View
2
Download
0
Category
Preview:
Citation preview
IBC
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Biodiversity of Africa –Observation and Sustainable Management for our Future!
September 29 - October 3, 2008Spier / Stellenbosch / Republic of South Africa
Genetic diversity of wild Coffee (Coffea arabica) and its implication
for conservation
Kassahun Tesfaye, Feyera Senbeta, Tamiru Oljira,Solomon Balemi, Govers, K., Endashaw Bekele, Borsch, T.
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Ecosystem
Species
Genes
Biodiversity
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Objectives:-
• To clarify the maternal parentship among closely related Coffea species.
• To characterize cpDNA microsatellites & to detect SNPs within C. arabica to observe infraspecific variation among wild populations C. arabica.
• To evaluate if individuals from wild populations in forests are genetically different from landraces.
• To evaluate the relationships of wild C. arabica populations throughout Ethiopia & also to understand the patterns of distribution.
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
ChloroplastChloroplast DNA DNA MicrosatellitesMicrosatellites
--High levelHigh level--
Intraregional Intraregional GeneticGenetic DiversityDiversity
--LowLow levellevel--
Interregional Interregional GeneticGenetic DiversityDiversity
--Medium levelMedium level--
GeneticGenetic DiversityDiversity of of Coffea arabicaCoffea arabica in in EthiopiaEthiopia
ConservationConservation and and UseUse PlanningPlanning
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
•• CpDNA is maternally inherited CpDNA is maternally inherited
•• Intron & spacerIntron & spacerusually variable usually variable within species within species
•• Contain hyperContain hyper--variable variable microsatelites microsatelites
•• To explain the genetic diversity To explain the genetic diversity in an evolutionary contextin an evolutionary context
CpDNA
Plants have 3 genomesPlants have 3 genomes
Chloroplast DNA MicrosatellitesChloroplast DNA Microsatellites
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
• Screening cpDNA for its most variable regions for 17 taxa ( 5.5 %)• Seven microsatellites (MS1, MS2, MS3, MS5, & MS7)
Chlorplast regions selectedregions selected
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
C. arabica wild (Bonga-II, C016)
C. arabica wild (Bale-I, C034)
C. arabica wild (B. Kontir-III, C035)
C. arabica wild (Yayu-IV, C036)
C. arabica wild (Boginda-II, C037)
C. arabica ‘Blue Mountain’ (C002)
C. arabica ‘Caturra Yellow’ (C007)
C. eugenioides (C010)
C. stenophylla (C015)
C. salvatrix (C011)
C. liberica (C008)
C. congensis (C009)
C. arabica x liberica (C003)
C. canephora (C013)
C. kapakata (C014)
Psilanthus leroyi (C033)
5 changes
1891
8 71
5 100
2270
20
20
24
2797
11
5 78
5 59
11
14 100
1
11
• 7.2 kb of cp-genome sequenced for 17 taxa
• C. arabica exhibits no cp-genome diversity (unlike most plants!)
• Very recent origin
• C. eugenioides sister to C. arabica
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
• An ancestor of C. eugenioides is evidenced to be the maternal parent for C. arabica.
• Both C. arabica & C. eugenioides are recently diverged within Coffea.
• C. arabica has a single origin (one polyploidisation event).
Summary of Chloroplast data
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
InterregionalInterregional diversity assessment diversity assessment
• 10 regions of wild coffee
• 1 sample per landrace
• 150 individuals
I to IV - Core CoCE sites (wild Coffee)
V to X - Additional wild Coffee sites
O - Landraces (Farmer‘s varieties )
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
• Inter Simple Sequence Repeats-ISSR
CACACACACACA
GTGTGTGTGTGT
TGTGTGTGTGTG
ACACACACACAC
PCR
CACACACACACA
GTGTGTGTGTGT
TGTGTGTGTGTG
ACACACACACAC
Bale Yayu
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
0.1
II-5-15II-5-2
YemenI-5-4II-1-20
II-1-24Blue-Mountain
EritreaCherchero-H
Fendisha-HIV-4-5
X-1-9Buna-Abasha-SW
IX-1-5IX-1-6IX-1-4
EritreaBuna-Dima-H
