discussion about how
it will be carried out.
Assuming that QTL are identified (and I'm certain that at least some will be),
markers will be targeted to these intervals to more closely map the underlying QTL. The
first question is where additional markers will come from, but secondarily, better
resolution will require additional recombinants at some point. Do the PIs expect that the
recombination present within their pedigrees is sufficient to identify markers very
closely linked to the QTL?
Finally, the actual translation to breeding never seems to show up. Toolkits, QTL
populations, and so on are fine, but where is the breeding program that will select based
on the QTL, recombine desired plants, etc. That seems to be a step away....maybe
there's no possibility of getting to this stage in four years, but I would have liked
to know more about the actual application to an actual cultivar development-as opposed to
In summary, the concept is great, but the implementation of the concept across a series
of diverse species is not clear. Whether the appropriate resources (markers, pedigree
info, etc.) are available is just not documented well enough. And the vertical
integration sounds great, but it seems that traits have already been identified, germplasm
is being evaluated-where does the vertical integration actually show up in the work to be
The PIs have clearly thought about working undergraduate and graduate students into
projects, and they should be commended for that. The undergrad program is needed to get
students thinking plants. However, the curriculum is a bit ambitious-graduate students
often have problems with plant breeding concepts and molecular technologies. To expect a
sophomore to take a course in that is simply unrealistic. Still, the idea of developing a
cohort of students from different universities who can come together in the summer and
possibly integrate study abroad efforts is really good, and a strong aspect of this
project. The assessment methodology is not clear to me, however.
The grad program is fine, particularly partnering the undergrads with a grad student.
While this is often done, having a formalized structure for this mentoring activity is
As far as the extension component....well, the proposal has many ideas, but they are
somewhat diffuse. And I'm really not sure of the need for/value of extensive
programs to highlight translational genomics to producer groups and the like. Something
that is of interest, however, are programs discussing plant breeding in general (and the
PIs mention this)-how are the new cultivars developed, with what traits, etc. This is
something farmers and others are interested in. I suggest focusing generally on plant
breeding, and within that framework, discuss how all types of technology and methods can
be used. There's nothing magical about translational breeding-in fact, amazing
things have been bred without any modern technologies at all-so having that integrated
into a broader program of education/extension on plant breeding and cultivar development
would be preferable.
Overall, these programs are somewhat more fully realized than is often the case on these
I like aspects of this project very much-the undergrad program, linking undergrads with
grads, discussing phenotyping and plant breeding in the extension area, and conceptually
the development of breeders toolboxes. However, the implementation of some of these ideas
is either sketchy or unrealistic, and considerable detail of importance is not provided.
The project objectives are clearly outlined and integrated to address effective Rosaceae
breeding and integrated development of the human resources. All 3 project components are
substantially addressed, with research and education leading and extension built up from
communication across the ranks from stakeholder to researcher and student. Research
focuses on the "low-hanging-fruit" that would make the outputs very viable to
engage education and extension in an interactive experience. There is therefore a balance
where the research products would be able to reach the stakeholder in the minimal time.
The RosCAP proposes to address the dwindling plant breeding student population head-on by
kindling and supporting an interest from undergraduate-graduate level onwards, using an
original way by allowing students to continue in their chosen undergraduate field of
interest but train them in modern breeding methodologies. This is very appropriate for a
multi-disciplinary approach of doing science, each specialty contributing with different
required expertise with a common goal, and will foster team science from these selected
individuals. The main research focus of utilizing Pedigree Genotyping (PG) is a very
attractive approach to the analysis of gene/locus-phenotype correlations which has its
basis in human genetics and animal breeding and uses robust statistical systems and
software proven in the Rosaceae. The research, education and extension components are
completely integrated through the program, with unique solutions and vertical
communication of problems and modern solutions.
Under each objective gaps in the field are identified which are addressed by inputs,
outputs, outcomes (short/long-term) and evaluation steps. Each of these steps provides
lists/table of achievable goals that are followed through the input to evaluation process.
For example, in objective 1 undergraduate and graduate education are targeted, which
results can be queried in the evaluation process of where the students end up contributing
from their education, which should be traceable within the project duration. Objective 3
on translation breeding infrastructure is exemplified by a focus on germplasm phenotyping
which is supported by software/statistical support, databases/webportal development. The
success of integration of these procedures will be tested by the achievement of the
selected trait improvements that are targeted across the crops and are addressed under
Objective 4 of the proof-of-concept of the RosCAP translational pipeline which provide a
set of expected deliverables across research, education and extension. Although the
strategy relies on the integration of the RosCAP activities, each objective and focus
result is selected to be independent and therefore can be successful by itself, and yet
contribute to the whole RosCAP.
