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Plant Breeding & Genetics Group

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Plant Breeding & Genetics Group 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 0.05H52_0206 3.2 A10133 3.7 A11281A11283 12.5 A3012 13.0 A61467 13.2 A17246 15.8 5149877 19.1 5232930 21.7 52_1426 27.1 A9236A9242 45.5 A35937 49.9 A6527 53.6 A32314 54.8 A34399 55.7 A45497 56.3 A58614 A17329A15122A38678 Doubled haploids 56.9 A33142A11195A39423 A10578A33144 57.2 A35635 57.5 A23020A19878A57310 57.8 A23663 58.1 A52323A45139A54566 59.2 A21751 61.6 53_0654 C13P_LOD:2.7_a: M15H_LOD:5.8_a: 62.2 51_1128C14H_LOD:5.5_a: A62366A16750A62372C14TW_LOD:6.8_a: 64.6 A14013 65.2 A27948 65.8 A58627 C13H_LOD:10.3_a: 66.0 A28098 66.2 A23036 C14P_LOD:9.4_a: 66.4 A53775 - C14LR_LOD:3.5_a:5.6 1.3 C13BC_LOD:6.4_a: 66.5 A13235 - C13BP_LOD:3.1_a:0.4 - 1.7 67.1 A523244.8 - A28510A40667A257840.9 70.6 A38634 C13TKW_LOD:14.3_a: C14H_LOD:6.7_a: 72.3 51_122151_0671 - C14HD_LOD:7.4_a: 5.2 C13HD_LOD:8.6_a: C15HD_LOD:6.3_a: M15HD_LOD:8.3_a: C13H_LOD:12.3_a: C14L_LOD:4.8_a: 52_0441 C14Y_LOD:6.9_a: 72.9 M15M_LOD:5.3_a:6.8 C14TW_LOD:7.6_a: C13P_LOD:5.1_a: 74.6 A39562 M15H_LOD:8.2_a: - 74.8 A59246 6.1 75.5 A2132 - 76.0 A21727 3.3 76.4 A31634A39567A8401 77.6 A33667 78.8 A33802A24436 - 5.4 C15BSR_LOD:5.5_a:7.1 C14L_LOD:3.7_a: - C14BSR_LOD:6.6_a:5.5 - 80.0 52_0713 5.2 - 318.1 - - - - 1.7 2.8 2.1 - 5.6 1.5 80.6 52_0392 1.8 - - - 2.9 2 82.9 A4388A44540 1 A60826 92.5 C15HD_LOD:3.3_a: 93.1 A16532A40446A16546C13BC_LOD:3.1_a: 93.7 A16543 97.3 A28760 101.6A56808A56807A15768 - A10413 4.6 102.2A39511A62319 102.8A39701 105.751_135553_1427 51_051852_0526- 111.9 - 2.3 120.1A40885A40886 1.6 133.252_001853_0098 135.752_054952_116852_0795 138.1A29949 139.3A35656 52_1061A50994A50443 139.9A42576A57844 140.5A50995 141.1A42579 161.6A56719 162.8 A3016 163.1A56725 163.4A15237 163.8A56720 164.2A15242 165.1A26145A6950 Genetics and Breeding 168.95366981 180.353_0524 185.4A17309 187.2A47689A52248 189.0A61559 191.4A19829A19833A19834 194.451_0805 200.451_0783 201.151_009553_092953_0930 202.6A10668 204.1A10672A10673 208.3A25187 210.153_0635 214.451_0819 C13ST_LOD:3.7_a: 216.2A10187 216.9A11995 C13BC_LOD:3.2_a: 227.0A45575 C14SPS_LOD:2.9_a: 229.0 A3583 229.6A39117 236.1A12032 237.4A44849A61082 A6348 C13BG_LOD:5.9_a:75.1 237.8 - 238.6A32892 1.9 244.4A45211 A2340752_1018A43929 - 247.8 C13ST_LOD:31.2_a: A43332 2.3 - 0.8 249.0A44323A44334 C13WC_LOD:16.5_a: C13AA_LOD:35.3_a: Publication, Variety/Germplasm release C13FAN_LOD:36.9_a: C13ST_LOD:35.2_a: 250.2A55919A51223 C13WP_LOD:30.1_a: 251.952_0829 C13ME_LOD:11.4_a: 254.051_0869 262.6A63287A60753A60754 263.2A10542 C13BG_LOD:5_a:66.7 264.952_1141 268.5A31352 276.8A32988A32982A31257 - 279.8A14908 4.6 - - - 18.7 280.4A12049A12052 0.3 4.7 - - 39.6 A61914 0.6 283.1 - 287.1A44414A22962A597180.9 288.8A19168A55993 289.4A54195 290.0A37358 291.253_0382 293.651809_R 294.15784_F569307 The Relationships between Development and Low Temperature Tolerance 294.751_085751_0322 295.953_0958 297.1514026953_148151_0401 298.3512816752448_R 298.951881_F54750752048_F 300.653_12925139089 in Barley Near Isogenic Lines Differing for Flowering Behavior. Cuesta- 301.2548097 302.5546054 303.752_1155 Marcos, A. et al. 2015. Plant and Cell Physiology Volume 56, Issue 12 Pp. 305.653_0769 2312-2324. 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 - External Symptom Internal Symptom cause severe disease on potato A gene, RMc1(blb), controlling resistance derived from Solanum bulbocastanum has been identified and SB 22 roots Russet Burbank root s resistant to M. chitwoodi susceptible to M. chitwoodi used in breeding resistant potato lines. 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 BWA Illumina Hi-seq 2000 SB22 genome Genome alignments Samtools SNP calling Resistant Susceptible VCF Tools 68,180 contigs Genetically Engineered Trees Steve Strauss Distinguished Professor Oregon State University [email protected] 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
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