Plant Breeding & Genetics Group. Shaun Townsend Co-Director PBG

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1 Plant Breeding & Genetics Group Shaun Townsend Co-Director PBG

2 Outline Introduction PBG Genetic Research Program personnel Research areas Questions

3 Introduction PBG is one part of a larger genetic research component at OSU Plant-based genetic research Primarily in support of plant breeding efforts Initially formed by members of Crop & Soil Sciences and Horticulture

4 Hops Two programs: Shaun Townsend, OSU, Aroma Hops John Henning, USDA, Aroma and bittering hops

5 Hop Challenges Expensive production system Infrastructure & labor Plants immature until third growing season Brewing chemistry extremely complex Dioecy

6 Genetic Approaches Traditional (statistical) Heritability, co-inheritance, BLUP Induced mutations Molecular biology Marker development, genetic diversity, gene discovery Possibly gene editing and transformation

7 OSU Aroma Hops Task is to develop new aroma hop cultivars suitable for the craft beer industry and adapted to Oregon growing conditions. Traits include yield, maturity date, disease resistance, brewing profile

8 Traditional Approaches Understanding heritability of important traits Best Linear Unbiased Predictor (BLUP) Provides information to guide breeding strategy by partitioning observed or measured variation for a trait into genetic and non-genetic causes Superior male genotypes identified

9 Traditional Approaches Induced mutations Subtle changes Limited genetic change Replacement hop cultivars

10 USDA Hops Program Led by John Henning Started in 1933 Most public hop cultivars developed by this program

11 Molecular Approaches Marker development for Marker-Assisted Selection (MAS) Disease resistance, plant sex Sequence the genome Gene discovery Fix pedigree errors Assess genetic diversity

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13 Barley Hordeum vulgare 2n = 2x = Gbp ~ 30,000 genes Self-pollinated (hermaphroditic)

14 The OSU Barley Project Crossing Doubled haploids Genetics and Breeding Publication, Variety/Germplasm release The Relationships between Development and Low Temperature Tolerance in Barley Near Isogenic Lines Differing for Flowering Behavior. Cuesta- Marcos, A. et al Plant and Cell Physiology Volume 56, Issue 12 Pp H _ A A11281 A A A A _ A9236 A A A A A A A58614 A17329 A15122 A A33142 A11195 A39423 A10578 A A A23020 A19878 A A A52323 A45139 A A _ _ A62366 A16750 A62372 A A A A A A A A52324 A28510 A40667 A A _ _ _ A A A A A31634 A39567 A A A33802 A _ _ A4388 A A A16532 A40446 A A A A56808 A56807 A15768 A A39511 A _1355 A _ _ A _ _0018 A _ _ A _ _ A _ A50994 A50443 A42576 A A A56719 A A56725 A A A A A A _ A A A61559 A A _0805 A19833 A _ _ A _ _ A A25187 A _ _ A A A A39117 A A A A A32892 A A A _1018 A43929 A A44323 A _0829 A55919 A _ A A10542 A60753 A _ A A A14908 A32982 A A A61914 A A A19168 A22962 A A54195 A A _ _R _F C14L_LOD:4.8_a:-5.2 C13H_LOD:12.3_a:-5.6 C14BSR_LOD:6.6_a:5.5 C13H_LOD:10.3_a:-5.2 C14H_LOD:6.7_a:-5.4 C15BSR_LOD:5.5_a:7.1 C14L_LOD:3.7_a:-4.6 C13ST_LOD:3.7_a:-1.9 C13BG_LOD:5.9_a:75.1 C14TW_LOD:6.8_a:-0.9 C14P_LOD:9.4_a:-6.1 M15H_LOD:8.2_a:-2 C13BC_LOD:3.2_a:-2.3 C13P_LOD:2.7_a:-1.3 C13BC_LOD:6.4_a:-3.3 C15HD_LOD:3.3_a:-1.6 C13ME_LOD:11.4_a:-0.9 C13BC_LOD:3.1_a:-2.3 C14SPS_LOD:2.9_a:-0.8 C14LR_LOD:3.5_a:5.6 C13BG_LOD:5_a:66.7 M15H_LOD:5.8_a:-1.7 C14H_LOD:5.5_a:-4.8 C13BP_LOD:3.1_a: _ _ _ _ _ _F 52448_R _ _F _ _ M15M_LOD:5.3_a:6.8 C13P_LOD:5.1_a:-1.8 C13HD_LOD:8.6_a:-2.8 M15HD_LOD:8.3_a:-1.5 C13FAN_LOD:36.9_a:-39.6 C13AA_LOD:35.3_a:-18.7 C13ST_LOD:35.2_a:-4.7 C13ST_LOD:31.2_a:-4.6 C13WP_LOD:30.1_a:-0.6 C13WC_LOD:16.5_a:-0.3 C14TW_LOD:7.6_a:-1 C13TKW_LOD:14.3_a:-2.9 C14Y_LOD:6.9_a: C14HD_LOD:7.4_a:-1.7 C15HD_LOD:6.3_a:-2.1

