Public Bean Breeding in Ontario Research Update

AAFC/U of G Bean Breeding ProgramOPCC Research Day; March 23, 2012

Outline • Breeding Objectives

• Historical Improvement in Bean Varieties

• Disease Resistance

• N-Fixation studies

• G x E Interaction

• New and upcoming varieties

AAFC/UofG Bean Breeding Program Objectives

Objective GrowerSeed

Company Buyer Processor Consumer Variation Heritability Selection Parental Progeny Elite

AgronomicsYield H L-M H

Maturity H H H

Canopy Architecture M L-M H

Biotic stress Resistance/ToleranceCBB H M H

Anthracnose H H H

BCMV H H H

White Mould L L L

Root Rot L L L

SCN H ? L

Abiotic Stress ToleranceN use efficiency M M L

End-User TraitsSeed Appearance H H H

Cooking/Canning H M L

Non/Slow Darkening ? H M H

Composition M ? L

Protein M ? L

Starch M ? L

Health Promoting ? ? ?

Value Chain Prospects of gain Selection

CONTRIBUTION OF GENETIC IMPROVEMENT IN YIELD INCREASE AND DISEASE RESISTANCE IN NAVY BEANS RELEASED IN CENTRAL CANADA

SINCE 1930’s.

Navabi, A., A. Burt, T. Rupert, T. H. Smith, C. Gillard and K. P. Pauls

Yield Gain in Navy Bean Varieties since 1940s

Yiel

d (K

g ha

-1)

2400

2600

2800

3000

3200

3400

3600

3800

4000

4200

4400

Year of Release1940 1950 1960 1970 1980 1990 2000 2010

AC Compass

AC Cruiser

AC Hensall

AC Mast AC Trident

Centralia Corvette

Crestwood ExRico_23

HR177

Apex

HR200

Harofleet

Harokent

Lightning

Michelite

Nautica

Rexeter

OAC Laser

OAC Rico

OAC Seaforth

OAC Speedvale

OAC Thunder

Saginaw Sanilac

Seafarer

Vista

Y = 17.6x – 31650

P < 0.01

Change in Canopy Height Over TimeC

anop

y H

eigh

t (cm

)

Year of Release

4344454647484950515253545556575859606162

1940 1950 1960 1970 1980 1990 2000 2010

AC Compass

AC Cruiser

AC Hensall

AC Mast

AC Trident

Centralia

Corvette Crestwood

ExRico_23

HR177

Apex

HR200

Harofleet

HarokentLightning

Michelite

Midland

Nautica

Rexeter

OAC Laser

OAC Rex

OAC Rico

OAC Seaforth

OAC Speedvale

OAC Thunder

Saginaw

Sanilac

Seafarer

Vista

Y = 0.16x - 259.45

p < 0.01

Change in “Time to Maturity” over TimeD

ays

to M

atur

ity

73

74

75

76

77

78

79

80

81

82

83

84

85

86

87

88

89

90

Year of Release1940 1950 1960 1970 1980 1990 2000 2010 2020

AC Compass

AC Cruiser

AC Hensall

AC Mast

AC Trident

Centralia

Corvette

Crestwood ExRico_23

HR177

Apex

HR200 Harofleet

Harokent

Lightning

Michelite

Midland

Nautica

Rexeter

OAC Laser

OAC Rex OAC Rico

OAC Seaforth OAC Speedvale

OAC Thunder

Saginaw

Sanilac

Seafarer

Vista

CB

B S

core

(0-5

)

0

1

2

3

4

5

Year of Release

1940 1950 1960 1970 1980 1990 2000 2010 2020

Michelite

Corvette

Sanilac

Saginaw

Seafarer

ExRico23Harofleet

Harokent

Midland

OAC Rico

Seaforth

Crestwood

CentraliaVista

Laser

Speedvale

Hensall

Compass

Thunder

TridentAC Mast

Cruiser

OAC Rex

Nautica

Lightning

HR177

Apex

HR200Rexeter

OAC 09-4

Gain in CBB Resistance Since 1940s

Race 73 ResistanceA

nthr

acno

se (r

ace

73) S

core

(1-1

0)

