Plant Breeding & Genetics Group

Shaun TownsendCo-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

Genetics and Breeding

Publication, Variety/Germplasm release

Doubled haploids

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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.

Crossing

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 42Doubles 84Moldy Kernels 61Poorly Filled Nuts 25

Nut Length 68Nut Shape Index 65Nut Compression Index 88Nut Weight 63Percent Kernel 87Fiber 56Blanching 64

Relative Husk Length 91Nuts per Cluster 67Catkin Elongation Time 68Nut 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

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

Solanum sp.

64 %21%

10%

NASS 2014

PNWNorth Central Eastern

Southwest

5%

Adapted from Knowles et al (2010)

USA Potato Production 2014

PNW Potato Industry

Processing Industry Fresh Market – Table stock RussetsChipping Specialty – Reds, yellows, etc.Dehy Industry – Potato starch, flour,

etc.

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

Breeding Objectives

Overall Goal:Release & commercialize new potato varieties that will directly benefit all segments of the PNW potato industry

Serious pathogen -cause severe disease on potato

A gene, RMc1(blb), controlling resistance derived from Solanum bulbocastanum has been identified and used in breeding resistant potato lines.

Russet Burbank root s

susceptible to M. chitwoodi

SB 22 roots

resistant to M. chitwoodi

External Symptom Internal Symptom

Columbia Root Knot Nematode

Solanum bulbocastanumDunal

• Wild, diploid potato

• Source of late blight resistance genes

• Source of tuber resistance to Columbia Root Knot Nematode (CRKN)

• Accession SB22 (PI 275187)

BWA

VCF Tools

Samtools

Resistant Susceptible

Illumina Hi-seq 2000 SB22 genome

Resistant Susceptible

SNP calling

68,180 contigs

Genome alignments

Identification of Molecular Markers

Steve StraussDistinguished ProfessorOregon State University

Steve.Strauss@OregonState.Edu

Genetically Engineered Trees

• 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)

Focus in Strauss lab

Study organisms: Poplar plantations

Rapid cycling eucalypts recently proven in

Strauss laboratory

Field trials: Coleopteran resistant Bt-

cottonwoods in eastern Oregon field trial

Control GE

August 2015

RNA interference for sterility (suppression of

endogenous flowering genes)

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 Fusariumroot 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

Introgressedchromosomal 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, cerealBob 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

Infected seed Non-infected seed

Disease can also reduce quality

- Fusarium head blight

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