Coffee Breeding Update

with new tools

HCA Conference 2003

Chifumi Nagai
Hawaii Agriculture Research Center
 Coffee Breeding and Selection
Traditional tools New tools
Existing varieties DNA markers
Quality evaluation Genetic Engineering
Foreign germplasm
(Cupping)
Hybridization
Flavor chemistry
Visual selection
Data collection
Backcross

New coffee varieties

with high yielding and superior quality

with rust and nematode resistance

having cupping quality
 HARC Coffee Program
• Breeding and Selection
HCGA/State,DOA 1997-
• Molecular Markers
USDA grant (CMBRU)
Ray Ming, Heather Pearl, C. Nagai
• Transgenic coffee for nematode resistance
USDA grant ( T-STAR )
Brent Sipes, D. Schmit. H. Atkinson, Roxana Cabos,
C.Nagai
• Green Bean Chemistry
USDA grant (CMBRU)
Mel Jackson, Cathy Cavaletto, Shawn Steiner, C.
Nagai
 Coffee Breeding and Selection

HARC- team
C. Nagai, B. Osgood, R. Ming, M. Jackson,
L. Poland, K. Wiever, J. Buenafe, J. Clayton

UH
C. Cavaletto, N.Nagai and S. Bittenbender,

Hawaii Coffee Growers’ Association (HCGA)

Kauai Oahu Molokai
red Catuai Maui
yellow Catuai mokka hyb. mokka
red Catuai Promecafe red Caturra
red Catuai Kona
‘Guatemalan’
typica
‘Old Hawaiian’
Hawaiian
Common Field
Kunia, HARC
planted April,1998

Crosses (spring 1999)

Group # of crosses
mokka and other arabica varieties 66
with Promecafe (Catimor) 53 H99 - series
with Icatu 8 Progeny
mokka and other selfs 40

Total 167
 New Cultivar Development
using Mokka Hybrids
Goal:
The introgression of Mokka flavor traits into high yielding
and larger bean size cultivars

•Mokka was introduced to the UH coffee germplasm collection in the mid

1950s

•Commercially cultivated on Maui (Kaanapali Coffee Co). The accession is

now considered to be a Mokka hybrid.

•The cupping quality of Mokka hybrid is considered excellent but bean size is
very small ( about 30-40% of Red Catuai beans).

•In 1999, we made crosses focused on increasing mokka seed size while
maintaining its excellent cupping quality.
Example of Progenies from 1999 Cross

• Tree height
Red Catuai x Mokka hyb
Red catuai dwarf x mokka
hyb
Red Catuai x typica
Yel Caturra x mokka
• Cupping Quality
• Increase bean Size
Yellow catuai x Margogipe
Mokka hyb. Self
Mokka x Red Catuai
Red Catuai x SL28
Mokka hyb self
Red Catuai x 6661
 Cherry and green bean) size
of families with mokka and
Margogipe crosses
Fall 2002

Cross# Parentage n 100 fruit wt Green bean

gram gram
H99-34 KA17-5 x Margog 3 241 ± 3 41.7 ± 0.2
(Y. catuai)

H99-36 MA1-12 x Margog 5 258 ± 17 42.9 ± 4.3

(mokka)
H99-22A MA1-12 self 5 179± 9 29.2 ± 1.4
(mokka select )
H99-101 KA16-4 self 6 148 ± 1 25.5 ± 1.7
(Y. catuai)
Potential New cultivar

H99-36:
MA1-12 x Margogipe
(mokka)
 Cupping of 3 genotypes of coffee
harvested at Kunia in 2002-03 Season
By Cathy Cavaletto’s Panel ( April 2003)
Cupping Panel: 7 trained cuppers (Judge)

Genotypes ( 2 hybrids + 1 parent)

H97-1700: Yellow Catuai (KA17C)
H99-34: KA17 x Margogipe
H99-36: MA1-12(mokka) x Margogipe

Replication: 3 days
 Cupping Results
ANOVA

_________________________________________________________
Source df Dry Wet Acidity Flavor Body
aroma
________________________________________________
Judge 6 ** ns *** ns **
Genotype 2 ns ns ns ns ns
Rep 2 ns ns ns ** ns
Residual 43
_________________________________________
**: significant at P = 0.01
***: significant at P= = 0.001
ns= not significant
 Propagation of Selected Hybrids
by cloning
Preparation of trees Cloning
Induction of vertical shoots
1. Shoot tip culture

