Enabling Marker-Assisted Breeding in Rosaceae I... · Enabling Marker-Assisted Breeding in Rosaceae...
Transcript of Enabling Marker-Assisted Breeding in Rosaceae I... · Enabling Marker-Assisted Breeding in Rosaceae...
Enabling Marker-Assisted Breeding in Rosaceae
Dedicated to the genetic improvement of U.S.
rosaceous cropswww.rosbreed.org
Project Director
Amy IezzoniMichigan State [email protected] x 1391
Team Leaders
BreedingJames Luby
University of [email protected]
Socio‐Economics Chengyan Yue
University of [email protected]
Marker‐Assisted Breeding PipelineCameron Peace
Washington State [email protected]
Breeding Information Management SystemGennaro FazioUSDA‐ARS Plant Genetic Resources [email protected]
GenomicsDorrie MainWashington State [email protected]
StakeholderJim McFersonWashington Tree Fruit Research [email protected]
Pedigree‐Based Analysis Eric van de Weg
Plant Research International – Netherlands [email protected]
ExtensionCholani WeebaddeeMichigan State [email protected]
GenotypingNahla BassilUSDA‐ARS National Clonal [email protected]
RosBREED is a multi‐state, multi‐institution project dedicated to genetic improvement of U.S. rosaceous crops by targeted applications of genomics knowledge and tools to accelerate and increase the efficiency of breeding programs. This Coordinated Agricultural Project is funded through the Specialty Crops Research Initiative by a combination of federal and matching funds.
What is RosBREED?
RosBREED Team Members
Marco BinkPlant Research International, [email protected]
Tom GradzielUniversity of California ‐ [email protected]
Susan BrownCornell [email protected]
James Hancock Michigan State [email protected]
David ByrneTexas A&Md‐[email protected]
Raymond JussaumeWashington State [email protected]
John Clark University of [email protected]
Vicki McCrackenWashington State [email protected]
Carlos CrisostoUniv. of California – [email protected]
Nnadozie OraguzieWashington State [email protected]
Thomas DavisUniv. of New [email protected]
Gregory ReighardClemson [email protected]
Kate EvansWashington State [email protected]
Alexandra Stone Oregon State [email protected]
Chad FinnUSDA‐ARS , Corvallis, OR [email protected]
Mykel TaylorWashington State [email protected]
Karina GallardoWashington State [email protected]
Dechun WangMichigan State [email protected]
Ksenija GasicClemson [email protected]
Kenong XuCornell [email protected]
RosBREED Project Associates
Riaz Ahmad (U. of Calif. – Davis)[email protected]
Steven McKay (U. of Minn.)[email protected]
Matt Clark (U. of Minn.)[email protected]
John McQueen (Oregon State Univ.)[email protected]
Daniel Edge‐Garza (Wash. State Univ.)[email protected]
Paul Sandefur (U. of Arkansas)[email protected]
Lise Mahoney (U. of New Hampshire)[email protected]
Travis Stegmeir (Michigan State Univ.)[email protected]
International Partners and Nature of Partnership
Collaborators and Nature of Collaboration
Pedigree Based Analysis ‐ Plant Research International, Netherlands Hans Jansen ‐ Institute for Hort Plant Breeding
Chris Maliepaard ‐ Plant Breeding
Roeland Voorrips ‐Centre for Plant Breeding & Reproduction Research.
Sequencing/Molecular Groups
Amit Dhingra ‐ Dept of Hort. & Landscape Arch., Washington State Univ., Pullman, WA 99164
Bryon Sosinski ‐ Dept. of Hort Sci North Carolina State University, Raleigh, NC 27695
Vladimir Shulaev ‐ Virginia Tech & Virginia Bioinformatics Institute Blacksburg, VA 24061‐0477
Riccardo Velasco ‐ Biology Department Istituto Agraraio San Michele. Trento, Italy
Sequencing/Molecular Groups
David Chagné ‐ Plant & Food Research Palmerston North, 4474, New Zealand
Lee Meisel ‐ Center of Plant Biotechnology, Ecology & Natural Resources. Andres Bello Univ Santiago, Chile
Jasper Reese ‐Dept of Biotechnology, Univ of the Western Cape, Bellville, 7535, South Africa
Dan Sargent ‐ Department of Plant Breeding and Genetics, East Malling Research, East Malling, UK.