2

3

4

5

6

7

8

9

Year of Release1940 1950 1960 1970 1980 1990 2000 2010

AC Compass

AC Cruiser AC Hensall

AC Mast Centralia

Corvette

Crestwood ExRico_23 HR177

Apex HR200

Harofleet

HarokentMichelite

NauticaOAC Laser

OAC Rico

OAC Seaforth

OAC Speedvale

OAC Thunder

Saginaw

Sanilac

Seafarer

Vista

Rexeter

Cultivar and Germplasm Development; breeding pipelineCrossing

Head Rows (n = 2000) (Low CHU)

F1 (n=200) Top and Backcross

F2 -Fn (ON – Puerto Rico)3 - generations per year

F2 -FnModified Bulk

F5 Bulk Populations (n = 200) 2 locations (High and low CHU)

Preliminary Yield Trials (2 locations; High and Low CHU)Mesoamerican: E, M, and F Andean: E, M, and F

Advanced Yield Trial (2 locations; High and Low CHU)Mesoamerican: E, M, and F Andean: E, M, and F

Ontario Dry Bean (White & Colored) Registration Trials4-6 locations per year for two years

F2 -Fn3 - 4 generations per year SSD

Germplasm Introduction CIAT C-BATDBCNInternational

Cooking / Canning Quality Pre Cooking (Instrumental)Post Cooking (Instrumental)Post Cooking (Visual)NIR (Protein, Starch, Poly Sach)

Marker screeningSU91 (CBB), UBC420 (CBB), SAS13 (Anth.), SW13 (BCMV)

Resource-PoorEnvironment Testing

Field Screening

Head Rows (n = 2000) (High CHU)

Field Disease NurseriesCBBAnthracnoseWhite mouldRootRot

Growth Room Disease TestingCBBAnthracnoseBCMV

Resistance/Tolerance to Biotic Stress Breeding, Genetics and Genomics

CBB Resistance Marker Frequencies (2009) CBB Marker

GP Yield Trial N SU91 UBC420

Preliminary YT Early 56 0.00 0.00

Preliminary YT Mid 56 0.00 0.00

Preliminary YT Late 56 0.02 0.00

Advanced YT 42 0.17 0.00

Preliminary YT Early 56 0.39 0.09

Preliminary YT Mid 56 0.54 0.07

Preliminary YT Late 56 0.57 0.09

Advanced YT Early 36 0.42 0.06

Advanced YT Mid 36 0.14 0.08

Advanced YT Late 36 0.39 0.00

And

ean

Cra

nan

d K

idne

y

Mes

oam

eric

anN

avy

and

Bla

ck

SU91 and UBC420: SCAR markers associated with CBB resistance

Studying CBB QTLxQTL interaction (MSc Thesis Kelli Durham)

(Durham et al. Plant Breeding, Submitted)

