Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers

Genetic diversity was studied using RAPD markers among119 coffee (Coffea arabica L.) individuals representing 88 accessions derived from spontaneous and subspontaneous trees in Ethiopia, the primary centre of species diversity, six cultivars grown locally in Ethiopia, and two accessions derived from the genetic populations Typica and Bourbon, spread in the 18^th century, which gave rise to the most currently grown cultivars. Twenty-nine polymorphic fragments were used to calculate a similarity index and construct dendrograms. The Ethiopian material was separated from the Typica- and Bourbon-derived accessions and classified in four groups: one with most of the collected material from southwestern Ethiopia and three from southern and southeastern Ethiopia. Almost all detected diversity was found in the southwestern group while the southern and southeastern groups presented only 59% of identified markers. The genetic distances were low between the southwestern group and the southern and southeastern groups, and between the southwestern group and the Typica- and Bourbon-derived accessions. The cultivated coffee derived from the genetic populations Typica and Bourbon appeared little differentiated from wild coffee growing in the southwest. The results supported the hypothesis that southwestern Ethiopian coffee trees could have been introduced recently in the south and southeast. A separate analysis of the 80accessions classified in the southwestern group allowed identifying particular spontaneous- and subspontaneous-derived accessions and redundancies in the collected material from southwestern Ethiopia. RAPD markers did not detect any within-collection polymorphism except for two trees that were identified as off-types in the CATIE field genebank. This revised version was published online in July 2006 with corrections to the Cover Date.     

Responses of different arabica coffee (Coffea arabica L.) clones to varied environmental conditions

Different improved coffee arabica crosseshaving resistance to coffee berry diseaseand leaf rust, plus a standard cultivar,were grown under a range of environmentalconditions in a series of field trials inKenya. The effects of location and year ofproduction and their interactions with theclones were determined for berry yield.These data were used to estimate andcompare methods of analysis of GEI. An AMMImodel, joint regression model and ANOVAwith repeated measurements were used toinvestigate these interactions. The resultsindicated the relative effects of theclones and the environmental conditions,with Meru being the location where therewas greatest discrimination between theclones, probably because it was bettersuited for coffee. Clones,environments and joint regressions combinedaccounted for 31.20% of the interaction,leaving a residual of 68.80%. Significantresidual mean squares showed therelationship between clones andenvironments not to be strictly linear,thus indicating that regression analysisdid not always provide good estimates ofindividual clonal performance acrossenvironments. High correlations wereobtained between mean yield and regressioncoefficients and between ecovalence andmean square deviations as well as thecoefficient of determination. Resultsshowed that the improved clones surpassedthe standard cultivar both in terms ofyield and stability.Different analyses of the various aspectsof genotype response enabled the 21 clonesto be classified into different similaritygroups based on their performance andphenotypic stability as measured by variousstability parameters and the use of biplotsfrom the AMMI analysis.     

A new source of resistance against coffee leaf rust from New-Caledonian natural interspecific hybrids between Coffea arabica and Coffea canephora

The development of cultivars resistant to coffee leaf rust caused by the fungal pathogen Hemileia vastatrix is a priority in coffee breeding. However, only very few descendants of interspecific hybrids between Coffea arabica and diploid relative species have been used as resistance source. Identification of new sources of resistance appeared therefore particularly worthwhile. Hybrid plants derived from interspecific hybridization between C. arabica and Coffea canephora and found in neo‐natural coffee tree populations of New Caledonia were therefore investigated. Amplified Fragment Length Polymorphism and microsatellites amplification were used to evaluate the genetic diversity of 14 hybrid plants, and rust resistance was evaluated by inoculation with a panel of rust races representing a large variability in virulence. An important genetic diversity was characterized in hybrid plants originating from introgressions into C. arabica from various C. canephora progenitors. On the 14 plants tested for leaf rust resistance, eight appeared resistant to all races investigated. Such plant material should represent a highly valuable resource for C. arabica breeding against coffee leaf rust.     

Detection by simple sequence repeat markers of introgression from Coffea canephora in Coffea arabica cultivars

Microsatellites or simple sequence repeats (SSR) were used to assess polymorphism among 16 Coffea arabica and four Coffea canephora accessions, and to identify DNA introgression fragments from C. canephora in four C. arabica lines. Thirty‐one primer pairs allowed for the identification of 92 polymorphic alleles distributed over 37 loci. The C. arabica accessions derived from the genetic bases ‘Typica’ and ‘Bourbon’ were grouped separately according to their genetic origin. Two genotypes derived from a spontaneous hybrid (C arabica×C. canephora) were classified with the C. canephora accessions from Central Africa. Coffea canephora from West Africa were separated from the other accessions studied. Four alleles related to introgression (i.e. present in C. canephora and introgressed lines, and absent in C. arabica) were identified. The SSR markers were used successfully for characterization of a particular cultivar (‘Veranero’) from Costa Rica, which is known for its late maturity.     

