Genetic diversity of wild Coffee (Coffea arabica)and its ...€¦ · C. arabica ‘Blue Mountain’ (C002) C. arabica ‘Caturra Yellow’ (C007) C. eugenioides (C010) C. stenophylla

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.


Ecosystem

Species

Genes

Biodiversity


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.


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


•• 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


• Screening cpDNA for its most variable regions for 17 taxa ( 5.5 %)• Seven microsatellites (MS1, MS2, MS3, MS5, & MS7)

Chlorplast regions selectedregions selected


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


• 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


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 )


• Inter Simple Sequence Repeats-ISSR

CACACACACACA

GTGTGTGTGTGT

TGTGTGTGTGTG

ACACACACACAC

PCR

CACACACACACA

GTGTGTGTGTGT

TGTGTGTGTGTG

ACACACACACAC

Bale Yayu


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


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


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


Intraregional diversity assessment diversity assessment

• Three regions(Yayu, B.Kontir & Bale)

• 250 individuals(Yayu & B.Kontir)

• ISSR marker system

Yayu

B. Kontir

Bale


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

...


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.


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)


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.


In situ gene bank-Yayu

Naturally regenerated seedlings were collected from different forest population


In situ gene bank• Totally 5,000 coffee seedlings were

disseminated for the 3 farming community-Year 2007


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


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


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


C o C EC o C E

Capacity Building andCapacity Building and ResearchResearchActivitiesActivities in AAUin AAU


C o C EC o C E

Capacity Building andCapacity Building and ResearchResearchActivitiesActivities in AAUin AAU


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EIAREIAR IBCIBCAAUAAUNeesNees

Thank you very much

Documents

Genetic diversity of wild Coffee (Coffea arabica)and its ...€¦ · C. arabica ‘Blue Mountain’ (C002) C. arabica ‘Caturra Yellow’ (C007) C. eugenioides (C010) C. stenophylla