CBB Resistance Breeding in Ontario

Navy BeanXAN 159

Masterpiece

PI319443P. acutifolius

PI319441

UI 114

OAC Rico

HR 13 621

Centralia

HR67

NY5268 HR93 1843

Apex

ICA Pijao

PI440795P. acutifolius Midnight

HR 20 728

OAC Rex

Ex Rico 23

G 40001

A 775

A 769

XAN 263

Vax 4RAB73

BAT1579

HR452X

Avanti

Seafarer

C-20Jamapa

73130-E2-B

Nep-2

Crestwood

HR14818

Kippen

Rexeter

Narda

5XGryphon

W72988

OAC 99-1

PI324685

OAC Speedvale

ICB10

PI207262

OAC Seaforth

233B

UnknP. vulgaris

P. coccineus

OAC 09-4OAC 09-3ACUG 10-6

Envoy

Sel 1308

2X

AC Compass

HR135

ACUG 11-7

CBB test of newly-developed line ACUG11-7

ACUG11-7 OAC Rex OAC09-3 Sanilac

+SU91+BC420

+SU91 +SU91

Pathogen isolatesNo. 12 No. 18 No. 118No. 98

Nautica

OAC 09-3

Apex

Rexeter

CBB Resistance Breeding in Ontario Kidney and Cranberry beans

PI319441

UI 114

XAN 159

Masterpiece

PI319443P. acutifolius

Camelot

Redhawk

Isles

AC Calmont

ACUG 10-D1

Darkid

Montcalm

Redhawk

Isles

AC Calmont

ACUG 10-D3

ACUG 10-C1

Ferg Cran 1

SVM T H

Cran 09

HR 202-4973

2x

Navabi et al., unpublished

Quantitative measurement of CBB disease severity: Image analysis (Assess® 2.0 )

OAC 09-3: spscbbr136/PI207262//ICB-10/Vax4/3/Speedvale/Avanti//99-1/OAC Rex

Marker-assisted selection for CBB Resistance in common bean

Association between disease severity and marker SU91

SU91 marker to select resistant bean plants; How efficient ?

Xie et al. 2012 Phytopathology 102:434

SelectedF5 Subset

UnselectedF5 Population

0

1

2

3

4

5

CB

B S

core

(0-5

)Gs

BC1 F1Enriched

F2SU91 Selection F5Generation advance

No. 12 No. 18 No. 

118No. 98

Nautica

OAC 09-3

Apex

Rexet er

Sanilac X        OAC 09-3

Field

AUDPC Growth room

Marker p R2 p R2 SU91 *** 0.40 *** 0.27 SU91-CG10 *** 0.28 *** 0.23 SU91-CG11 *** 0.42 *** 0.36

Allele

Field AUDPC Growth room

Lsmean Std.

Error p Lsmean Std.

Error p A 39.95 1.45 *** 4.30 0.15 *** H 29.81 1.68 *** 3.53 0.17 *** B 25.33 1.17 *** 2.96 0.12 ***

Co-dominant marker SU91-CG11 is a good replacement for SU91

SU91-CG11 genotyping

Sanilac

OAC 09‐3RIL

RIL

464 bp425 bp

Single marker QTL analysis Lsmean of SU91-CG11 in CBB tests

Efficiency of MAS (SU91 and SU91-CG11) in direct selection in three way crosses (TCF4 )

R S

1600 lines / 4 populations

45 lines/subset

R (0‐2.5)  and S (4‐5)

Phenotypes

False positives

False negatives

False positives

False negatives

Nautica//Apex/MBE7 2% 2% 2% 2%

Nautica//Rexeter/Apex 2% 7% 2% 7%

Compass//Apex/MBE7 2% 20% 2% 16%

Compass//Rexeter/Apex 4% 7% 4% 0%

SU91 SU91-CG11

Population

Selection gain following one cycle of SU91-selection in BC1F1SU91 used in F2 enrichment

SelectedF5 Subset

UnselectedF5 Population

0

1

2

3

4

5

CB

B S

core

(0-5

)

Gs

BC1 F1Enriched

F2SU91 Selection F5Generation advance

OMAFRA Project (2011-2014)Combining Anthracnose Resistance with Resistance to other Major Diseases in Ontario Common Bean (Phaseolus vulgaris L.) Germplasm

• Study 1. Monitoring the Pathogen in ON (Spread/Virulence).

• Study 2. genotypic and phenotypic characterization of breeding materials.

• Study 3. Genetics of resistance to anthracnose in Ontario bean germplasm.

• Study 4. Pyramiding resistance to Anthracnose (Co42), CBB and BCMV.

• Research Team: A. Burt (PDF), M Vazin (MSc student), B Hall (KTT), TH Smith, M McDonald, KP Pauls, A. Navabi.