Herman Silva ‐ Center of Plant Biotechnology, Ecology & Natural Resources. Andres Bello Univ Santiago, Chile
INRA – Breeding & Genetics teams
Beatrice Denoyes‐Rothan ‐ Unité de Recherche des Espèces Fruitières (UREF), INRA CR Bordeaux.Villenave d'Ornon, France
Elisabeth Dirlewanger ‐ Unité de Recherche des Espèces Fruitières (UREF), INRA CR Bordeaux.Villenave d'Ornon, France
Charles‐Eric Durel‐ Unité de Génétique et Horticulture (GENHORT), INRA CR Angers, Beaucouze, France
Francois Laurens ‐ Unité de Génétique et Horticulture (GENHORT), INRA CR Angers, Beaucouze, France
Jose Quero Garcia ‐ Unité de Recherche des Espèces Fruitières (UREF), INRA CR Bordeaux.Villenave d'Ornon, France
Benedicte Quilot‐Turion ‐ Unité de Génétique et Amélioration des Fruits et Légumes (UGAFL), INRA CR Avignon, France
AlcalaCookPartickavan SickleHirst
Watkins
Karp
AbbottBuellGardiner
ChengSimon
Ross
AP Color KeyIndustry
Extension
Scientific
AllenCarrDoddGrimKorson
BierlinkCurtisPerrySparksSeavertBliss
Baugher
Professional interests of RosBREED Advisory Panel members
Stokes
Moffitt
GoldbergerOlmsteadShermanArusArvai
RosBREED has three Advisory Panels, representing industry, scientific, and extension interests. Panel members broadly represent the diversity of Rosaceae by crop, region, and professional expertise.
RosBREED Industry Advisory Panel
Jim Allen: President New York Apple Association, Fishers, NY (http://www.nyapplecountry.com/) Board of Trustees, US Apple Association (http://www.usapple.org/)
Phil Baugher: Co‐owner Adams County Nursery, Aspers, PA (http://www.acnursery.com/) Chair, US Apple Association Research Committee
Henry Bierlink: Director Washington Red Raspberry Commission, Lynden, WA (http://www.red‐raspberry.org) National Berry Crops Initiative (http://www.nationalberrycrops.org/)
Chalmers Carr III: CEO Titan Peach Farms, Inc., Ridge Spring, SC (http://www.titanfarms.com/default.asp) Board of Directors, South Carolina Peach Council (http://www.scpeach.com/about.htm)
Fred Cook: National Research Department Manager Driscoll’s Strawberry Associates, Watsonville, CA (http://www.driscolls.com/ )
Robert Curtis: Senior Manager, Production Research Almond Board of California, Modesto, CA (http://www.almondboard.com)
Bill Dodd: President Ohio Fruit Growers Marketing Association, Newcomerstown, OH (http://www.ohioapples.com/ohio_apples_fgma.htm) Board of Trustees, US Apple Association
Bruce Grim: Director Washington Marketing Associations, Wenatchee, WA (http://www.themarketingassociations.org/) Executive Director, Washington State Horticultural Association (http://www.wahort.org/) President, Board of Trustees, US Apple Association
Philip Korson: President Cherry Marketing Inst., Inc., Lansing, MI (http://www.cherrymkt.org/)
Kevin Moffitt: President Pear Bureau Northwest, Portland, OR (http://www.usapears.com/)
Chrislyn Particka: Research Director Sakuma Bros. Inc. Burlington, WA (http://sakumabros.com)
Tom Stokes: CEO Tree Top Inc, Selah, WA (http://www.treetop.com/) Board of Trustees, US Apple Association
Gary van Sickle: Research Director California Tree Fruit Agreement, Reedley, CA, (http://www.eatcaliforniafruit.com/index.asp)
RosBREED Extension Advisory Panel
Jessica Goldberger: Asst. Professor, Dept. of Rural Sociology, Washington State Univ. Professional interests: agricultural knowledge, science, and technology (http://www.crs.wsu.edu/facstaff/goldberger/goldberger.html)
Peter Hirst: Assoc. Professor, Dept. of Horticulture, Purdue Univ. Professional interests: tree fruit production systems and physiology, physiological genetics of flowering and fruit development in Rosaceae; state Extension specialist; undergraduate and graduate education (http://www.hort.purdue.edu/hort/people/faculty/hirst.shtml)
David Karp: Associate, Agricultural Experiment Station, UC Riverside Professional interests; freelance food journalist and photographer
