Genetic diversity of wild Coffee (Coffea arabica) and its implication for conservation

Transcription

1 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. Biodiversity of Africa Observation and Sustainable Management for our Future! September 29 - October 3, 2008 Spier / Stellenbosch / Republic of South Africa IBC

2 Biodiversity Ecosystem Species Genes

3 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.

4 Chloroplast DNA Microsatellites -High level- Interregional Genetic Diversity -Medium level- Intraregional Genetic Diversity -Low level- Genetic Diversity of Coffea arabica in Ethiopia Conservation and Use Planning

5 Chloroplast DNA Microsatellites CpDNA is maternally inherited Plants have 3 genomes Intron & spacer usually variable within species Contain hyper-variable microsatelites CpDNA To explain the genetic diversity in an evolutionary context

6 Chlorplast regions selected Screening cpdna for its most variable regions for 17 taxa ( 5.5 %) Seven microsatellites (MS1, MS2, MS3, MS5, & MS7)

7 C. arabica wild (Bonga-II, C016) Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia C. arabica wild (Bale-I, C034) C. arabica wild (B. Kontir-III, C035) 7.2 kb of cp-genome sequenced for 17 taxa C. arabica wild (Yayu-IV, C036) C. arabica wild (Boginda-II, C037) C. arabica exhibits no cp-genome diversity (unlike most plants!) Very recent origin C. arabica Blue Mountain (C002) C. arabica Caturra Yellow (C007) C. eugenioides (C010) C. stenophylla (C015) C. eugenioides sister to C. arabica 24 C. salvatrix (C011) 11 C. liberica (C008) C. congensis (C009) 1 C. arabica x liberica (C003) C. canephora (C013) 11 C. kapakata (C014) Psilanthus leroyi (C033) 5 changes

8 Summary of Chloroplast data 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).

9 Interregional 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 )

10 Inter Simple Sequence Repeats-ISSR CACACACACACA GTGTGTGTGTGT GTGTGTGTGTGT TGTGTGTGTGTG ACACACACACAC ACACACACACAC PCR Bale Yayu

11 Yemen Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia I-5-4 II-1-20 Interregional NJ tree Landraces & Cultivars different from Wild individuals 0.1 II-5-15 II-1-24 Blue-Mountain Eritrea Cherchero-H Fendisha-H X-1-9 Buna-Abasha-SW IX-1-5 IX-1-6 IX-1-4 Eritrea Buna-Dima-H X-1-3 X-1-11 X-1-1 Bukuri-H Kurme-S CoCE-14 CoCE-10 CoCE-11 Aruso Kubania-H Buna-Abasha-SW Muyerra-H Qonga-S Shumbure-H Bun-Guracha-H Borojetti-SW II-5-2 IV-4-5 Walisho-S Dega-S V-1-15 I-2-1 I-2-2 I-2-5 III-1-11 III-5-1 III-5-6 III-1-4 IV-5-10 IV-4-15 IV-5-1 I-2-9 I-2-13 I-5-3 II-3-11 II-4-4 III-5-2 III-1-5 I-2-6 II-5-12 San-Ramon Sendi-SW II-1-21 VII-1-8 II-4-2 I-4-2 I-4-3 I-4-4 I-4-6 II-3-7 IV-5-17 IV-5-23 V-2-5 VII-1-2 V-2-2 V-1-17 V-2-4 V-2-1 V-1-6 V-1-8 VII-1-5 VII-1-7 VII-1-4 IV-1-10 IV-1-15 Bedessa-SW III-6-23 III-6-24 VIII-1-9 Abadero-H II-5-5 II-5-6 III-5-3 VIII-1-7 IX-1-3 IV-1-3 IV-5-8 I-5-1 BeleteF IV-4-9 I-4-5 II-5-1 Kuburi-SW IV-4-24 CoCE-5 Bronz-Woshi III-1-9 III-5-4 VIII-1-20 VIII-1-21 Buna-Magala-SW V-2-3 VIII-1-14 II-1-22 II-4-1 II-3-3 X-1-5 X-1-7 III-1-2 III-6-20 IV-1-19 VIII-1-2 VII-1-3 INTER REGIONAL IV-1-1 C046-I-4-1 V-1-20 IV-5-15 IV-4-21 C. eugeniodes IX-1-1 Landraces & Cultivars Wild individuals Wild individuals Wild individuals Wild Yayu & B. Kontir

