Apple Rootstock Selection

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Information about Apple Rootstock Selection
Business & Mgmt

Published on February 16, 2014

Author: organicgrant



An overview of apple rootstock development and selection

Concepts of Apple Rootstock Breeding and Selection: A Journey Through the Development of New Apple Rootstocks G. Fazio, H. Aldwinckle, T. Robinson

Introduction Breeding work for the Geneva® rootstocks was initiated by Drs. Cummins and Aldwinckle in 1967. The USDA/Cornell program is actively breeding and selecting new rootstocks (about 2,500 in the pipeline) – Dr. Aldwinckle and Dr. Robinson represent Cornell University in the program. The program, has always focused on developing yield efficient, disease resistant rootstocks (fire blight, etc). It is now focusing on characterization of other important traits such as replant disease resistance, drought tolerance, cold tolerance, etc.

Apple Harvest Doud family farm (1916, Miami Co. Indiana)

Auvil Fruit Farm (Vantage, WA 2005 – next to Columbia River)

Benefits from the implementation of dwarfing rootstocks Less sprays Less ladder accidents Increased productivity

Improving Rootstocks for Superior Tree Performance Fruit Color and Quality Fruit Size Disease Resistance Plant Architecture – Dwarfing Molecular mapping and selection tools Genomics Yield and productivity (Nutrition) Precocity Abiotic Stress Resistance (Cold) Disease Resistance Fire blight ($40M 2000 epidemic, MI) Replant disease complex TRANSGENIC ROOTSTOCKS for a plethora of traits

Active Apple Rootstock Breeding Programs 1970s and 80s Quebec Malling Sweden Norway Russia Vineland Poland Japan Michigan Geneva Germany Czech

Active Apple Rootstock Breeding Programs 2005 Russia S. Korea Japan China Geneva New Zealand

New and Experimental Apple Rootstocks in the U.S. Polish Czhec Malling Russia Vineland Quebec Japan Germany Geneva P.14 JTE-B AR-86-1-20 Bud 57-195 V.1 SJP84-5218 JM1 Supp. 1 G.11 P.22 JTE-C AR-86-1-25 Bud 60-160 V.2 SJP84-5217 JM2 Supp. 2 G.16 JTE-D AR-295-6 Bud 61-31 V.3 SJP84-5198 JM3 Supp. 3 G.41 AR-931-15 Bud 62-396 V.4 SJP84-5162 JM7 Supp. 4 G.65 AR-440-1 Bud 64-194 V.7 SJP84-5231 Marubakaido PiAu 56-83 G.935 AR-680-2 Bud 65-838 SJP84-5174 G.30 AR-486-1 Bud 67-5(32) SJP84-5189 CG.2001 AR-628-2 Bud 70-8-8 SJP84-5180 CG.2003 AR-69-7 Bud 70-20-21 CG.2006 AR-360-19 Bud 71-3-150 CG.2022 M.20 Bud 71-7-22 CG.2034 CG.2406 CG.3142 CG.3736 CG.3902 CG.4001 CG.4002 CG.4003 CG.4004 CG.4005 CG.3001 CG.4011 CG.4013 CG.4018 CG.4019 CG.4021 CG.4038 CG.4049 CG.4088 CG.3007 CG.4094 CG.4113 CG.4172 CG.4210 CG.4213 CG.4214 CG.4247 CG.4288 CG.3029

Geneva Rootstock Selection Traits TRAIT Fire Blight resistance Phytopthora resistance Replant Disease Complex Wholly apple aphid res. EVALUATION YEARS 1 or 7 1 1 or 7 1 LOCATION Greenhouse/Field Greenhouse Greenhouse/field Greenhouse Juvenility - Spines 3-4 Field/Stoolbed Stoolbed rooting 3-4 Field/Stoolbed Growth habit - Brittleness 3-4 Field/Stoolbed Dwarfing 8-12 Orchard Precocity 8 Orchard Suckering 8 Orchard Yield – Biennial bearing 12 Orchard Cold hardiness Drought tolerance Graft union compatibility 15 Orchard 4 Orchard 5 Orchard

Insects and diseases of apple rootstocks Fire blight (Erwinia amylovora) Crown rot, root rot (Phytophthora spp.) Woolly Apple Aphid (Eriosoma lanigerum) Southern Blight (Sclerotium rolfsii) White root rot (Rosellinia necatrix) Texas root rot (Phymatotrichum omnivora)

Apple Rootstock Breeding: Resources and Activities Orchard Production Lab & Greenhouse -Seedling inoculations -Molecular markers -Tissue culture -Plant pathology -ETC. -Individual yield and growth -Disease incidence -Scion compatibility -ETC. Nursery -Liner production -Tree Production -Stoolbed evaluation -Transplant Evaluation -ETC. Apple Rootstock Breeding is a very resource intensive endeavor.

