Out of Africa: tracing the genomic footprints of the Vietnamese Robusta coffee

Authors: VI, TRAM - Cirad, France; LE, THI NHU - Vietnam Nationall University; CUBRY, PHILIPPE - Cirad, France; PHAM, VIET HA - Vietnam Nationall University; NGUYEN, VAN TOAN - Vietnam Nationall University; Zhang, Dapeng; PONCET, VALERIE - Cirad, France

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/28/2025
Publication Date: 5/28/2025
Citation: Vi, T., Le, T., Cubry, P., Pham, V., Nguyen, V., Zhang, D., Poncet, V. 2025. Out of Africa: tracing the genomic footprints of the Vietnamese Robusta coffee. PLOS ONE. https://doi.org/10.1371/journal.pone.0324988.
DOI: https://doi.org/10.1371/journal.pone.0324988

Interpretive Summary: Coffee plays an important role in beverages worldwide, as well as in the environment, economy and culture in many countries. There are two main types of coffee, Arabica and Robusta, produced from two different species, Coffea arabica and Coffea canephora, respectively. Robusta accounts for approximately 40% of global coffee production. Robusta coffee was introduced to Vietnam in the 1900s. Since then, it has become one of the most important crops in Vietnam, with a massive impact on the livelihood of local farmers. Understanding the genetic diversity of Vietnamese cultivated varieties, is a prerequisite for effective conservation and utilization of Robusta genetic resource in coffee production and breeding. In this study, we traced the African origin of Robusta accessions cultivated in the Central Highlands of Vietnam, using a new generation of DNA markers. We found that the Vietnamese Robusta coffee was primarily derived from Congolese Robusta materials, originated from the Congo basin. but there was also a diversity from other genetic sources dispersed in backcrossed hybrids. These germplasm groups have been widely used in crossbreeding to develop ”elite” clones. The results increased our understanding of the coffee genetic resources available in Vietnam. This information will be used by coffee researchers and the coffee industry to improve the effectiveness in conservation and utilization of Robusta genetic resources in coffee breeding.

Technical Abstract: Coffee plays an important role in beverages worldwide, as well as in the environment, economy and culture in many countries. Coffea canephora (Robusta coffee) exhibits a genetic diversity strongly structured in its native habitat, the tropical forests of Africa. Only a part of this diversity contributed to the diffusion of Robusta across the world. In this study, we traced the African origin of Robusta accessions cultivated in the Central Highlands of Vietnam. A total of 126 accessions from the Vietnam germplasm collection were characterized, including ancient, elite and local cultivated clones. Their genetic diversity and origin were inferred through comparison with wild reference samples, using a new set of 261 genome-wide SNPs. A core set of 45 accessions that maximize the genetic distance and allelic richness were identified. The full genome sequence of these individuals helped to trace the origin of chromosome segments back to the different genetic groups in Africa. Ancestral origin from a Congolese group of the Congo basin (group ER) presented in all the Vietnamese accessions, although in varying proportion. Admixtures, with different distributions on the genome, from at least one other groups (D in Guinean region, AG in Atlantic coastal region of central Africa, and OB in Congo basin) were found in 31 individuals. Vietnamese Robusta coffee was primarily derived from Congolese Robusta materials, but there was also a diversity from other genetic sources dispersed in backcrossed hybrids. These germplasm groups have been widely used in crossbreeding to develop ”elite” clones. The results provided better understanding of the genetic resources available in Vietnam, which will be useful for establishing sustainable breeding strategies.