Unveiling unexpected Coffea arabica genetic diversity in Southeast Asia: Timor-Leste and the Philippines

While the genetic resources of Coffea arabica L. in its native habitat (Ethiopia and South Sudan) and primary domestication center (Yemen) have been recently thoroughly described, the available genetic diversity of the species in Southeast Asian secondary domestication centers remain unexplored. Nevertheless, since the eighteenth century, this region of the world has been key for the internationalization of coffee production beyond Ethiopia and Yemen. It has provided a unique source of disease resistant breeding material originating from interspecific crosses in Timor-Leste. In this paper, we explore through ten robust single sequence repeats markers the genetic diversity of 228 C. arabica samples surveyed in two contrasting countries: Timor-Leste and the Philippines. An unexpected genetic diversity is revealed, including some new alleles specific to the region. We show that the interspecific crosses between C. arabica and C. canephora Pierre ex A. Froehner have not been uncommon and that the present populations of Timor Hybrids most likely derive from several interspecific crosses. These results shed new light on the importance of C. arabica’s genetic resources in Southeast Asia and help guiding future genetic resource conservation paying attention to remote islands where the species was introduced during the past three centuries.