15 Integrating genetics and breeding at a Land Grant University Locus/alleles Phenotype Mechanism Vrn1, Vrn2, Vrn3 Growth habit Loss of function deletions Ppd1, Ppd2 Flowering time Loss of function deletions

16 Barley contributions to beer flavor Deschutes + 6 and the Oregon Promise

17 Hazelnut Program Led by Shawn Mehlenbacher Only hazelnut breeding program in the U.S. Hazelnut production is centered in Oregon

18 Hazelnut Breeding Objectives A. Blanched kernel market (for chocolate, baked goods) (93% of world crop is sold as kernels, 7% sold in-shell) 1. Bud mite resistance 5. Easy pellicle removal 2. Round nut shape 6. Few defects 3. High percent kernel 7. Early maturity 4. Precocity 8. Free-falling nuts 5. High yield B. Resistance to eastern filbert blight (EFB) 1. Simply inherited resistance ( Gasaway & >50 others) 2. Quantitative resistance (e.g. Tonda di Giffoni, Sacajawea )

19 Hazelnut Quantitative Traits Trait Heritability (%) Good Kernels 42 Doubles 84 Moldy Kernels 61 Poorly Filled Nuts 25 Nut Length 68 Nut Shape Index 65 Nut Compression Index 88 Nut Weight 63 Percent Kernel 87 Fiber 56 Blanching 64 Relative Husk Length 91 Nuts per Cluster 67 Catkin Elongation Time 68 Nut Maturity 86 Most traits are highly heritable. Mehlenbacher et al., 1993; Yao & Mehlenbacher, 2000

20 Eastern Filbert Blight Fungus Anisogramma anomala, 2-year life cycle. Cankers girdle and kill branches. We now have > 100 sources of resistance. We use single R-genes and quantitative resistance.

21 Sources of Very High EFB Resistance in C. avellana (greenhouse tests) Accession Origin LG* S-alleles 1. Gasaway Unknown Zimmerman Barcelona x Gasaway Ratoli Spain Georgian OSU Rep. of Georgia OSU Univ. Minnesota OSU Southern Russia (VIR) Culpla Spain Crvenje Serbia Uebov Serbia Moscow N02 Russia (Moscow)? Moscow N23 Russia (Moscow)? Moscow N26 Russia (Moscow)? Moscow N27 Russia (Moscow)? Moscow N37 Russia (Moscow)? Farris OSU Lansing, Michigan? C. avellana COR 157 Finland? Amarillo Tardio Chile (Chillan)? 2 2 *Linkage Group assigned using microsatellite markers

22 Pacific Northwest Potato Breeding and Variety Development Program Jointly funded by USDA-NIFA & Potato Commissions of ID, OR & WA

23 Solanum sp. Range of ploidy: 2X, 3X, 4X and 5X Most cultivated potatoes are tetraploid (2n=4x=48) The basic chromosome number is 12 Haploid genome size is ~900 mb

24 USA Potato Production 2014 PNW North Central Eastern 64 % 21% 10% 5% Southwest NASS 2014 Adapted from Knowles et al (2010)

25 PNW Potato Industry Processing Industry Fresh Market Table stock Russets Chipping Specialty Reds, yellows, etc. Dehy Industry Potato starch, flour, etc.