Studying the Inheritance of Anthracnose (Race 73) resistance in ACUG 10-1

(MSc Thesis, Maryam Vazin; Jan 2011-present)

ACUG 10-1: OAC_Rex/A98083//AC_Compass/B98143/3/RESW2138/B981045//B98213/Kippen

Anthracnose Virulence and Distribution in Ontario

• Anthracnose race 73 was discovered in Ontario in 2003

• Since that time race 73 has been thought to be the dominant race in Ontario

• 24 samples collected including 16 site specific samples: 8 from HDC (on map) and 8 from Brian Hall, and 8 cultures from sub-samples of HDC seed sorting rejects

• Samples have been cultured, DNA extraction and screening on differential cultivars is underway

• DNA will be used to sequence the Internal transcribed spacer (ITS), a standard marker for fungal identity. Results will show distribution of clonal colonies of Colletotrichum lindemuthianum

Differential cultivar Michelite

(1) 

immediately following inoculation with 

standardized suspension of conidia 

Anthracnose Virulence and Distribution in Ontario

• Screening results are so far consistent with the hypothesis that the predominant Anthracnose race present in Ontario is race 73.

Anthracnose on green bean media to 

produce sporulating

culture for 

inoculating differential lines

Anthracnose Virulence and Distribution in Ontario

Anthracnose VirulenceRaces

Differential Line

GP Binary No.

Res Gene 23 31 73 2047 Elora 2010(0-10)

Elora 2011(0-10)

Michelite MA 1 Co-11 S S S S 1.3 5.7

MDRK AN 2 Co-1 S S R S 1.3 3.0

Perry Marrow AN 4 Co-13 S S R S 1.0 1.7

Cornell 49242 MA 8 Co-2 R S S S 4.0 5.1

Widusa AN 16 Co-15,Co-93 S S R S 0.7 3.1

Kaboon AN 32 Co-12 R R R S 1.0 3.0

Mexico 222 MA 64 Co-3 R R S S 10.0 9.0

PI 207262 MA 128 Co-43, Co-9 R R R S 0.3 1.0

TO MA 256 Co-4 R R R S 1.7 1.7

TU MA 512 Co-5 R R R S 0.7 1.9

AB136 MA 1024 Co-6,co-8 R R R S 0.3 1.1

G2333 MA 2048 Co-42,Co52,Co7 R R R R 0.1 1.1

BCMV Resistance in the Breeding Pipeline BCMV

GP Yield Trial N SW13

Preliminary YT Early 56 0.79

Preliminary YT Mid 56 0.70

Preliminary YT Late 56 0.77

Advanced YT 42 0.31

Preliminary YT Early 56 0.82

Preliminary YT Mid 56 0.88

Preliminary YT Late 56 0.75

Advanced YT Early 36 0.83

Advanced YT Mid 36 0.81

Advanced YT Late 36 0.81

And

ean

Mes

oam

eric

an

SW13: SCAR marker linked to I gene

White Mold Tolerance

Root Rot Tolerance

Resistance to Soybean Cyst Nematode

0 200 400 600 800 1000 1200 1400

Sherwin (resist soy)Gts 564

ACUG 10-6Seafarer

OAC 07-2Sanilac

T154-051ACUG 10-3

T10303T9903Reliant

AC CruiserOAC 07-3OAC RexLightning

OAC 09-3OAC 09-4

HR177-3719AC Mast

IndiOAC Seaforth

HR200-4345T10704

HR206-4170Gts 544

ACUG 10-1Ex Rico 23

VistaViscount

OAC ThunderAC Compass

T95-051OAC DublinACUG 10-5

T9905ACUG 10-4

HR205-4457Nautica

AC CalmontACUG 10-2

EtnaHooter

HR199-4857MajestyAC Elk

OAC RedstarMontcalmRed Rider

SVM Taylor HortRCAT Harwich

No of Cysts / 6 Roots

Folate Content Inheritance Studies (MSc Thesis Sarita Khanal)

g7740.0g6802.4

G680_B36.1

g45774.6

g457_B111.6g321117.7g2581120.1

g2020183.6

LG2

Othello                                     F1                 

Redhawk

100 150 200 250 300 3500

5

10

15

20

25

Folate content (g/100g)

