Ecological speciation through host-shift has been proposed as a major route for the appearance of novel fungal pathogens. The growing awareness of their negative impact on global economies and public health created an enormous interest in identifying the factors that are most likely to promote their emergence in nature. In this work, a combination of pathological, molecular and geographical data was used to investigate the recent emergence of the fungus Colletotrichum kahawae. C. kahawae emerged as a specialist pathogen causing coffee berry disease in Coffea arabica, owing to its unparalleled adaptation of infecting green coffee berries. Contrary to current hypotheses, our results suggest that a recent host-jump underlay the speciation of C. kahawae from a generalist group of fungi seemingly harmless to coffee berries. We posit that immigrant inviability and a predominantly asexual behaviour could have been instrumental in driving speciation by creating pleiotropic interactions between local adaptation and reproductive patterns. Moreover, we estimate that C. kahawae began its diversification at <2200 bp leaving a very short time frame since the divergence from its sibling lineage (c. 5600 bp), during which a severe drop in C. kahawae's effective population size occurred. This further supports a scenario of recent introduction and subsequent adaptation to C. arabica. Phylogeographical data revealed low levels of genetic polymorphism but provided the first geographically consistent population structure of C. kahawae, inferring the Angolan population as the most ancestral and the East African populations as the most recently derived. Altogether, these results highlight the significant role of host specialization and asexuality in the emergence of fungal pathogens through ecological speciation.

Coffee berry disease (CBD) caused by Colletotrichum kahawae is a major constraint to Arabica coffee ( Coffea arabica ) production in Africa. One source of resistance to the disease is a natural interspecific hybrid between C. arabica and C. canephora and its derivatives. This study is aimed at deciphering the genetic basis of the host resistance and identification of molecular markers associated with it. CBD is a mature stage disease and in the absence of a mature mapping population, early detection of disease reaction phenotypes of mapping individuals is required. Two F 2 populations from crosses of cv. Catimor (resistant) and cv. SL28 (susceptible) were screened for resistance by a two step procedure. First, half of each population was screened 6 weeks after germination by inoculating hypocotyls with the pathogen. The surviving seedlings (G1) were considered to be resistant and were raised in a nursery together with the other unscreened halves (G2). Secondly, after one year, all the seedlings (G1 + G2) were screened by inoculation. Analysis of 57 microsatellites and 31 AFLP markers in 56 and 95 seedlings from G1 and G2, respectively, were performed. Eight AFLP and two microsatellites markers linked tightly to the resistant phenotype were identified and mapped to one unique chromosomal fragment introgressed from C. canephora . The gene conferring the resistance was localized within an 11 cM segment. It is concluded that the locus carries a major resistance gene designated Ck -1, which is likely to be synonymous to the T gene described in previous studies.

Biochemical composition appears to be influenced by both genetic factors and plant growth conditions. The main objective of this study was to evaluate the biochemical composition of selected Ruiru 11 sibs and its relationship with cup quality. Thirty four (34) Ruiru 11 sibs grown in three different locations in Kenya were used in this study. The experiment was laid out in a Randomized Complete Block Design with three replications. Coffee cherries were picked during the peak harvesting period between 2009 and 2011. The cherries were wet processed and graded into different grades based on size, shape and density. Fifty (50) grams of the dry coffee beans per sib per replication were frozen at -80 ºC before grinding (< 0.5 mm particle size) in liquid nitrogen as specified by the Association of Official Analytical Chemists (AOAC). The samples were packed in small plastic bottles and stored at -80 ºC awaiting extraction of biochemical components. Caffeine, trigonelline and total chlorogenic acids were extracted and purified using classical methods and analysed using High Pressure Liquid Chromatography (HPLC). For the lipids, the sample was subjected to Soxhlet extraction using n-hexane. The study demonstrated the existence of high variation in biochemical composition among Ruiru 11 sibs. Significant correlations were observed between biochemical and cup quality traits indicating that biochemical composition plays a major role in determining the sensory quality of coffee. The growing environment was also found to have an effect on biochemical composition as portrayed by high locational variations.