Apple Rootstock Breeding and Selection Protocols Stage 1 Stage 2 Stage 3 Stage 4 Stage 5 Stage 6 Stage 7 Stage 8 Stage 9 Stage 10 Years 1-2 Objective 1.1 Years 3-4 Years 5-6 Years 7-12 Years 10-15 Years 16-18 Years 19-21 Years 22-24 Years 25-27 Years 27-30 1. Select elite parents Critical Juncture: Molecular information about allelic constitution at disease resistance loci and about other important traits can be used to bypass first test orchard. 2. Generate F1 populations 3. Stratify and plant populations 4. MAS for dwarfing, precocity, disease resistance, etc. 5. Disease screening 6. Plant selected stools Repeated inoculations with Fireblight, Wooly Apply Aphid, Phytophtora, Powdery Mildew and comparison to known standards 7. Stool selection 8. Propagation and grafting 9. First test orchard 10. First test evaluation and selection 11. Elite stoolbed establishment 12. Stress tolerance tests - drought, cold hardiness, graft union strength 13. Elite liner and tree production 14. Elite stoolbed selection and distribution to nurseries 15. Intermediate replicated orchard 16. Intermediate orchard evaluation 17. Commercial stoolbed evaluation 18. NC-140 and cooperator trials (national and international) 19. Commercial production ramp up Patent and UPOV protection 20. Comercial sale Contingent on goodness of MAS Highly replicated first test orchard at multiple sites Test orchard Evaluation and Selection Elite stoolbed establishment Stress tolerance tests - drought, cold hardiness, graft union strength Elite stoolbed selection and distribution to nurseries Commercial stoolbed evaluation and distribution of trees to trial sites NC140 and cooperator trials (national and internationa) Commercial production ramp up Commercial sale Feedback from Horticultural Traits evaluations, disease resistance evaluations, stress tolerance evaluationswill be combined with molecular data and used in subsequent cycles of selection. Elite material from these evaluations are used as parents in subsequent cycles. These Stress Tolerance Tests willl have to be highly replicated at each location - therefore only a few selections at a time will be tested. Grower cooperators in cold or drought prone areas in the US will be selected for cold hardiness and drought stress. For graft union compatibility and strength a set of rootstocks will be grafted with multiple scions and graft unions tested after 3 years.

Breeding and Selection of Apple Rootstocks - Simplified 10,000 Number of genotypes observed Number of replications per genotype Number of plants 1000 Transgenic “value-added” traits 100 10 1 1 2 3 4 5 6 7 8 Time (3 year stages) 9 10 B. Johnson

Criteria for Parent Selection – Phenotype and Molecular Markers Dwarfing Precocity Disease Resistance Fire Blight AD13 SCAR scab marker (Boudichevskaia et al. 2006) Phytopthora Powdery Mildew Apple Scab Yield and Field Performance “New” Gene Pools EM M01 SCAR powdery mildew marker (Evans et al. 2003)

New Gene Pools at the Plant Genetic Resources Unit (PGRU) Geneva, New York Malus - Apple - 3995 accessions 2430 clones (grafted) and 1565 seedlots from wild 2808 wild Malus seedlings from 310 populations from Kazakhstan, Russia, China & Turkey

Malus sieversii from Kazakhstan 1989 - 1996 Site 9 w/ depletion by grazing animals Excellent apple-scab resistance from some sites Site 5 Site 6

Gene Pool Identification – Combining SSR, SCAR Markers MM.111 PiAu5683 M.2 MM.106 M.13 P.14 M.1 M.7P.18PiAu5111 J-TE-C V.1 M.27 M.11 G.65 M.10 M? M.3 0.81 G.41 0.14 G.202 J.9 Pi80 M.9T337 B.118 PiAu514 M.9 M.26 J-TE-G M.8 M.20 M.25 V.7 V.2 G.11 G.30 G3007 G.935 G5179 R.5 III III Alnarp M.4 O.3 B.9 P.1 B.491 JM.10 -0.52 -0.52 1.00 0.47 0.47 -1.19 II -0.06 G.16 Novole Maruba NAGA -0.59 -1.11 -1.86 -1.86 -1.03 -0.59 -0.15 I 0.29 0.29 G3007 G.935 O.3 G5179 G.202 G.30 G.11 B.9 M.8 M.20 J.9 JM.10 J-TE-G Pi80 M.9 M.9T337 V.2 M? P.1 P.14 G.16 V.1 G.41 M.27 G.65 PiAu5111MW M.10 M.13 M.26 Alnarp PiAu514 M.1 M.2 M.4 M.11 M.3 PiAu5683 M.7 PiAu5111 P.18 R.5 V.7 J-TE-C M.25 MM.106 MM.111 B.491 B.118 Maruba NAGA Novole 0.00 0.72 0.21 0.42 Coefficient 0.63 0.83