Freq

uenc

y

Mea

n

• Screening Bean Germplasm for N use Efficiency and N Fixation

• Genetic Studies of N fixation ability in Bean

Nitrogen Use Efficiency and improving N Fixation in Common Bean; Mehdi Farid (PhD student)

Sanilac

ACUG 10-6

OAC 09-3

R 99

A

B

N2Fixation Efficiency  (N0 )

+0.4

‐0.4 +0.4

‐0.4

N2Fixation

 Efficiency (N

AS

Relative Biomass (N = 0)

+0.4

‐0.4 +0.4‐0.4 +0.4

‐0.4

Relative Biomass (N = 100

)

AS

Genotype x Environment Interactions in Ontario Pulse Committee Variety Trials

• Making effective decisions on variety performance is important, and exceedingly difficult in years where there are large and significant differences in variety performance, particularly cross- over interactions, between testing locations

2011

How often do locations fall into the same SREG grouping?

•Eliminating locations never tested together, 7 or 8 locations can be examined

•SREG groupings are inconsistent across years, making weak non-COI clusters that have no correlation with historical environmental or yield data.

Kemptville College

Elora

Woodstock

St. Thomas

Ailsa Craig

Kippen Exeter

Brussels

Kemptville College

Elora

Woodstock

Kippen

Granton

Brussels

St. Thomas

•Long running genotypes can be used to examine the relative contribution of GxE parameters to the variance of yield

•Twenty-five genotypes each in the trials from 10 – 23 years, span the whole data set

•Site nested within year has, by far, the largest effect size

Next steps

Using the common sub-set of genotypes, we can analyze 3 years at a time to get variance partitions across years and locations.

Use data from long-term check varieties to answer complicated questions– e.g. is the performance at Site X over time or average performance across sites a

better predictor of a varieties’ performance at Site X?

Breeding Alternate PulsesMung Bean (Vigna radiate)

Yield

ID Origin Hvblty Mat Ht 100SW kg/haPHLV 193 Philippines 2.4 88.0 85.7 6.0 1089.2AVRDC V-2182 Philippines 1.7 87.8 61.1 7.5 634.9AVRDC V-2184 Philippines 2.1 93.8 87.7 6.6 747.0

AC HarosproutHRC release 1.9 82.8 59.2 6.3 929.0

IMGM check 3.8 84.8 67.6 6.2 1030.8LSD 0.3 1.6 4.7 0.3 140

2010 lines (Navy Bean)

2010 - 11 data; 12 site-years

Yield Maturity Ht Hvblty100 SW CBB ANTH.

ID Sponsor Kg/ha days cm (1-5) gr (0-5) Race 73

AC Compass 2757.4 92.3 50.9 3.2 22.0 S S

Rexeter 3246.3 101.6 57.4 2.6 21.2 R S

ACUG 10-1 UG HDC 2834.8 93.4 54.9 2.4 24.8 S R

ACUG 10-6 UG HDC 3329.2 99.8 56.9 2.5 22.7 R S

HR206-4170 AAFC 2967.0 99.9 56.4 2.6 22.2 R S

2011 lines (Navy Bean)

Yield Maturity Ht Hvblty 100 SW CBB ANTH.