2. Root induction of cuttings

Kunia H99- fields Using misting/ bottom heat

3. Bioreactor of somatic embryos

(root stock production)
 Summary and plan ‘03-’04
• Field Trial at Kauai Coffee- “FT7” design
Germinated Seeds from selected hybrids at MWü
Ship seedlings to Kauai (9/03)
Plant seedlings at 2 fields, Kauai Coffee(12/03)
Data collection (5/04-)

• Field planting of 2002 hybrids ( 7/03) ü

• Harvest and data collection of H99- series at Kunia (10-
12/03)
• Crosses using new germplasm and selected genotypes
(12/03-3/04)
• Send selected individuals for rust resistance tests.
• Make new crosses of selected F1 plants
 DNA Marker Study
2002-2003
Ray Ming, Heather Pearl and C.
Nagai

• Genetic evaluation of Fukunaga and

newly introduced coffee
• DNA analyses of green beans
• Development of coffee populations for
QTL mapping
• Construction of a genetic map of
Arabica coffee
Coffee leaves
DNA
 Bourbon1
Bourbon3
Typica-H1
Typica-H2
Typica-K6
Typica-H3
Genetic Relationships Within and Typica-K2
Typica-H4
Typica-H5
Typica-K10
Between Coffea Species Typica-K7
Typica-K9
Typica-K3
Typica-H8
Typica-H9
Typica-H7
Typica-K1
Typica-K11
Typica-K32
Brown- Bourbon Typica-K33
Typica-K8
Catuai8
Typica-K4
Typica-K34
Green- Typica MH3
MH2
MH5
MH6
MH7
Catuai1
Blue- Catuai/Caturra Catuai2
Catuai5
Caturra1
Caturra2
Catuai3
Catuai4
Lt. Blue- Mokka hybrid Typica-K12
Typica-K13
MH8
Catuai6
Typica-K5
Catimor4
Pink- Catimor Catimor5
Catimor7
Catimor8
Catuai9
Black- Diploid Species MH4
Catuai10
Bourbon4
Catimor6
Bourbon2
MH1
Typica-H6
Catuai7
Catimor1
Catimor3
Catimor2
C-canephora
C-liberica
Deweveri
0.41 0.56 0.71 0.85 1.00
Genetic Similarity (Cophenetic coefficient = .99)
Application of Fingerprinting:

– Determine the genetic relationship of Fukunaga (Coffea

liberica, deweveri) trees from various sources in Kona
and other trees showing liberica traits

– Examine the differences between newly introduced

cultivars and long established Hawaiian cultivars such
as Kona typica
Samples
Arabica (2n=44) 30 smples
– tetraploid and self fertile
– Blue Mountain(Jamaica), Blue Mountain (HARC)
Kona Typica, Mokka, Laurina, tall Mokka Hybrid,
Bourbon, Mundo Nova
New Brazilian cultivars : Icatu, Obata, and Tupi

Liberica “Fukunaga “ (2n=22) 20 samples

– diploid and self-sterile
– torlelet nematodes , used as root stock for Kona typica

Canephora (robusta) 2 samples

– diploid and self-sterile
 List of Fukunaga samples from Kona
(collected by Mario Sarracin 11/20/01)

Sample Name Source Additional Information

KES1 UH Kainaliu H-Field, Marc Meinsner's selec. From P.Ito's original trees
KES2 UH Kainaliu H-Field, Marc Meinsner's selec. From P.Ito's original trees

KES (Original) UH Kainaliu C. liberica dewevrei (Fukunaga)

