docEnabling Marker-Assisted Breeding in Rosaceae
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Enabling Marker-Assisted Breeding in Rosaceae
Enabling Marker-Assisted Breeding in Rosaceae Project Director Dedicated to the genetic improvement of U.S. rosaceous crops www.rosbreed.org Amy Iezzoni Michigan State University [email protected] 517.355.5191 x 1391 Team Leaders Breeding James Luby University of Minnesota [email protected] Socio‐Economics Chengyan Yue University of Minnesota [email protected] Marker‐Assisted Breeding Pipeline Cameron Peace Washington State University [email protected] Breeding Information Management System Gennaro Fazio USDA‐ARS Plant Genetic Resources Unit [email protected] Genomics Dorrie Main Washington State University [email protected] Stakeholder Jim McFerson Washington Tree Fruit Research Commission [email protected] Pedigree‐Based Analysis Eric van de Weg Plant Research International – Netherlands [email protected] Extension Cholani Weebaddee Michigan State University [email protected] Genotyping Nahla Bassil USDA‐ARS National Clonal Germplasm [email protected] What is RosBREED? 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. RosBREED Team Members Marco Bink Plant Research International, Netherlands [email protected] Tom Gradziel University of California ‐ Davis [email protected] Susan Brown Cornell Univ. [email protected] James Hancock Michigan State University [email protected] David Byrne Texas A&M d‐[email protected] Raymond Jussaume Washington State University [email protected] John Clark University of Arkansas [email protected] Vicki McCracken Washington State University [email protected] Carlos Crisosto Univ. of California – Davis [email protected] Nnadozie Oraguzie Washington State University [email protected] Thomas Davis Univ. of New Hampshire [email protected] Gregory Reighard Clemson University [email protected] Kate Evans Washington State University [email protected] Alexandra Stone Oregon State University [email protected] Chad Finn USDA‐ARS , Corvallis, OR [email protected] Mykel Taylor Washington State University [email protected] Karina Gallardo Washington State University [email protected] Dechun Wang Michigan State University [email protected] Kenong Xu Cornell University [email protected] Ksenija Gasic Clemson University [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 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 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 Professional interests of RosBREED Advisory Panel members 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. AP Color Key Industry Extension Scientific Bierlink Curtis Perry Sparks Seavert Bliss Alcala Cook Particka van Sickle Hirst Abbott Buell Gardiner Allen Carr Dodd Grim Korson Goldberger Olmstead Sherman Arus Arvai Baugher Moffitt Watkins Cheng Simon Stokes Karp Ross 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) What need does RosBREED address? 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 crops and traits will be targeted in RosBREED? 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. RosBREED core breeders Apple Washington State Univ (Kate Evans) Cornell Univ (Susan Brown) Univ of Minnesota (James Luby) Sweet cherry Washington State Univ (Nnadozie Oraguzie) Tart Cherry Michigan State Univ (Amy Iezzoni) Peach Clemson Univ (Ksenija Gasic) Univ of Arkansas (John Clark) Texas A&M (David Byrne) Univ of California (Tom Gradziel) Strawberry Michigan State Univ (James Hancock) USDA‐ARS Corvallis (Chad Finn) Univ of New Hampshire (Tom Davis) Why now? 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. What is the technology that will be developed and adopted? 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. Why are we working together as a crop family? 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. What are the targets for success? 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. Marker‐Assisted Breeding 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: Gene: Marker: MAPS: MASS: The genetic code that controls the structure and function of all organisms, including fruit crops. A specific segment of DNA that codes for a certain trait. A specific DNA segment that is close to a gene of interest and can be used to predict the presence of the gene. Marker‐assisted parent selection 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. 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: RosBREED Meetings & Workshops Timeline YR 1 YR 2 Meeting Location Target Audience Theme RosBREED I San Diego, CA Jan 7-8, 2010 RosBREED Participants, Advisory Panel Members, & Collaborators RosBREED Orientation & Planning SNP Summit Seattle, WA May 2010 RosBREED Genomics team participants & Collaborators Design genotyping platforms in coordination with international partners. ASHS Workshop Palm Springs, CA August 2010 Non-core breeders & local Advisory Panel Members RosBREED Introduction to non-core Rosaceous crop breeders • Breeding teams perform data analysis. • Overview of RosBREED goals, accomplishments, deliverables to date. •Feedback from AP Members & Collaborators • Breeding teams perform data analysis. • Overview of RosBREED goals, accomplishments, deliverables to date. •Feedback from AP Members & Collaborators RosBREED II East Lansing, MI Week of March 3rd, 2011 RosBREED Participants, Advisory Panel Members, & Collaborators RosBREED III East Lansing, MI Week of March 5th , 2012 RosBREED Participants, Advisory Panel Members, & Collaborators Participatory Workshops 4 locations* 2012 Core and non-core breeders Local Advisory Panel Members Assist in MAB adoption by breeders Stakeholder education YR 3 RosBREED IV TBD 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 Members Assist 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 YR 4 * Participatory workshops will be located in NY, MI, SC, AR, TX, CA, WA, MN, and NH. 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 Coe Cedar Lake Research and Consulting LLC Role: External evaluation of RosBREED outreach acitivies [email protected] RosBREED I Agenda Wednesday, 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 RosBREED would 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 University A342‐E PSSB East Lansing, MI 48824 517.355.5191 x 1432 Cell: 517.230.5506 [email protected] Joan Schneider – Project Assistant for Budget Michigan State University A288 PSSB East Lansing, MI 48824 517.355.5191 x 1359 [email protected]
