Plant Breeding & Genetics Group Shaun Townsend Co-Director PBG
Outline Introduction PBG Genetic Research Program personnel Research areas Questions
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
Hops Two programs: Shaun Townsend, OSU, Aroma Hops John Henning, USDA, Aroma and bittering hops
Hop Challenges Expensive production system Infrastructure & labor Plants immature until third growing season Brewing chemistry extremely complex Dioecy
Genetic Approaches Traditional (statistical) Heritability, co-inheritance, BLUP Induced mutations Molecular biology Marker development, genetic diversity, gene discovery Possibly gene editing and transformation
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
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
Traditional Approaches Induced mutations Subtle changes Limited genetic change Replacement hop cultivars
USDA Hops Program Led by John Henning Started in 1933 Most public hop cultivars developed by this program
Molecular Approaches Marker development for Marker-Assisted Selection (MAS) Disease resistance, plant sex Sequence the genome Gene discovery Fix pedigree errors Assess genetic diversity
Barley Hordeum vulgare 2n = 2x = 14 5.3 Gbp ~ 30,000 genes Self-pollinated (hermaphroditic)
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. 2015. Plant and Cell Physiology Volume 56, Issue 12 Pp. 2312-2324. 5H 0.0 52_0206 3.2 A10133 3.7 A11281 A11283 12.5 A3012 13.0 A61467 13.2 A17246 15.8 5149877 19.1 5232930 21.7 52_1426 27.1 A9236 A9242 45.5 A35937 49.9 A6527 53.6 A32314 54.8 A34399 55.7 A45497 56.3 A58614 A17329 A15122 A38678 56.9 A33142 A11195 A39423 A10578 A33144 57.2 A35635 57.5 A23020 A19878 A57310 57.8 A23663 58.1 A52323 A45139 A54566 59.2 A21751 61.6 53_0654 62.2 51_1128 64.6 A62366 A16750 A62372 A14013 65.2 A27948 65.8 A58627 66.0 A28098 66.2 A23036 66.4 A53775 66.5 A13235 67.1 A52324 A28510 A40667 A25784 70.6 A38634 72.3 51_1221 51_0671 72.9 52_0441 74.6 A39562 74.8 A59246 75.5 A2132 76.0 A21727 76.4 A31634 A39567 A8401 77.6 A33667 78.8 A33802 A24436 80.0 52_0713 80.6 52_0392 82.9 A4388 A44540 92.5 A60826 93.1 A16532 A40446 A16546 93.7 A16543 97.3 A28760 101.6 A56808 A56807 A15768 A10413 102.2A39511 A62319 102.851_1355 A39701 105.751_0518 53_1427 111.9A40885 52_0526 120.152_0018 A40886 133.252_0549 53_0098 135.7A29949 52_1168 52_0795 138.1A35656 139.352_1061 139.9 A50994 A50443 A42576 A57844 140.5A50995 141.1A56719 A42579 161.6 162.8A56725 A3016 163.1A15237 163.4A56720 163.8A15242 164.2A26145 165.15366981 A6950 168.953_0524 180.3A17309 185.4A47689 187.2A61559 A52248 189.0A19829 191.451_0805 A19833 A19834 194.451_0783 200.451_0095 201.1A10668 53_0929 53_0930 202.6A10672 204.1A25187 A10673 208.353_0635 210.151_0819 214.4A10187 216.2A11995 216.9A45575 227.0 229.0A39117 A3583 229.6A12032 236.1A44849 237.4 A61082 237.8A32892 A6348 238.6A45211 244.4A23407 247.8 52_1018 A43929 A43332 249.0A44323 A44334 250.252_0829 A55919 A51223 251.951_0869 254.0A63287 262.6A10542 A60753 A60754 263.252_1141 264.9A31352 268.5A32988 276.8A14908 A32982 A31257 279.8A12049 280.4A61914 A12052 283.1A44414 287.1A19168 A22962 A59718 288.8A54195 A55993 289.4A37358 290.053_0382 291.251809_R 293.65784_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:0.4 294.151_0857 569307 294.753_0958 51_0322 295.95140269 297.15128167 53_1481 51_0401 298.351881_F 52448_R 298.953_1292 547507 52048_F 300.6548097 5139089 301.2546054 302.552_1155 303.753_0769 305.6 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:-318.1 C14HD_LOD:7.4_a:-1.7 C15HD_LOD:6.3_a:-2.1
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
Barley contributions to beer flavor Deschutes + 6 and the Oregon Promise
Hazelnut Program Led by Shawn Mehlenbacher Only hazelnut breeding program in the U.S. Hazelnut production is centered in Oregon
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 )
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
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.