Pollen longevity and artificial cross-pollination in Coffea arabica L

Summary Various aspects of pollen longevity, in vitro germination of pollen and controlled pollination in Coffea arabica were investigated. High pollen viability could be maintained for more than two years, much longer than previously reported, by storing it under vacuum at 18°C. The most satisfactory method of in vitro germination of pollen was the hanging drop in a Van Tieghem cell, with a 10°, sucrose solution. For artificial cross-pollination it is necessary to carry out emasculation and bagging at the latest one day before anthesis. The stigmas of unpollinated flowers remained receptive for at least nine days.This paper is published with permission of the Director, Coffee Research Station, Ruiru, Kenya     

Breeding for low seed caffeine content of coffee (Coffea L.) by interspecific hybridization

Summary Seeds from open-pollinated flowers collected from hybrids of several Coffea species were analysed for caffeine content. The caffeine content was not always intermediary to that of the parents; higher and lower values were found. Diploid F₁ hybrids between accessions of C. eugenioides and C. salvatrix showed the lowest seed caffeine content. Seeds of the tetraploid hybrids C. arabica × C. salvatrix or C. arabica × C. eugenioides hybrids presented low caffeine content. The possibility of breeding coffee to reduce the caffeine content in the seeds by interspecific hybridization of C. arabica with other Coffea species is discussed.     

Breeding for resistance to coffee berry disease in Coffea arabica L. II. Inheritance of the resistance

Summary The inheritance of resistance to coffee berry disease (CBD) has been studied by applying a preselection test to F₂ progenies of a half diallel cross between 11 coffee varieties with different degrees of resistance and to sets of parental, F₁, F₂, B₁₁ and B₁₂ generations of crosses between resistant and susceptible varieties. True resistance to CBD appears to be controlled by major genes on three different loci. The highly resistant variety Rume Sudan carries the dominant R- and the recessive K-genes. The non-allelic interaction between these two genes is of a duplicate nature. The R-locus has multiple alleles with R ₁R₁alleles present in Rume Sudan and the somewhat less effective R ₂R₂alleles in a variety like Pretoria, which also has the K-gene. The moderately resistant variety K7 carries only the recessive K-gene. The arabica-like variety Hibrido de Timor (a natural interspecific arabica x robusta hybrid) carries one gene for CBD resistance on the T-locus with intermediate gene action. It probably inherited this gene from its robusta parent. There is circumstantial evidence that the resistance to CBD is of a stable nature, but it is advisable to accumulate in one genotype as many resistance genes as possible by combining in the breeding programme the resistance of Rume Sudan with that of Hibrido de Timor.     

The evaluation of arabica coffee cultivars for resistance to coffee berry disease: Some comments

Summary The preselection test as used in the Kenya arabica coffee breeding program was critically examined prior to use in a similar program in Uganda, since the criticism by Van der Graaff (1982) of the an der Vossen et al., scaling technique for measurement of seedling resistance to Colletotrichum coffeanum may alter the interpretation of results.The published data were re-analysed using non-parametric statistical techniques and it is concluded that, despite the criticism, the method appears to give satisfactory results. It is suggested however, that the mode of the distribution obtained by the selection test be considered as a suitable alternative to the mean in the interpretation of results.     

Genetic diversity for RAPD markers between cultivated and wild accessions of Coffea arabica

Summary Random amplified polymorphic DNA (RAPD) markers have been successfully employed to analyse the genetic diversity among cultivated and subspontaneous accessions of Coffea arabica. The narrow genetic base of commercial cultivars was confirmed. On the other hand, a relatively large genetic diversity was observed within the germplasm collection demonstrating the importance of collecting missions. Results suggested an East-West differentiation in Ethiopia, the primary centre of diversification of C. arabica. The large heterosis effect reported in intergroup hybrids could be related to such genetic differentiation. RAPD method appeared to be effective in resolving genetic variations and in grouping germplasm in C. arabica.     

Prediction of genetic value for coffee production in Coffea arabica from a half-diallel with lines and hybrids

Genetic analysis of yield and morphological traits has been carried out in Coffea arabica from a half-diallel including the parental lines. The trial was established in west Cameroon with completely randomized single-tree plots. Observations included yield (four years), stem diameter, height and number of primaries. General combining abilities (GCA) and specific combining abilities (SCA) as heritabilities and genetic correlations were estimated. A significant SCA variance was observed for all the traits. Morphological traits, stem diameter, plant height and number of primaries, were genetically correlated to the yield. The hybrids were, on average, better performing than lines. There was no clear relationship between performance of lines and their general combining ability. Contribution of the seven lines to the SCA sum of squares was shown to be unequal for all the studied traits, one parent (Java) being far the most interactive. This variation of interactivity seemed to be related to different levels of residual heterozygosity among parental lines. Indirect prediction of yield using morphological traits gave the same value for expected genetic gain as the prediction based on cumulated yield over four years. The multitrait indirect selection for yield operated in a different way as far as GCA and SCA are concerned. The application of these results to coffee breeding strategies involving hybrid selection is discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

