Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.
Summary
Coffee species such as
Coffea canephora
P. (Robusta) and
C. arabica
L. (Arabica) are important cash crops in tropical regions around the world.
C. arabica
is an allotetraploid (2
n
= 4
x
= 44) originating from a hybridization event of the two diploid species
C. canephora
and
C. eugenioides
(2
n
= 2
x
= 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single‐nucleotide polymorphism (
SNP
) array for coffee trees. A total of 8580 unique and informative
SNP
s were selected from
C. canephora
and
C. arabica
sequencing data, with 40% of the
SNP
located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065
SNP
s (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high‐density genetic map by adding 1307
SNP
markers, whereas 945
SNP
s were found segregating in the Arabica mapping progeny. A panel of
C. canephora
accessions was successfully discriminated and over 70% of the
SNP
markers were transferable across the three species. Furthermore, the canephora‐derived subgenome of
C. arabica
was shown to be more closely related to
C. canephora
accessions from northern Uganda than to other current populations. These validated
SNP
markers and high‐density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.
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