Mercy Olmstead: Asst. Professor, Department of Horticultural Sciences, University of Florida‐IFAS, Professional interests: Stone Fruit Extension Specialist (http://hos.ufl.edu/stonefruit)
Ron Perry: Professor, Dept. of Horticulture, Michigan State Univ. Professional interests: extension and research in cherry and apple orchard systems (http://www.hrt.msu.edu/faculty/perry.htm)
Clark Seavert: Professor and Center Director, North Willamette Research and Extension Center, Oregon State Univ. Professional interests: economics, risk management and decision tools for ornamental, nursery, and berry crops (http://oregonstate.edu/dept/NWREC/Staff/Seavert/Seavert.html)
Jamie Sherman: Asst. Professor, Dept. of Plant Sciences and Plant Pathology, Montana State Univ. Professional interests: wheat genetics and Outreach Coordinator for USDA‐NRI WheatCAP (http://plantsciences.montana.edu/facultyorstaff/faculty/sherman/sherman.html)
Brian Sparks, Group Editor, American/Western Fruit Grower: Willoughby, OH Professional interests: trade and web‐based publication covering U.S fruit production (http://www.growingproduce.com/americanfruitgrower/)
Chris Watkins: Professor, Dept. of Horticulture, Cornell Univ., Assoc. Director for Cornell Cooperative Extension Professional interests; postharvest physiology and management of apple, pear, peach, and cherry; state‐wide agricultural extension activities (http://hort.cals.cornell.edu/people/faculty.cfm?netId=cbw3)
RosBREED Scientific Advisory Panel
Albert Abbott: Professor, Dept of Biological Sciences, Clemson Univ. Research areas; structural genomics of Prunus, sequencing of peach genome (http://www.clemson.edu/cafls/departments/genbiochem/people/aabbott.html)
Pere Arús: Head, Plant Genetics Dept., Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cabrils, Spain Research areas: molecular tools for plant genetics; comparative genomics and application of molecular markers in Rosaceae breeding co‐PD: European Integrated Research Project ISAFRUIT (http://www.isafruit.org/Portal/about.php)
Joe Arvai, Professor of Judgment and Decision Science, Michigan State Univ. Research areas: testing theories of decision‐making in the absence of formalized decision support; developing decision aids to improve decision quality
Frederick Bliss: Professor Emeritus, Univ. of California, Davis and Sr. Director, R&D Special Projects, Seminis Vegetable Seeds, Woodland, CA Research areas: genomics, genetics, and breeding of fruit and vegetable crops; research administrator in public and private sectors; commercialization of breeding products
Robin Buell: Assoc. Professor, Dept. of Plant Biology, Michigan State Univ. Research areas: genomic aspects of plant biology and plant pathogens; high throughput sequencing, functional genomics, comparative genomics, and bioinformatics (http://www.plantbiology.msu.edu/faculty/faculty‐research/robin‐buell/)
Lailing Cheng: Assoc. Professor, Dept. of Horticulture, Cornell Univ., Ithaca, NY Research areas: plant nutrition, fruit physiology, molecular, cellular, and whole plant response to abiotic stress in apple, cherry, grape; undergraduate and graduate education (http://hort.cals.cornell.edu/cals/hort/people/faculty.cfm?netId=lc89)
Susan Gardiner: Principal Scientist, The Horticultural and Food Research Inst. of New Zealand (Plant & Food Research [PFR]) Research areas: leads Gene Mapping Team integrated with PFR breeders in several Rosaceae crops, including, apple, apple rootstock, pear, peach/nectarine and apricot
Carolyn Ross: Asst. Professor, Dept. of Food Science, Washington State Univ. Research areas: sensory analysis and consumer preferences of fruit and fruit products, including fresh and processed apple, pear, and cherry and wine (http://sfs.wsu.edu/facultystaff/Ross.html)
