Genetic variation in cultivated coffee (Coffea arabica L.) accessions in northern New South Wales, Australia

Genetic consistency within varieties is essential to quality assurance for any agricultural product. While the Australian coffee industry targets high quality coffee, there is observed morphological variation within coffee varieties in New South Wales plantations. This variability may result from environmental, genetic and/or management factors. Genetic factors can be tested by molecular markers which can also shed light on the questions concerning crop quality management. A review of the literature showed low genetic variation in C. arabica. Hence four different molecular marker systems were used in this study to detect possible genetic variation within and between varieties of local coffee grown in Northern New South Wales (NNSW), Australia. Genetic variation in eighty-four seed propagated coffee (C. arabica) accessions, mainly from two commercial varieties (K7 and CRB) in NNSW, were tested using various PCR-based marker systems (RAPDs, ISSRs, SSRs and AFLPs). Eleven accessions from Central Highland, Vietnam, were used as reference material. While RAPD and ISSR did not distinguish intra-varietal molecular variation, SSR and AFLP data revealed the degree of genetic variability and the relationship among individuals within and between coffee varieties. Despite observed morphological variation within supposedly single variety plantations in NNSW, the genetic variation, measured by genetic distance, revealed in this study was very low (K7: 0.193; CRB: 0.205). There exists genetic variation between different farms sharing the same cultivar (K7) which suggests differences in the management of plantation establishment and sourcing of trees. The genetic variability is not aligned with off-type individuals observed in K7, but is with off-type CRB plants which is probably due to inter-varietal hybrids from unintentional outcrossing. The mean level of genetic identity between cultivars derived from the two distinct types of C. arabica is moderate (0.641). Although genetic variation within and among arabica cultivars is low, sufficient DNA polymorphism was found among some C. arabica accessions to allow differentiation. The results in this study suggested that even the elite cultivars, which have been exposed to intensive selection, still show a certain degree of genetic variation amongst individuals within each cultivar even though C. arabica is a predominantly selfing species and has a narrow genetic foundation. The congruence between AFLP and SSR data sets suggests that either method individually, or a combination, is applicable to genetic studies of coffee. SSR alone clearly distinguished and revealed inter-varietal heterogeneity but were more powerful when combined with AFLP.