ID Sponsor kg/ha days cm (1-5) gr (0-5) Race 73

Rexeter 2853.9 106.3 50.7 2.4 20.6 1.5 S

AC Compass 2617.6 96.0 46.3 2.8 23.0 4.3 S

ACUG 11-1 AAFC 2829.5 105.1 57.0 2.4 23.4 3.6 R

ACUG 11-2 UG 3038.6 98.8 47.7 2.2 25.1 4.1 R

ACUG 11-3 UG 3185.4 104.5 52.4 2.3 25.5 0.6 S

ACUG 11-4 AAFC 2726.0 101.8 53.2 2.4 24.5 3.4 S

ACUG 11-5 UG 2479.9 104.2 56.6 2.2 22.6 2.6 R

ACUG 11-6 UG 2762.1 101.1 51.7 1.9 21.1 2.0 R

ACUG 11-7 AAFC 2437.5 104.7 48.9 2.6 23.0 1.0 R2011 data; 6 locations

Forthcoming Black Beans 2010 lines

Yield Lodging Maturity 100 SW CBB Purple Color

NAME_ID (kg/ha) Hvblity (1-5) (days) gr (0-5) Visual Colorometer

AC Harblack 2457.4 3.8 3.9 95.6 20.6 3.8 3.0 1.7

Zorro 3332.8 1.8 2.3 98.1 22.1 3.9 1.1 0.6

ACUG 10-B1 AAFC 3553.0 2.6 2.1 102.9 26.5 3.0 1.1 0.5

ACUG 10-B3 AAFC 3138.3 2.0 2.0 99.6 21.5 3.6 1.5 0.7

LSD (P < 0.05) 350.8 0.36 0.5 1.4 0.8 0.8 0.4 0.3

2011 data

Yield Lodging Maturity 100 SW CBB Purple Color

NAME_ID (kg/ha) Hvblity (1-5) (days) gr (0-5) Visual Colorometer

AC Harblack 2457.4 3.8 3.9 95.6 20.6 3.8 3.0 1.7

Zorro 3332.8 1.8 2.3 98.1 22.1 3.9 1.1 0.6

ACUG 11-B1 AAFC 3609.0 3.4 3.5 94.6 24.2 2.3 3.1 1.3

ACUG 11-B2 AAFC 3781.3 3.3 3.5 99.6 29.1 3.4 1.3 0.9

ACUG 11-B3 AAFC 3438.5 3.3 3.1 95.0 25.7 2.8 3.5 1.8

LSD (P < 0.05) 350.8 0.36 0.5 1.4 0.8 0.8 0.4 0.3

Forthcoming Black Beans 2011 lines

2011 data

HR202 Cranberry Bean

Yield Maturity100 SW Ht

Hvblt y BCMV

NAME_ID 2009 2010 20113-year

average days gr cm (1-5) Race 1 Race15

Hooter 2729.6 3300.6 2957.3 2729.6 99.3 65.0 45.4 3.0 R R

Etna 2302.4 3218.0 2594.0 2302.4 89.9 63.7 40.4 2.9 R R

Red Rider 2725.2 3594.3 3075.6 2725.2 98.2 62.6 46.6 2.8 S IR

HR202-4973 2695.1 3531.7 2935.2 2695.1 98.2 66.6 47.8 3.0 R R

HR202 (% Hooter, Etna) 107.1 108.4 105.7 107.1

HR202 (% Mean) 103.1 103.5 101.5 103.1

ACUG 10-D3 Dark Red Kidney Bean Calmont/5/Isle/Redhawk/4/Montcalm/3/Darkid//Camelot/XAN 159

Yield (kg/ha) Maturity 100 SW CBB BCMV

NAME_ID 2010 20112-year average days gr (0-5) Race 1 Race15

AC Calmont 3047.9 2432.5 2740.2 97.5 57.6 4 R R

Red Hawk 2620.1 2293.8 2457 93.3 55.6 4 R R

Majesty 2994.4 2979.2 2986.8 95.2 70.4 3.8 R R

ACUG 10-D3 3143.3 2328.2 2735.7 93.9 58.6 2.5 R R

ACUG 10-D3 (% Redhawk) 120 101.5 111.3

Acknowledgment