Phil Simon: Research Geneticist, USDA‐ARS and Professor, Dept. of Horticulture, Univ. of Wisconsin‐Madison Research: vegetable breeding and genetics; biochemistry of culinary and nutritive factors, terpenoids, and sugars in carrots and garlic (http://www.horticulture.wisc.edu/faculty/facultylist.php) Vice Chair: U.S. Plant Breeding Coordinating Committee (http://cuke.hort.ncsu.edu/gpb/pr/pbccmain.html)
Apple PeachWashington State Univ (Kate Evans) Clemson Univ (Ksenija Gasic)Cornell Univ (Susan Brown) Univ of Arkansas (John Clark)Univ of Minnesota (James Luby) Texas A&M (David Byrne)
Univ of California (Tom Gradziel)Sweet cherryWashington State Univ (Nnadozie Oraguzie) Strawberry
Michigan State Univ (James Hancock)Tart Cherry USDA‐ARS Corvallis (Chad Finn)Michigan State Univ (Amy Iezzoni) Univ of New Hampshire (Tom Davis)
U.S. Rosaceae crop industries face numerous limitations to profitability and sustainability. Overcoming these barriers requires rapid development and deployment of new cultivars with improved characteristics to meet dynamic industry and market needs and consumer preferences. This project seeks to identify breeding trait targets based on knowledge of what industry sectors and consumer’s value, and utilize genomics information to develop a sustainable technical platform to accelerate and increase the efficiency of cultivar development and adoption.
What need does RosBREED address?
RosBREED will focus on fruit quality traits for four rosaceous crops: apple, peach, cherry and strawberry. Market‐based information will be used to objectively quantify the importance of fruit quality traits that will be targeted for marker‐assisted breeding.
What crops and traits will be targeted in RosBREED?
RosBREED core breeders
2010 is a watershed year for Rosaceae with the anticipated release of the peach, apple, and strawberry genome sequences. In addition over 250 major genes and marker‐trait associations have been identified in rosaceous crops. Yet a huge gap exists as this genetic information is rarely used to improve plant breeding. RosBREED will bridge that gap and ensure that future breeding efforts leverage genomics and genetics information to more efficiently reach the cultivar improvement goals.
Why now?
The central technology to be used in this project is marker‐assisted breeding (MAB). An eight‐stage MAB Pipeline will be established, and demonstrated with markers for high impact traits, to assist breeders in improving the efficiency of their programs. RosBREED will develop the community resource of a genome‐scanned, comprehensively phenotyped (for fruit quality) reference database on pedigree‐linked breeding germplasm. Pedigree‐Based Analysis will be used to functionally characterize alleles at detected QTLs, describing the genotypic value of breeding parents. The genome scans for each of the major crop groups (apple, peach, strawberry, and cherry) will exploit ancestral genomic relationships across Rosaceae, and focus on shared fruit quality genes. Software will be developed for breeder access to databases and decision‐support analytical tools, incorporating such features as trait economic values, cost‐efficiency calculation of (marker‐assisted) seedling selection schemes, cross planning, and breeder‐friendly interfacing of genomics information.
What is the technology that will be developed and adopted?
RosBREED is rooted in our vision that the common ancestry of the diverse Rosaceae genera can be harnessed to leverage knowledge and resources across commodity boundaries. For example…
…the same gene that controls the presence of red pigment (skin and flesh) in apple likely controls the presence of red pigment in cherry.
Why are we working together as a crop family?
The marker‐assisted breeding approach will be adopted and implemented by the core breeders as a cost effective strategy for improving the efficiency of their programs. Stakeholders will appreciate how the use of genomics information can be harnessed to develop new varieties that meet market needs and consumer preferences.
What are the targets for success?
