Genetic diversity based on AFLP markers in germplasm of the Brazilian national Coffea arabica trial

Brazil is the world largest producer and exporter of Coffea arabica. In this country, numerous breeding programs have generated a great multiplicity of cultivars with expressive productivity that are adapted to the different regions. Evaluating genetic diversity is critical since it provides parameters for defining breeding strategies. We estimated the genetic diversity among and within 32 cultivars of the Brazilian Coffee Trial using AFLP markers. This trial is composed of the main cultivars developed and some under development by Empresa De Pesquisa Agropecuaria do Estado de Minas Gerais (EPAMIG), Fundacao PROCAFE, Instituto Agronomico de Campinas (IAC), and Instituto de Desenvolvimento Rural do Parana (IDR-Parana). A total of 982 AFLP fragments were generated, of which 97.35% were polymorphic. The percentage of polymorphic loci ranged from 22.8 to 50.5%, with genetic diversity varying from 0.06 to 0.16. Variable levels of genetic diversity observed among cultivars probably derived from the diverse germplasm sources and methods used in the genetic breeding programs, the number of advanced generations of each cultivar, as well as genetic recombination or cross-fertilization during breeding programs. Bayesian cluster analysis, principal component analysis, and Neighbor-Net showed three divergent genetic groups, with a high genetic differentiation index (FST = 0.46). The pairwise FST also revealed high divergence among cultivars. IDR-Parana had the cultivars with the highest genetic variability among these four Brazilian coffee breeding centers. We found that AFLP markers allowed us to distinguish the cultivars/progenies in the Brazilian National Trial. We conclude that Brazilian coffee germplasm still has considerable genetic variability for the development of new cultivars with high productivity, resistance to disease, superior beverage quality, and adaptation to diverse edaphoclimatic conditions in the different producing regions.