Sources of Very High EFB Resistance in C. avellana (greenhouse tests) Accession Origin LG* S-alleles 1. Gasaway Unknown 6 3 26 1. Zimmerman Barcelona x Gasaway 6 1 3 2. Ratoli Spain 7 2 10 3. Georgian OSU 759.010 Rep. of Georgia 2 4 20 4. OSU 408.040 Univ. Minnesota 6 15 27 5. OSU 495.072 Southern Russia (VIR) 6 6 30 6. Culpla Spain 6 9 10 7. Crvenje Serbia 6 6 23 8. Uebov Serbia 6 12 16 9. Moscow N02 Russia (Moscow)? 6 20 10. Moscow N23 Russia (Moscow)? 6 30 11. Moscow N26 Russia (Moscow)? 1 29 12. Moscow N27 Russia (Moscow)? 19 23 13. Moscow N37 Russia (Moscow)? 1 6 14. Farris OSU 533.029 Lansing, Michigan? 3 11 15. C. avellana COR 157 Finland? 9 25 16. Amarillo Tardio Chile (Chillan)? 2 2 *Linkage Group assigned using microsatellite markers
Pacific Northwest Potato Breeding and Variety Development Program Jointly funded by USDA-NIFA & Potato Commissions of ID, OR & WA
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
USA Potato Production 2014 PNW North Central Eastern 64 % 21% 10% 5% Southwest NASS 2014 Adapted from Knowles et al (2010)
PNW Potato Industry Processing Industry Fresh Market Table stock Russets Chipping Specialty Reds, yellows, etc. Dehy Industry Potato starch, flour, etc.
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
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
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 275187)
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
Genetically Engineered Trees Steve Strauss Distinguished Professor Oregon State University Steve.Strauss@OregonState.Edu
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)
Study organisms: Poplar plantations
Rapid cycling eucalypts recently proven in Strauss laboratory
Field trials: Coleopteran resistant Btcottonwoods in eastern Oregon field trial Control GE
RNA interference for sterility (suppression of endogenous flowering genes) August 2015
Policy analysis relevant to GE crops and trees many lab contributions
Vegetable Breeding & Genetics Various species Snap beans Snap peas Broccoli Tomatos Cucurbits Traditional and organic production
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
Indigo Rose Tomato Introgressed chromosomal segments from a wild relative into tomato High levels of healthful flavanoids
Ornamental Breeding & Genetics Various landscape ornamentals Maples Cape hyacinth Sweetbox Flowering currant Many others
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)
Genetic Work Interspecific hybridization in Lilac Heritability of floral traits in Hibiscus syriacus Cytogenetics of various woody shrubs
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
Program Goal Increase profitability of growing wheat for Oregon producers How: Boost production - yield Decrease costs - disease resistance Boost demand - high quality
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
Barley Yellow Dwarf Virus 30-40% yield loss Resistance gene bdv2 from Oklahoma germplasm Moving gene into Oregon germplasm
Wheat Mosaic Virus Soil-borne Only control is genetic resistance sbwm1 gene from midwest and New York
Disease can also reduce quality - Fusarium head blight Infected seed Non-infected seed
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
Other Programs Jennifer Kling - Quantitative genetics Kelly Vining - Mint breeding & genomics Laurent Deluc - Grape genomics Chad Finn - USDA, Berry breeding & genetics