This approach, usually shortened to MAB, uses genetic markers, usually DNA‐based tests, to monitor the presence of desirable and undesirable genes in breeding plants. RosBREED will focus on enabling breeders of apple, peach, cherry, and strawberry breeders to make more informed selection of the best parents to combine and the best seedlings to advance in cultivar development. Selection for improved fruit quality traits including texture, size, and flavor will thereby be enabled prior to planting young trees or plants in evaluation orchards or field plots, and set the stage for similar advances in other Rosaceae crops.
DNA: The genetic code that controls the structure and function of all organisms, including fruit crops.
Gene: A specific segment of DNA that codes for a certain trait.Marker: A specific DNA segment that is close to a gene of interest and can be
used to predict the presence of the gene.MAPS: Marker‐assisted parent selectionMASS: Marker‐assisted seedling selection
Apple Texture is an example of an important trait that influences consumer preference for apple fruit. Firm, juicy, crisp‐fleshed apples are more desirable than those with soft and mealy flesh.
Marker‐Assisted Breeding
A gene that influences the maintenance of apple texture is known –Md‐ACS1. One variant of this gene results in normal production of the ripening hormone ethylene in fruit. The other variant results in much less ethylene, allowing fruit to maintain excellent texture for longer periods. A DNA marker is available that acts like a flag for the Md‐ACS1 gene, indicating which variant is present.
Breeders can now determine which variants each potential parent has, and thereby design crosses that will yield a large proportion of seedlings with low ethylene production. Those offspring carrying the “wrong” variant can also be weeded out at the very young seedling stage. The breeders avoid wasting resources producing and growing inferior trees.
Selected text courtesy of:
* Participatory workshops will be located in NY, MI, SC, AR, TX, CA, WA, MN, and NH.
RosBREED Meetings & Workshops
Timeline Meeting Location Target Audience Theme
YR 1
RosBREED ISan Diego, CA
Jan 7-8, 2010
RosBREED Participants,
Advisory Panel Members, &
CollaboratorsRosBREED Orientation & Planning
SNP SummitSeattle, WA
May 2010
RosBREED Genomics team
participants & CollaboratorsDesign genotyping platforms in
coordination with international partners.
ASHS WorkshopPalm Springs, CA
August 2010
Non-core breeders & local
Advisory Panel MembersRosBREED Introduction to non-core
Rosaceous crop breeders
YR 2 RosBREED II
East Lansing, MI
Week of March 3rd,
2011
RosBREED Participants,
Advisory Panel Members, &
Collaborators
• Breeding teams perform data analysis.
• Overview of RosBREED goals,
accomplishments, deliverables to date.
•Feedback from AP Members &
Collaborators
YR 3
RosBREED III
East Lansing, MI
Week of March 5th ,
2012
RosBREED Participants,
Advisory Panel Members, &
Collaborators
• Breeding teams perform data analysis.
• Overview of RosBREED goals,
accomplishments, deliverables to date.
•Feedback from AP Members &
Collaborators
Participatory
Workshops
4 locations*
2012
Core and non-core breeders
Local Advisory Panel MembersAssist in MAB adoption by breeders
Stakeholder education
YR 4
RosBREED IVTBD
2013
RosBREED Participants,
Advisory Panel Members, &
Collaborators
• Breeding teams perform data analysis.
• Overview of RosBREED goals,
accomplishments, deliverables to date.
•Feedback from AP Members &
Collaborators
•Final recommendations and program
evaluation
Participatory
Workshops
5 locations*
2013
Core and non-core breeders
Local Advisory Panel MembersAssist in MAB adoption by breeders
Stakeholder education
Regional
Workshops
NY, SC, WA, CA
2013
Regional extension specialists.
Non-core breeders
Industry representatives
MAB training
Technology transfer
Engage stakeholder community
Michael Coe’s Table 1
Will be added when converted to PDF
Michael Coe’s Table 2
Will be added when converted to PDF
Dr. Michael CoeCedar Lake Research and Consulting LLCRole: External evaluation of RosBREED outreach acitivies
RosBREED I AgendaWednesday, January 6, 2010 – Arrive
Evening ‐ Jim McFerson & Amy Iezzoni will coordinate dinner plans for participants who arrive in the afternoon.