26 Breeding Objectives Develop new russet potatoes Dual purpose russet varieties (ID) Individual market oriented russet varieties (OR) Breeding for resistance to major pests and diseases PVY, Verticillium wilt, Zebra Chip, TRV, PMTV, CRKN, Scab etc. Breeding of specialty potatoes Reds/yellows/purples High anthocyanins, minerals, carotenoids, Nutrients, Flavor Breeding for cold sweetening resistance and high nutrient efficiency Low acrylamide, low N input Overall Goal: Release & commercialize new potato varieties that will directly benefit all segments of the PNW potato industry

27 Columbia Root Knot Nematode Serious pathogen - cause severe disease on potato A gene, R Mc1(blb), controlling resistance derived from Solanum bulbocastanum has been identified and used in breeding resistant potato lines. External Symptom SB 22 roots resistant to M. chitwoodi Internal Symptom Russet Burbank root s susceptible to M. chitwoodi

28 Solanum bulbocastanum Dunal Wild, diploid potato Source of late blight resistance genes Source of tuber resistance to Columbia Root Knot Nematode (CRKN) Accession SB22 (PI )

29 Identification of Molecular Markers Resistant Susceptible Illumina Hi-seq 2000 BWA SB22 genome Genome alignments SNP calling Samtools Resistant VCF Tools Susceptible 68,180 contigs

30 Genetically Engineered Trees Steve Strauss Distinguished Professor Oregon State University

31 Focus in Strauss lab Genetic engineering approaches to tree breeding, with a focus on poplar (cottonwood) and eucalypts Emphasis on containment for social and regulatory acceptance given wild relatives, long distance gene flow capability Genomic analysis of role of structural polymorphisms in poplar heterosis GWAS analysis of genes that control variation in capability for genetic engineering (major new, $4 million NSF project)

32 Study organisms: Poplar plantations

33 Rapid cycling eucalypts recently proven in Strauss laboratory

34 Field trials: Coleopteran resistant Btcottonwoods in eastern Oregon field trial Control GE

35 RNA interference for sterility (suppression of endogenous flowering genes) August 2015

36 Policy analysis relevant to GE crops and trees many lab contributions

37 Vegetable Breeding & Genetics Various species Snap beans Snap peas Broccoli Tomatos Cucurbits Traditional and organic production

38 Disease Resistance in Bean Genetic resistance in beans to Fusarium root rot Screened 148 bean varieties in Oregon Associated morphological traits to resistance Used Single Nucleotide Polymorphism (SNP) to identify markers for MAS Created a linkage map

39 Indigo Rose Tomato Introgressed chromosomal segments from a wild relative into tomato High levels of healthful flavanoids

40 Ornamental Breeding & Genetics Various landscape ornamentals Maples Cape hyacinth Sweetbox Flowering currant Many others

41 Plant Sterility Genetic work to support plant breeding effort Ploidy manipulation to induce sterility (ie. triploids) in nonnative species Mutagenesis via chemical and physical means Traditional genetic research (ex. heritability)

42 Genetic Work Interspecific hybridization in Lilac Heritability of floral traits in Hibiscus syriacus Cytogenetics of various woody shrubs

43 Winter Wheat Breeding Program Soft white winter wheat Cakes, cookies, pancakes Hard white winter wheat Noodles, bread Hard red winter wheat Bread, rolls, cereal Bob Zemetra

44 Program Goal Increase profitability of growing wheat for Oregon producers How: Boost production - yield Decrease costs - disease resistance Boost demand - high quality

45 Disease Resistance In some cases, genetic resistance is the only option Barley Yellow Dwarf (BYDV) Wheat Mosaic Virus (sbwmv) Viruses have a great impact on yield and quality

46 Barley Yellow Dwarf Virus 30-40% yield loss Resistance gene bdv2 from Oklahoma germplasm Moving gene into Oregon germplasm

47 Wheat Mosaic Virus Soil-borne Only control is genetic resistance sbwm1 gene from midwest and New York

48 Disease can also reduce quality - Fusarium head blight Infected seed Non-infected seed

49 Fusarium head blight - Fungal disease that infects the head and seed - Disease reduces yield and seed quality - Pathogen produces a toxin making the seed useless for animal and human consumption - Source of resistance gene Fhb1 and QTLs Michigan and New York germplasm - Breeding program transferring Fhb1 and QTL for FHB resistance into OSU germplasm

50 Other Programs Jennifer Kling - Quantitative genetics Kelly Vining - Mint breeding & genomics Laurent Deluc - Grape genomics Chad Finn - USDA, Berry breeding & genetics