Haitian coffee agroforestry systems harbor considerable, dynamic and under-reported varietal mixture and genetic diversity

Authors: PATRICK, MILLET - Institute For Research And Development (IRD); ALLINNE, CLEMENTINE - Institute For Research And Development (IRD); VI, TRAM - Institute For Research And Development (IRD); VERLEYSEN, LAUREN - Flanders Research Institute For Agriculture; COUDERIC, MARIE - Flanders Research Institute For Agriculture; RUTTINK, TOM - Ghent University; Zhang, Dapeng; SOLANO-SANCHEZ, WILLIAM - Catie Tropical Agricultural Research; TRANCHANT, CHRISTINE - Institute For Research And Development (IRD); JEUNE, WESLEY - Quisqueya University; PONCET, VALERIE - Institute For Research And Development (IRD)

Submitted to: Agriculture, Ecosystems and Environment
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/11/2024
Publication Date: 4/16/2024
Citation: Patrick, M.C., Allinne, C., Vi, T., Verleysen, L., Couderic, M., Ruttink, T., Zhang, D., Solano-Sanchez, W., Tranchant, C., Jeune, W., Poncet, V. 2024. Haitian coffee agroforestry systems harbor considerable, dynamic and under-reported varietal mixture and genetic diversity. Agriculture, Ecosystems and Environment. https://doi.org/10.1371/journal.pone.0299493.
DOI: https://doi.org/10.1371/journal.pone.0299493

Interpretive Summary: Coffee production has played a unique role in rural Haiti, as an important contributor to rural livelihoods and local ecosystems. However, little is known about the varietal composition and on -farm genetic diversity in this country. Using a new generation of DNA fingerprinting technology, we analyzed coffee samples from 28 farms in historically important coffee growing regions in Haiti. Our analyses revealed considerable genetic diversity in Haitian farms. The analysis of genetic structure revealed different varietal groups including Typica, Bourbon, and Catimor groups. There are also groups of farmer selections that are not represented in the reference panel. Across the study areas, we found both diversified farms and monovarietal farms with traditional Typica variety. This study is the first to genetically characterize Haitian C. arabica coffee varieties. Our results show that some coffee farms are repositories of historical varieties while others are generators of new diversity through genetic mixing. The result provides a scientific data to address challenges faced by Haiti coffee farmers and increase the sustainability of coffee agroecosystems. This information will be used by coffee growers and coffee industry to produce special coffee based on identified varieties. The information will also be used by coffee researchers to sustainably conserve cacao genetic resources in Haiti and the other Caribbean countries.

Technical Abstract: Though facing significant challenges, Haitian Coffee (Coffea arabica) agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. However, little is known about their genetic diversity and the variety mixtures used. There is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 diverse farms in historically important coffee growing regions of Northern and Southern Haiti. We performed targeted multiplex amplicon sequencing and KASP-genotyping of SNP markers on our samples, as well several Ethiopian and commercial accessions from international collections. This allowed us to assign Haitian samples to varietal groups. Our analyses revealed considerable genetic diversity in Haitian farms, higher in fact than many farmers realize. Notably, genetic structure analyses revealed the presence of clusters related to Typica, Bourbon, and Catimor groups, another which was not represented in our reference accession panel, and several admixed individuals. Across the study areas, we found both diversified farms and monovarietal farms with the historical and traditional Typica variety. This study is, to our knowledge, the first to genetically characterize Haitian C. arabica variety mixtures and report the limited cultivation of C. canephora (Robusta coffee) there. Our results show that some coffee farms are repositories of historical, widely abandoned varieties while others are generators of new diversity through genetic mixing. Future study may reveal adaptive potential and suggest ways of mobilizing this diversity to address challenges faced by farmers and increase the sustainability of coffee agroecosystems.