Thursday, January 7, 2010 – (Agenda focuses on involving Advisory Panel Members) Meeting Location: Windsor Room, Town and Country Hotel, Mission Valley
San Diego, CA 8:00 – 8:30 Welcome, agenda and self‐introductions – Amy Iezzoni 8:30 – 9:30 Project Overview with time for questions ‐ Amy Iezzoni 9:30 ‐ 9:45 Break 9:45 – 11:45 RosBREED Core breeding programs –Amy Iezzoni moderator. 11:45 – 1:15 Lunch (walk to Mission Valley Food Court) 1:15 – 1:30 Introduction of RosBREED activities – Cameron Peace (Moderator for afternoon session) 1:30 – 2:00 Activity 1 Socio‐Economics – Chengyan Yue 2:00 – 3:00 Activities 2‐4 Genomics‐PBA‐BIMS‐MAB Pipeline – Cameron Peace 3:00 – 3:30 Break 3:30 ‐ 4:00 Activity 5 Extension – Cholani Weebadde 4:00 ‐ 4:15 Activity 5d – Outreach impact evaluation – Michael Coe 4:15 – 5:00 Discussion with AP members ‐ Jim McFerson, moderator 6:00 RosBREED buffet dinner at the Marriott Courtyard San Diego Mission Valley. Synergy Room. (595 Hotel Circle South)
RosBREED I Agenda con’t
Friday, January 8 – (Agenda targets within‐project educational and organizational needs) Meeting Location: Windsor Room, Town and Country Hotel, Mission Valley
San Diego, CA 8:00 – 8:15 Overview of day’s activities – Jim Luby (Moderator of morning session) 8:15 – 8:45 PediMap demo – Roeland Voorrips 8:45 – 9:45 Introduction to FlexQTL and discussion of software targets – Marco Bink & Eric van de Weg 9:45 – 10:15 Break 10:15 – 12:15 Breeder Discussion (Eric, Jim, Dechun, Marco, Nahla, Cameron) Make sure the breeders know what their goals are for the 2010 growing season, including PBG goals for 2010. 12:15 – 1:30 Lunch (Walk to Mission Valley Food Court)
Cholani moderates afternoon session 1:30 – 2:00 PBGworks demo and discussion – Alex Stone (available for Q&A from 2‐3) 2:00 – 4:00 Concurrent activities
Activity 1: PediMAP hands on sessions with breeders split into 3 groups (Prunus, Malus and Fragaria) ‐ Roeland Voorrips & Eric van de Weg
Activity 2: SE breeder interviews
Activity 3: DNA marker polymorphism discussion – Nahla 4:00 – 5:00 Wrap up – Cholani Weebadde and Audrey Sebolt: Identification of any knowledge gaps or organizational items that need to be addressed. Discussion of how progress and potential problems should be communicated to the Administrative Team and/or Team Leaders
Advisory Panel Members
Questions to be thinking about for our discussion at 4:15 PM
1. How can RosBREED build interactive communications on goals, activities, outcomes, and impacts that are mutually beneficial to both RosBREED members and stakeholder groups?
2. How can RosBREED advance the idea that the benefits from RosBREED activities are not defined by state or crop boundaries but should be viewed as regional or national benefits?
3. How can RosBREED communicate goals, activities, outcomes, and impacts to the general public of consumers and tax payers?
4. Are there other projects or on‐going research activities where collaboration with RosBREEDwould produce significant synergies? What are these opportunities?
5. Are there any methods or plans of work that could be done differently to better meet project goals?
6. Are there any misunderstandings of our project that we need to address (e.g. RosBREED is not about GMOs. RosBREED will only help growers who have access to Club varieties)?
7. What was good about RosBREED I?
8. What recommendations do you have for next year so we can make RosBREED II the best use of your time?
RosBREED Staff
Audrey Sebolt – Project Assistant for Communications
Michigan State UniversityA342‐E PSSBEast Lansing, MI 48824517.355.5191 x 1432Cell: [email protected]
Joan Schneider – Project Assistant for Budget
Michigan State UniversityA288 PSSBEast Lansing, MI 48824517.355.5191 x [email protected]