12 Conservation and Use of Wild Populations Fendisha-H of Coffea arabica in the Montane Rainforests of Ethiopia Interregional NJ tree Bonga - Spread all over the tree Boginda, Bale/Harrena & Anfilo; - Form its own groups 0.1 II-5-15 Yemen I-5-4 II-1-20 II-1-24 Blue-Mountain Eritrea Cherchero-H X-1-9 Buna-Abasha-SW IX-1-5 IX-1-6 IX-1-4 Eritrea Buna-Dima-H X-1-3 X-1-11 X-1-1 Bukuri-H Kurme-S CoCE-14 CoCE-10 CoCE-11 Aruso Kubania-H Buna-Abasha-SW Muyerra-H Qonga-S Shumbure-H Bun-Guracha-H Borojetti-SW II-5-2 IV-4-5 Walisho-S Dega-S V-1-15 I-2-1 I-2-2 I-2-5 III-1-11 III-5-1 III-5-6 III-1-4 IV-5-10 IV-4-15 IV-5-1 I-2-9 I-2-13 I-5-3 II-3-11 II-4-4 III-5-2 III-1-5 I-2-6 II-5-12 San-Ramon Sendi-SW II-1-21 VII-1-8 II-4-2 I-4-2 I-4-3 I-4-4 I-4-6 II-3-7 IV-5-17 IV-5-23 V-2-5 VII-1-2 V-2-2 V-1-17 V-2-4 V-2-1 V-1-6 V-1-8 VII-1-5 VII-1-7 VII-1-4 IV-1-10 IV-1-15 Bedessa-SW III-6-23 III-6-24 VIII-1-9 Abadero-H II-5-5 II-5-6 III-5-3 VIII-1-7 IX-1-3 IV-1-3 IV-5-8 I-5-1 BeleteF IV-4-9 I-4-5 II-5-1 Kuburi-SW IV-4-24 CoCE-5 Bronz-Woshi III-1-9 III-5-4 Bale VIII-1-20 VIII-1-21 Buna-Magala-SW V-2-3 VIII-1-14 II-1-22 II-4-1 II-3-3 X-1-5 X-1-7 III-1-2 III-6-20 IV-1-19 Anfilo VIII-1-2 Boginda VII-1-3 INTER REGIONAL IV-1-1 C046-I-4-1 V-1-20 IV-5-15 IV-4-21 C. eugeniodes IX-1-1 Landraces & Cultivars Wild individuals Wild individuals Wild individuals Wild Yayu & B. Kontir

13 Region Shannon s diversity index (H) & percentage of ISSR band polymorphism (P) Percent Polymorphism (%P) Di/tri_ Primers Tetra_ Primer Over all %P All primers Shannon s diversity Index (I) Di/tri_ Primers Tetra_ Primer Over all Index (I) All primers Bale (Harrena) Bonga Berhane Kontir Yayu/Geba Dogi Boginda Bench Maji Anfilo Daphe Mankira Sidamo Hararegh South West INTER REGIONAL

14 Intraregional diversity assessment Three regions (Yayu, B.Kontir & Bale) 250 individuals (Yayu & B.Kontir) Yayu B. Kontir ISSR marker system Bale

15 Intraregional UPGMA tree Yayu Conservation and Use of Wild Populations of Coffea arabica in the Montane Rainforests of Ethiopia B. Kontir IV-1-2 IV IV-1-4 IV-2-8 IV-1-5 IV-1-6 IV-2-9 IV-2-5 IV-1-14 IV-2-7 IV-1-24 IV-1-25 IV-2-4 IV-2-3 IV-1-8 IV-2-1 IV-1-11 IV-1-13 IV-1-12 IV-1-21 IV-1-22 IV-2-6 IV-2-12 IV-2-13 IV-2-14 IV-2-21 IV-2-18 IV-2-19 IV-2-20 IV-2-22 III-9-10 IV-2-15 III-8-24 III-8-25 III-9-1 III-9-2 III-9-3 III-9-6 III-9-14 III-9-7 III-9-5 III-9-11 III-9-21 IV-1-3 III-3-7 IV-1-9 IV-1-16 IV-2-2 IV-2-10 IV-2-23 III-10-2 III-10-5 III-10-9 III-10-7 III-10-6 III III III III III-10-8 III-10-3 III III III III III III III III III-9-24 III-9-25 SorreF2 III-1-3 III-1-7 III-1-19 Yayu - 1 Yayu - 2 B. Kontir- 9 Yayu- 1 & 2 B. Kontir-10 Coefficient IV-1-17 III-1-21 III-3-4 SorreF3 III-3-12 III-3-13 IV-1-20 III-1-16 III-1-18 III-1-20 III-1-22 III-3-10 IV-2-24 IV-2-25 III-3-3 III-1-13 III-1-14 III-3-2 III-1-15 III-1-2 III-3-14 III-1-17 III-1-23 III-1-25 III-1-26 III-1-24 III-1-11 III-9-26 III-3-9 III-3-15 III-3-16 III-3-17 III-3-18 III-3-19 III-3-20 III-3-21 III-3-22 III-3-23 III-3-1 III-9-17 III-9-16 III-9-12 III-9-20 III-9-13 III-9-19 III-9-15 III-9-9 III-1-27 III-8-4 III-8-1 III-8-2 III-8-20 III-8-19 III-8-17 III-8-18 III-8-5 III-8-8 III-8-14 III-8-12 III-8-10 III-8-11 III-8-9 III-8-13 III-8-15 III-8-3 III-8-23 III-8-21 III-8-22 III-816 III-10-1 III III IV-4-1 IV-4-4 IV-4-7 IV-4-10 IV-4-16 IV-4-19 IV-4-20 IV-4-17 IV-4-18 IV-4-25 IV-4-2 IV-4-6 IV-4-14 IV-4-8 IV-412 III-10-4 IV-4-13 IV-5-2 IV-4-21 IV-4-23 IV-4-23 IV-5-3 IV-5-4 IV-5-5 IV-5-7 IV-5-16 IV-5-18 IV-5-9 IV-5-6 IV-5-12 IV-5-13 IV-5-25 SorreF1 IV-5-14 IV-5-24 IV-5-20 IV IV-5-11 IV-5-22 III-9-22 III-9-23 B. Kontir 1 & 3 B. Kontir - 1 B. Kontir - 3 B. Kontir - 9 B. Kontir- 8 Yayu - 4 Yayu - 5 B. Kontir Yayu

16 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.

17 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)

18 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.