KES 16 KraigLee Kraig Lee C. liberica dewevrei (Fukunaga)
KES 6658 See MareM., Next to Arnold Diama 6658
CTS 2F TwigSmith Farm Flower Planted
CTS 2S TwigSmith Farm Seed Planted
CTS 3 TwigSmith Farm
CTS 4 TwigSmith Farm
CTS 5 TwigSmith Farm
CTS 6 TwigSmith Farm
CTS 7 TwigSmith Farm
CTS 9 TwigSmith Farm
CTS 10 TwigSmith Farm Looks like dewevrei type, not fruiting
CTS 11 TwigSmith Farm
CTS 12 TwigSmith Farm
CTS 13 TwigSmith Farm Reddish leaves, pointed, fruit not clustered, multiple verticals
CTS 14 TwigSmith Farm
CTS 15 TwigSmith Farm Seeds Taken
 Genetic Similarity Tree
BlueMountain3
KonaTypica4
KonaTypica3
Easily distinguishable
KonaTypica2
MokkaHybrid4
Mokka3
groups were seen
Luurina4
Luurina2
Luurina3
between the three
KonaTypica1
MundoNova1
MO2-7-2
species:
MundoNova2
Bourbon1
Bourbon2
MokkaHybrid3
Arabica
Tupi1
Mokka1
BlueMountain6
MO2-7-1
YellowBourbon1
BlueMountain4
BlueMountain5
5175-1
5175-2
MWBlueMountain1
MWBlueMountain1
Icatu2
Obata1
Obata2
Tupi2
Canephora1
Canephora2
KESLiberica1
Canephora
KESLiberica2
KESlibericaOrig
KESLiberica16
KESLiberica6658
CTSLiberica12
CTSLiberica2S
CTSLiberica2F
CTSLiberica4
CTSLiberica13
CTSLiberica3
CTSLiberica8
Liberica (Fukunaga)
CTSLiberica11
CTSLiberica14
CTSLiberica7
CTSLiberica6
CTSLiberica15
CTSLiberica5
CTSLiberica9
CTSLiberica10

0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00

Genetic Similarity Coefficient
 Species Specific Marker Bands:
Arabica
Marker
Band

Liberica
Marker
Band
 Genomic DNA analyses of
green beans

• Isolated DNA from commercially

processed green beans

• Tested DNA quality -- partially

degraded
Polymorphic DNA Markers
Linkage Groups
Mapping of arabica coffee Development of
a mapping population
P1: Promecafe1(C): X P2: Mokka (M) (1999)
T5175-1 MA2-7
large bean size, small bean size
low cupping quality, high cupping quality
Rust resistance rust susceptible
F1
(Pseudo F2)
130 progeny

F2
300 progeny
(will be planted 9/03)
 QTL (Quantitative Trait Locus) for
marker assisted selection
Find correlation between DNA markers
and coffee traits such as
Tree Characters
leaf shapes
tree height
branching angles
Bean Characters
bean size
yield
cupping quality
 Summary 2002-2003
• Developed a true F2 mapping population
with 323 progeny
• Constructed the first Linkage map of
Arabica coffee
( Pearl et al. 2003 submitted)
• Mapped QTLs for five traits
• Evaluated the possibility of applying DNA
markers on coffee green beans
• Fingerprinted a new set of coffee
germplasm including Fukunaga
Genetic Transformation of Coffee
for Nematode Resistance

Team: Roxana Cabos(UH), Brent Sipes(UH),

Don Schmitt(UH), Howard Atkinson(Leeds U)
and C. Nagai
Damage to M. konaensis Infested
Coffee Trees

Galls

Serracin et al ,2001
 Cystatin

• From Rice Flower

• Inhibitor for Cysteine
Proteinases
• Reduces Nematode
Growth & Fecundity
• Tested for Safety
• Field testing in
potato,rice, banana by
Atkinson’s group
Atkinson et al, 2001
 Coffee Tissue Culture

Callus from young leaves Somatic embryos Germination

Plants with roots Nursery

Production of Nematode Resistant Coffee
Plants by Genetic Engineering

Callus Induction of Coffee Leaves

Insertion of Cystatin Gene
Cystatin OcID86

Somatic Embryos

Agrobacterium
Selection & Regeneration -mediated transformation

Gene bombardment
Selection of Transgenic Somatic Embryos
and production of transgenic plants
Coffee Plantlets with cystatin gene

435 Plantlets Transformed w/Cystatin Constructs

 Acknowledgements

h Hawaii Coffee Growers Association

h University of Hawaii, Kainaliu Exp. Station
h Dr. Loren Gautz, University of Hawaii
h Dr. Mario Serracin
h Dr. H. Medina-Filho, Instituto Agronomico
de Campinas
h Jamaica Coffee Industry Board
h Susan Ancheta
h Laetitia Fournier, E.S.I.P.A