Crossing Parents – Stage 1

Crossing Parents – Stage 1

Seed Harvest – Stage 1 – 2,000-10,000 seeds per cross

Disease Screens – Stage 1 – 3,000 to 10,000 seedlings/year

Disease Screens – Stage 1 – 3,000 to 10,000 seedlings/year

Fire blight - Erwinia amylovora Major disease for apple rootstocks in North America Bacterial disease with strain differentiation Resistance sources available Rootstock infection routes: suckers injuries systemic movement of bacteria from scion

Fire Blight Screening – Stage 1 500 to 2,000 seedlings

Integration of Marker Assisted Selection – Stage 2 High throughput PCR markers – SCARs, SSRs Target traits: Dwarfing Powdery mildew resistance Scab resistance Wooly apple aphid resistance Use published and “in house” markers

Propagation and Evaluation of Layering Stool-Bed Properties

Harvest of Rootstock Liners – Evaluation of Rooting

Rootstock Liners in Tree Nursery for Budding/Grafting

First Test Orchard – Stage 3 3-10 replicates per rootstock genotype 50-100 different genotype selections every year All grafted with same scion Evaluated for 8-12 years

Early field selection of precocious genotypes – Stage 4

Expansion of Layering Beds to Increase Replications – Stage 4

Evaluation of Layering Stool Beds – Stage 5

Rootstock Liner Evaluation – Stage 5

Second Test for Resistance to Biotic Stresses – Stage 5 Inoculation with Wooly Apple Aphid (Eriosoma lanigerum) Water Logging test with Phytophthora Inoculation Fire Blight Inoculations with Multiple Strains

Replicated Orchard Trials in Multiple Locations – Stage 6 Precocity Yield Fruit Size Dwarfing Tree Survival Disease Incidence Tree Architecture Burr Knots

Cumulative Yield Efficiency Measurements Descriptive Statistics M.9 Variable: CUM-YEFF Anderson-Darling Normality Test A-Squared: P-Value: 0.5 2.0 3.5 5.0 17.106 0.000 8.0 95% Confidence Interval for Mu 2.59040 1.19212 1.42114 1.75248 3.70960 317 Minimum 1st Quartile Median 3rd Quartile Maximum 6.5 Mean StDev Variance Skewness Kurtosis N 0.24800 1.87200 2.20500 2.91550 8.18500 95% Confidence Interval for Mu 2.45867 2.08 2.18 2.28 2.38 2.48 2.58 2.68 2.78 2.72214 95% Confidence Interval for Sigma 1.10598 1.29292 95% Confidence Interval for Median 95% Confidence Interval for Median 2.13806 2.34268

Replicated Orchard Trials in Multiple Locations – Stage 6 Descriptive Statistics Variable: Suckers Anderson-Darling Normality Test A-Squared: P-Value: 10 40 70 100 130 160 95% Confidence Interval for Mu Mean StDev Variance Skewness Kurtosis N 21.1430 29.4424 866.858 2.55072 8.75868 317 Minimum 1st Quartile Median 3rd Quartile Maximum 190 27.087 0.000 0.000 2.000 9.500 29.166 204.000 95% Confidence Interval for Mu 17.889 5 15 25 24.397 95% Confidence Interval for Sigma 27.315 31.932 95% Confidence Interval for Median 95% Confidence Interval for Median 6.719 13.403

Timing of fire blight screens Number of genotypes observed Number of replications per genotype 9 Rootstock blight orchard trials Number of plants 1 Transgene mediated resistance Strain specific direct inoculation 5 screens 1 2 Time


Commercial Stool Bed Trials – Stage 7 On site trials of elite rootstocks at commercial nursery locations Evaluate liner productivity and quality under commercial conditions Generates nursery stock for major orchard trials (NC-140, large grower trials)

Program Protocol Trials with NC-140 Cooperators – Stage 8

Drought Tolerance Tests Work of Dr. PARRA

Graft Union Strength Tests Pictures Courtesy of Mike Parker (NC State University)

On Farm and Nursery Trials in Several U.S. Locations – Stage 9 Large scale trials planted in WA, PA, MI, NY Trials include 20-45 different genotypes

Nursery Tree Measurements on 10-15 Trees per Rootstocks Branch Length Tree Height Branch Angle 0=Flat 90=Upright Total Number of Branches Branch Height

Branch Angles of Brookfield Gala Trees on Several Dwarfing Rootstocks for 7 W hirls Branch Angle (0=Flat 90=Upright) 60 2034 2406 3041 50 40 4210 4213 4214 4814 5935 B9 G11 30 20 10 0 1 2 3 4 Whirl (3 branches) 5 6 7 G16 G? M9

Stages of Micro-Propagation Prior to Release – Stage 10

Commercial Release and Continued Testing – Stage 10 Program has released 6 new rootstock genotypes to date. G.16 and G.30 G.202, G.41, G.935, G.11 are commercially available in U.S. Release decision for six more elite rootstock genotypes expected in 2008.