The research goals are evenly distributed across the Rosaceae within the 3 sub-families
and the research topics of quality, resistance and horticultural traits. The PG system is
able to utilize multiple populations with many individuals screened for various traits in
multiple environments, some of which are the present focus, but will continue to provide
mapped traits in international collaborations beyond the project. It has therefore a broad
future, yet will be able to deliver within this project the low-hanging-fruit such as
virus resistance, apple quality and modulation of flowering for which the available
information has to be brought together in a concerted way, as proposed in the project.
The proposal in extension is to document and publicize the fruits of RosCAP translational
breeding through various events such as train-the-trainer workshops which will target
end-users such as consumers, stakeholders, breeders/producers, industry and the
production-chain. The translational breeding results will be used to vertically integrate
research, breeding, education and the end-users. Evaluation of the extension component
will be done by the extent of participation from different stakeholders and the adoption
of breeding tools by breeding programs. This proposal defines a cohesive extension
The educational component intends to capture talent at the undergraduate level, support
graduate study and groom them towards development of a modern plant breeder trained in
practical modern technologies with experience in multi-disciplinary and international
teams. The proposal has a good education plan as it nurtures talent of a select group who
would continue to perform and contribute directly after the project and for years to
The specific roles of the key personnel are described in the management plan, with 3
managers for education, translational breeding and administration. For each objective,
specific team leaders and key personnel are identified, their tasks being divided
regionally for education and extension or by specific expertise for the two research
objectives. These roles lead back to individual descriptions of the key personnel
The personnel show evidence of expertise. For education at different levels University
education in selected departments will be undertaken with the PI taking leadership. For
extension, Olmstead with a job title of "Area education educator" will take
leadership with a diverse team including the social sciences. The translational breeding
will be led by sub-family specialists and the infrastructure component by a specialist
team for leadership in databases, genotyping and phenotyping.
The project is very well imbedded in international collaboration with the primary groups
in the world working on the Rosaceae. Special contribution comes from software for
pedigree genotyping that strengthen the capabilities in translational genomics and
There are sufficient facilities and instrumentation documented in the participating labs
to be able to carry out the proposed work.
Although a clear plan is given for the project management structure, the timelines of
interaction between the different objectives and components are not provided. Attention
should be given to this as it is required for success of specific parts of the project
The budget is balanced, with the research component probably half, mainly supporting the
database and infrastructure parts. The education parts are strong providing the backbone
and the work-force for the research as well as extension components.
The project is relevant as the project addresses a crop family which is very valuable
with the Crop value of Rosaceae in 2007 being 8.2 billion. But because of the long time to
flower, breeding is difficult in some tree members, while others such as strawberry have
shorter cycles and are more amenable to genetics and functional genomics.
All three project components are fully integrated. The education plan is simple yet has a
potential to grow in different geographical regions and different levels and
multi-disciplines. The novel yet practical translational genomics and breeding program is
used as a focus to support extension and education activities.
In discussions and surveys from stakeholders and participants, the production of a white
paper and with supporting research and technological developments, the proposed strategy
is catered to use modern technology to serve stakeholders needs.
The involvement of different stakeholders has been there in the development of the plans
and is proposed to involve them throughout the project.
Evaluation is built into the plan at different levels and is addressed in the proposal
description. This process is planned to be used in an iterative way in developing the
The education component seems very bright to sustain interest in translational breeding,
even one crop of multi-discipline trained breeders can be an exceptional output of this
project that will sustain development for a generation. The extension program will be able
to reach out to multiple stakeholders demonstrating the promise and accomplishments of the
translational breeding program, which will refurbish the eroded educational and breeding
infrastructure in universities.
The thrust of the education is multi-disciplinary, encompassing undergraduate students
from different majors/interests into the program. The involvement of educational
activities are at different levels of translational breeding from phenotyping and
genotyping to databases and statistics etc, thus a broad range of disciplines all of which
are incorporated in the extension and education programs.
I am struck with the fact that throughout the proposal there has been very little
discussion on the development of markers. The markers are always referred to as
genome-spanning set of SSR markers, however when I look at the specific quoted
publications they are not very dense, and together with the low progeny size in the
different pedigreed populations would not contribute to high resolution mapping of
This is indirectly stated in section 4.B.2 on translating of available genomics data into
a breeders' toolkit, where the project peach genome sequence (end 2008) would be
used. However, that is quite an undertaking and there is no plan in this proposal to
develop these markers.
Similarly for apple in section 4.A.2 the plan is to narrow the broadly mapped QTL regions
(citations from Abstracts, question is if they are available) from a marker density of
1/20cM to 1/5cM. No plan for this is provided. A dependence on markers developed by others
might limit their use in commercial breeding applications, and this should be considered.