X-1-3X-1-11X-1-1Bukuri-HKurme-SCoCE-14CoCE-10CoCE-11
ArusoWalisho-S
Dega-SV-1-15
Kubania-HBuna-Abasha-SW
Muyerra-HQonga-SShumbure-H
Bun-Guracha-HBorojetti-SW
VIII-1-20VIII-1-21
Buna-Magala-SWV-2-3
BeleteFVIII-1-14
II-1-22II-4-1
C046-I-4-1II-3-3
X-1-5I-2-1
I-2-2I-2-5
III-1-11III-5-1
III-5-6III-1-4
IV-5-10IV-4-15IV-5-1
I-2-9I-2-13
I-5-3II-3-11
II-4-4III-5-2
III-1-5I-2-6II-5-12
San-RamonSendi-S W
II-1-21VII-1-8
IV-1-1IX-1-1
V-1-20IV-5-15
X-1-7III-1-2
III-6-20IV-1-19
IV-4-9I-4-5
II-4-2I-4-2I-4-3I-4-4
I-4-6II-3-7
IV-5-17IV-5-23
V-2-5VII-1-2V-2-2
V-1-17V-2-4
V-2-1V-1-6
V-1-8VII-1-5VII-1-7VII-1-4IV-1-10IV-1-15
II-5-1Kuburi-SW
Bedessa-SWIII-6-23III-6-24VIII-1-9
Abadero-HIV-4-24
VIII-1-2CoCE-5
Bronz-WoshiII-5-5
II-5-6III-5-3
III-1-9III-5-4
VIII-1-7IX-1-3
IV-1-3IV-5-8I-5-1
IV-4-21VII-1-3
C. eugeniodes
Landraces & Cultivars
Wildindividuals
Wild individuals
Wild individualsWild Yayu& B. Kontir
LandracesLandraces & &
CultivarsCultivars
different different
fromfrom
Wild Wild
individualsindividuals
INTER REGIONAL
InterregionalNJ tree
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
0.1
II-5-15II-5-2
YemenI-5-4II-1-20
II-1-24Blue-Mountain
EritreaCherchero-H
Fendisha-HIV-4-5
X-1-9Buna-Abasha-SW
IX-1-5IX-1-6IX-1-4
EritreaBuna-Dima-H
X-1-3X-1-11X-1-1Bukuri-HKurme-SCoCE-14CoCE-10CoCE-11
ArusoWalisho-S
Dega-SV-1-15
Kubania-HBuna-Abasha-SW
Muyerra-HQonga-SShumbure-H
Bun-Guracha-HBorojetti-SW
VIII-1-20VIII-1-21
Buna-Magala-SWV-2-3
BeleteFVIII-1-14
II-1-22II-4-1
C046-I-4-1II-3-3
X-1-5I-2-1
I-2-2I-2-5
III-1-11III-5-1
III-5-6III-1-4
IV-5-10IV-4-15IV-5-1
I-2-9I-2-13
I-5-3II-3-11
II-4-4III-5-2
III-1-5I-2-6II-5-12
San-RamonSendi-SW
II-1-21VII-1-8
IV-1-1IX-1-1
V-1-20IV-5-15
X-1-7III-1-2
III-6-20IV-1-19
IV-4-9I-4-5
II-4-2I-4-2I-4-3I-4-4
I-4-6II-3-7
IV-5-17IV-5-23
V-2-5VII-1-2V-2-2
V-1-17V-2-4
V-2-1V-1-6
V-1-8VII-1-5VII-1-7VII-1-4IV-1-10IV-1-15
II-5-1Kuburi-SW
Bedessa-SWIII-6-23III-6-24VIII-1-9
Abadero-HIV-4-24
VIII-1-2CoCE-5
Bronz-WoshiII-5-5
II-5-6III-5-3
III-1-9III-5-4
VIII-1-7IX-1-3
IV-1-3IV-5-8I-5-1
IV-4-21VII-1-3
C. eugeniodes
Bale
Boginda
Anfilo
Bonga- Spread all over
the tree
Boginda, Bale/Harrena & Anfilo;
- Form its owngroups
Landraces& Cultivars
Wild individuals
Wild individuals
Wild individualsWild Yayu& B. Kontir
INTER REGIONAL
InterregionalNJ tree
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Shannon’s diversity index (H) & percentage of ISSR band polymorphism (P)
0.220.400.1724.358.115.4South West
0.170.490.0825.080.710.3Hararegh
0.210.460.1417.654.87.7Sidamo
0.310.750.2025.783.910.3Mankira
0.250.600.1716.971.02.6Daphe
0.280.530.2120.367.77.7Anfilo
0.220.540.1318.267.75.1Bench Maji
0.270.590.1830.483.916.3Boginda
0.400.760.3035.893.620.5Yayu/Geba Dogi
0.340.560.2834.587.120.5Berhane Kontir
0.400.710.3141.993.628.2Bonga
0.250.530.1827.780.713.7Bale (Harrena)
All primersTetra_Primer
Di/tri_Primers
All primersTetra_Primer
Di/tri_Primers
Over all Index (I)
Shannon’s diversity Index (I)
Over all %PPercent Polymorphism(%P)
Region
INTER REGIONAL
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Intraregional diversity assessment diversity assessment
• Three regions(Yayu, B.Kontir & Bale)
• 250 individuals(Yayu & B.Kontir)
• ISSR marker system
Yayu
B. Kontir
Bale
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Coefficient0.79 0.84 0.89 0.95 1.00
IV-1-2IV-2-1 1IV-1-4IV-2-8IV-1-5IV-1-6IV-2-9IV-2-5IV-1-14IV-2-7IV-1-24IV-1-25IV-2-4IV-2-3IV-1-8IV-2-1IV-1-11IV-1-13IV-1-12IV-1-21IV-1-22IV-2-6IV-2-12IV-2-13IV-2-14IV-2-21IV-2-18IV-2-19IV-2-20IV-2-22III-9-10IV-2-15III-8-24III-8-25III-9-1III-9-2III-9-3III-9-6III-9-14III-9-7III-9-5III-9-11III-9-21IV-1-3III-3-7IV-1-9IV-1-16IV-2-2IV-2-10IV-2-23
III-10-2III-10-5III-10-9III-10-7III-10-6III-10-10III-10-13III-10-11III-10-12III-10-8III-10-3III-10-23III-10-21III-10-22III-10-14III-10-20III-10-16III-10-18III-10-19III-9-24III-9-25SorreF2III-1-3III-1-7III-1-19