Coffee leaf rust (CLR), caused by the fungus Hemileia vastatrix, is among the most important diseases affecting coffee all over the world. In Kenya, it is currently the second most important disease, and breeding coffee to obtain new resistant cultivars has been a priority. Over time, new rust pathogenic races able to infect hitherto resistant coffee genotypes have been registered. To date, 49 races of the pathogen have been characterized all over the world. The most recent races to be characterized are able to infect derivatives of Timor Hybrid (HDT), which is a major source of resistance in breeding programs. This work aimed to identify new races of the pathogen in Kenya, emphasizing infected leaves sampled from CLR resistant varieties and breeding lines collected from two sites (Ruiru and Koru). Twenty-four samples were characterized, out of which 22 samples corresponded to new races of the pathogen. A total of six new races (III, XVII, XXIII, XXXVI, XLI and XLII) were characterized, revealing three new virulence genes (v 1 , v 7 , v 8 ) and possibly a fourth virulence gene, the v 9 . This finding represents a serious threat to coffee production and also a challenge to coffee breeding programs that are in progress in Kenya.

BackgroundCoffee production in Africa represents a significant share of the total export revenues and influences the lives of millions of people, yet severe socio-economic repercussions are annually felt in result of the overall losses caused by the coffee berry disease (CBD). This quarantine disease is caused by the fungus Colletotrichum kahawae Waller and Bridge, which remains one of the most devastating threats to Coffea arabica production in Africa at high altitude, and its dispersal to Latin America and Asia represents a serious concern. Understanding the molecular genetic basis of coffee resistance to this disease is of high priority to support breeding strategies. Selection and validation of suitable reference genes presenting stable expression in the system studied is the first step to engage studies of gene expression profiling.ResultsIn this study, a set of ten genes (S24, 14-3-3, RPL7, GAPDH, UBQ9, VATP16, SAND, UQCC, IDE and β-Tub9) was evaluated to identify reference genes during the first hours of interaction (12, 48 and 72 hpi) between resistant and susceptible coffee genotypes and C. kahawae. Three analyses were done for the selection of these genes considering the entire dataset and the two genotypes (resistant and susceptible), separately. The three statistical methods applied GeNorm, NormFinder, and BestKeeper, allowed identifying IDE as one of the most stable genes for all datasets analysed, and in contrast GADPH and UBQ9 as the least stable ones. In addition, the expression of two defense-related transcripts, encoding for a receptor like kinase and a pathogenesis related protein 10, were used to validate the reference genes selected.ConclusionTaken together, our results provide guidelines for reference gene(s) selection towards a more accurate and widespread use of qPCR to study the interaction between Coffea spp. and C. kahawae.

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Arabica coffee (Coffea arabica L.) is known for the production of high quality beverage while Robusta coffee (Coffea canephora Pierre) has been characterized as a neutral, weak flavored and occasionally with strong acid and pronounced bitterness. Viable and reasonably fertile interspecific hybrids can easily be obtained from crosses between the allotetraploid C. arabica L. and induced autotetraploid forms of C. canephora P. This study was carried out to determine beverage quality characteristics and biochemical components of 15 coffee genotypes, nine of them being interspecific Arabusta F 1 hybrids. Beverage quality was determined by a panel of six judges using the prescribed sensory evaluation procedures, while caffeine, oil, trigonelline, total chlorogenic acids (CGA) and sucrose were analyzed in green coffee samples using recommended methodologies. The results indicated significant (p<0.05) variations among the genotypes for all the sensory attributes. The total score, which is a reflection of the broad coffee quality performance showed that SL34 and SL28 (which served as reference in sensory quality), were not significantly different from Arabusta hybrids SL34 x UT8, SL28 x UT8, N39 x UT8, SL34 x UT6, CaturraxUT6 and SL28 x UT6. The quality of some Arabusta hybrids was found to be similar to that of pure Arabica genotypes. Similarly, biochemical variables revealed significant (p<0.05) variations for caffeine, oil and sucrose, among genotypes except for CGA and trigonelline which were not significantly different. There were positive significant correlations between all the sensory characteristics. Sucrose showed significant (P<0.05) correlations with fragrance flavour, aftertaste and overall. Trigonelline showed a significant negative correlation with body and caffeine. All the Arabusta hybrids scored specialty grade (80 points and above for total score) and therefore future studies on their performance in many locations with more variable climatic conditions is recommended.