Large Scale Production of Rootstock Liners

Production of High Quality Nursery Trees and Adoption By Growers Nursery trees on Geneva 202 rootstocks and planted in high density orchard.

QTL Mapping of Apple Rootstock Yield & Disease Resistance Traits F2 0.0 1.5 2.6 3.7 4.8 7.7 12.0 CH02f06 E32M41-0208 E31M41-0089 G15-1250 CH02c02a E35M41-3500 E35M37-0318 15.4 17.0 E35M41-0193 E35M32-0272 22.5 23.5 E35M42-0282 E33M36-0192 1.20 Sieversii596280 Sieversii596283 Orientalis594101 PI594103 Sieversii596282 6589 Pi-Au56-83 NAGA Kansuenesis59409 AR486-1 Maruba M8 Asiatica594009 WijcikMacP18 Novole AR295-6 ReinetteSim Seiboldii594094 B9 YellowTrans J9 AR628-2 P1 Fusca589975 Pi-Au51-4 M26 Fusca589941EsopusSpitzenJM7 5046 NSpy Pi-Au51-11 J-TE-G B118 J-TE-CM27CrimsonBeauty P14 Tschonoskii58939 GoldenDel M7 JM4 V1 MM111 Supp4 Orientalis590015 M9 P22 NAKB337 B491 MM106 V2 G65 G16 Toringoides58939 Transitoria58942 6006G30 Transitoria58938 7707 5257179 4213 5030 54214 4013 4210 5935 6143 Ioensis590015 6210 50126874 5757 5087 3041 6969 6879 5890 Angustifolia5897 4814 G11 6253 3007 GH589882 4202 0.85 II 0.21 0.55 III -0.10 44.8 46.4 47.4 48.1 48.7 49.5 50.3 52.3 53.5 63.3 65.7 66.8 67.7 75.3 AD04-450 CH02c06 AA12-2200 E35M35-0178 E35M32-0460 E36M41-0590 CH03d10 E35M41-1000 E35M35-1500 E32M41-0650 CH02b10 C10-750 CH02a04y K13-350 E37M32-0113 E33M37-0172 E33M36-0194 CH05e03 E37M36-0195 CH03d01 NZ03c01z P14-750 E32M42-0340 F05-1500 -0.75 -1.05 -1.69 -1.40 -1.53 -0.42 Coronaria589976 Nertchinsk R5 -0.87 I -0.21 0.45 1.11 Dr. Wan Yizhen Construct a molecular map of Apple Rootstock using microsatellites, SNP, SCAR. Map and develop markers for plant architecture and disease resistance traits. Develop basic knowledge on Chinese apomictic species for seed propagated rootstocks. Transgenic approaches for improving rootstock performance.

Research Work on Apple Rootstocks Requires Many Collaborators and Institutions Cornell University: T. Robinson (Orchard Systems) I. Merwin (Horticulture - Replant) H. Aldwinckle (Plant Pathology) L. Cheng (Physiology) S. Brown (Scion Breeding) Michigan State University: R. Perry (Rootstocks) S. VanNocker (Genomics) Washington State University: B. Barrit (Scion Breeding) D. Main (BioInformatics) USDA ARS PGRU: A. Baldo (BioInformatics) P. Forsline (Apple Collection) USDA ARS AFRS Kearneysville: J. Norelli (Transgenics) C. Bassett (Stress Physiology) USDA ARS Wenatchee: M. Mazzola (Plant Pathology) Y. Zhu (Genomics) PENN State University: T. McNellis (Genomics) J. Schupp (Horticulture) Over 40 scientists as NC-140 collaborators Washington Tree Fruit Research Commission

BASIC SCIENCE Genomics, Proteomics Gene Discovery, Expression Physiology APPLIED SCIENCE Plant Breeding Genetic Transformation VERY APPLIED SCIENCE Horticultural Trait Evaluation Widespread Field Performance Field Recommendations NC-140 INDUSTRY, GROWERS, PROCESSORS, CONSUMERS

Genomic Revolution We know that M.7 rootstock is less precocious than M.9. Do we know why? We know that M.9 dwarfs more than M.26? Do we know why? Through Genomics much is being discovered about how rootstocks do all that they do. NSF funded project that aims to discover what genes are turned on and off in the apple scion by different rootstocks. (Dr. McNellis, Penn State) Tree architecture modified by apple rootstocks…. Wealth of new genetic material

The Geneva® Apple Rootstock Breeding Program THANK YOU Todd Holleran, Sarah Bauer, Yizhen Wan Funding from IDFTA, WTFRC, USDA, Cornell

The Road Ahead (2003 NC-140 Mtgs. Door County, Wisconsin)

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