IV-1-17III-1-21III-3-4SorreF3III-3-12III-3-13IV-1-20III-1-16III-1-18III-1-20III-1-22III-3-10IV-2-24IV-2-25III-3-3III-1-13III-1-14III-3-2III-1-15III-1-2III-3-14III-1-17III-1-23III-1-25III-1-26III-1-24III-1-11III-9-26III-3-9III-3-15III-3-16III-3-17III-3-18III-3-19III-3-20III-3-21III-3-22III-3-23III-3-1III-9-17III-9-16III-9-12III-9-20III-9-13III-9-19III-9-15III-9-9III-1-27III-8-4III-8-1III-8-2III-8-20III-8-19III-8-17III-8-18III-8-5III-8-8III-8-14III-8-12III-8-10III-8-11III-8-9III-8-13III-8-15III-8-3III-8-23III-8-21III-8-22III-816III-10-1III-10-24III-10-25IV-4-1IV-4-4IV-4-7IV-4-10IV-4-16IV-4-19IV-4-20IV-4-17IV-4-18IV-4-25IV-4-2IV-4-6IV-4-14IV-4-8IV-412III-10-4IV-4-13IV-5-2IV-4-21IV-4-23IV-4-23IV-5-3IV-5-4IV-5-5IV-5-7IV-5-16IV-5-18IV-5-9IV-5-6IV-5-12IV-5-13IV-5-25SorreF1IV-5-14IV-5-24IV-5-20IV-5-21IV-5-11IV-5-22III-9-22III-9-23
0.84 0.89 0.95 1.00
Yayu - 5
B. Kontir
Yayu
Intraregional UPGMA tree
Yayu
Yayu - 4
B. Kontir- 8
B. Kontir - 9
B. Kontir - 3
B. Kontir – 1 & 3
B. Kontir - 1
B. Kontir
Yayu - 1
Yayu - 2
B. Kontir- 9
Yayu- 1 & 2
B. Kontir-10
...
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
ISSRs show that: -
• Wild coffee populations can be clearly distinguished from landraces ”true wild coffee”.
• High levels of genetic diversity within geographical regions and vary from region to region.
• Even though Bonga, Yayu and Berhane Kontir showed higher diversity indices, it is observed that most regions have their unique genotypes.
• Individuals belonging to landraces often have lower genetic distances to each other than individual of wild populations.
• There is fine scale spatial genetic structuring among populations of Berhane Kontir and Yayu.
• Semidisturbed plots tends to show higher diversity than undisturbed.
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Recommendations for conservation & use planning
• Genetic evidence for true wild coffee - Justify conservation
• Unique genotypes in different regions - Multi-site in situ conservation approach
• The existing genetic divergence among regions –Prospects for use in national breeding (heterosis)
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Implementation-oriented research activities
Establishing coffee in situ gene bank:-
• The aim is to have a ‘copy’ of the genetic diversity in the natural populations at the forest margin.
• To re-introduced elite breeding materials originally came from the same forest into the forest margin to increase the yield and income of the local farmer.
– In situ gene bank have both conservation and use value for the local farmers who are fully dependent on wild coffee.
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
In situ gene bank-Yayu
Naturally regenerated seedlings were collected from different forest population
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
In situ gene bank• Totally 5,000 coffee seedlings were
disseminated for the 3 farming community-Year 2007
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Seeds of forest tree specieslike Cordia africana, Albiziagrandibracteata, Albizia gummifera, Acacia abyssinica, & Acacia mellifera were collected and raised in Nursery
-2,000 seedlings were disseminated
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Agreement were made with Youth Association organized to manage of the forest
- 10,000 seedlings of coffee along with 6,200 tree species were given for the association in Yayu. Leaders of the Association
Local Youth Association
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
Selection of elite individual coffee for re-introduction to the forest margin
-Jima Agricultural Research Center
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of EthiopiaCapacity Building andCapacity Building and ResearchResearchActivitiesActivities in AAUin AAU
C o C EC o C E
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
C o C EC o C E
Capacity Building andCapacity Building and ResearchResearchActivitiesActivities in AAUin AAU
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
C o C EC o C E
Capacity Building andCapacity Building and ResearchResearchActivitiesActivities in AAUin AAU
Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia
ZEF BonnZEF Bonn
EIAREIAR IBCIBCAAUAAUNeesNees
Thank you very much
Recommended