High regeneration potential in vitro of sunflower (Helianthus annuus L.) lines derived from interspecific hybridization

Successful selection of interspecific hybrid progenies with superior ability to regenerate shoots from apical meristems was performed in sunflower which now allows for the development of lines for improved biotechnological applications. Early generations of interspecific hybrids originating from crosses between the two H. annuus CMS lines ‘HA89’ and ‘Baso’, and 9 wild species were screened for their ability to regenerate in vitro. Evaluation of 36 progenies allowed to identify seven progenies from crosses involving H. mollis, H. giganteus, H. strumosus, and H. decapetalus which showed a significantly higher regeneration potential than the commercial hybrid ‘Albena’ regarding the number of shoots per explant. Among these progenies, 47.2 to 62.4% of explants produced shoots with an average of 2.3 to 3.5 shoots per cultured explant. Regeneration in vitro was significantly determined by the genotype. More than half of the investigated interspecific hybrids performed better than the inbred ‘HA89’ demonstrating that the high regeneration potential available in the wild species can be efficiently transferred to cultivated sunflower. The seven progenies with high regeneration potential in vitro were characterised by agronomic performance in the field. Two of the interspecific hybrids derived from H. strumosus and H. decapetalus not only showed a superior regeneration potential but also proved to be competitive to commercial hybrids with regard to important agronomic traits, e.g. fat content and TGW. This revised version was published online in July 2006 with corrections to the Cover Date.     

Resistance of Coffea arabica cv. Ruiru 11 tested with different isolates of Colletotrichum kahawae, the causal agent of coffee berry disease

Seven single conidia isolates of Colletotrichum kahawae varying in pathogenicity were used to inoculate hybrid progenies from 66 crosses ofCoffea arabica cv. Ruiru 11. The objective of this study was to investigate the effect of pathogen variation on resistance of the Ruiru 11 cultivar. The main effects of crosses and isolates were significant (p ≤0.05) while their interaction effects were non-significant. Partitioning variance components indicated that the proportion of phenotypic variance for resistance that is due to genetic effects was low. It was concluded that variation for resistance among hybrid progenies of the Ruiru 11 cultivar was probably due to differences in aggressiveness of the pathogen as reflected by the significant main effects of crosses and isolates in combination with other environmental factors which influence disease epidemics. The coffee berry disease pathogen is unlikely to have adapted to the cultivar because of the non-significant crosses × isolates interaction effects. This revised version was published online in August 2006 with corrections to the Cover Date.     

Bulked AFLP analysis for the assessment of genetic diversity in white clover (Trifolium repens L.)

The use of bulked leaf samples from individual plants for amplified fragment length polymorphism (AFLP) analysis was evaluated as a tool for assessment of genetic diversity in white clover (Trifolium repens L.). Bulking of leaf samples produced slightly simpler AFLP profiles compared to the combined profiles of individual plants from the same cultivar. Approximately 90% of bands which were present in individual plants were present in bulked samples of the same cultivar. The majority of those absent were rare bands, shared by less than 25% of individual plants. Replicate bulk samples gave almost identical banding patterns, demonstrating the robustness of the bulked AFLP technique. Cluster analysis of AFLP data derived from individual plants resulted in a phenogram similar to that produced from data derived from bulked samples of the same plants. AFLP analysis of bulked samples detected significant amounts of genetic variability among 52 cultivars and accessions with genetic similarity values ranging from 0.42 to 0.92. However, cluster analysis of AFLP data only partially reflected the geographic origin of cultivars and accessions and was not congruent with cluster analysis based on variation for morphophysiological characters. Bulked AFLP analysis provides a powerful tool for rapid assessment of genetic variability in white clover and may also be used for cultivar identification. This revised version was published online in August 2006 with corrections to the Cover Date.     

Development of a promising interspecific hybrid in black pepper (Piper nigrum L.) for Phytophthora foot rot resistance

For the first time in the history of black pepper cultivation, a partly fertile interspecific hybrid having partial resistance to the dreaded disease Phytophthora foot rot was developed through hybridizing Piper nigrum with the wild species Piper colubrinnum. Hybridity of interspecific progenies was established through morphology, anatomy, cytology, and molecular studies. The hybrid, whose chromosome number is 2n = 39, is a triploid hybrid between a tetraploid and diploid species. The hybrid designated as Culture P5PC-1 exhibited distinct anatomical and morphological feature with a large number of long spikes with reduced setting percentage. The RAPD primers OPE 07 and OPG 08 were identified as hybrid specific molecular markers. Functional evaluation revealed partial introgression of genes—responsible for Phytophthora foot rot resistance—into the hybrid. This hybrid is considered as a successful breakthrough for introgression of resistance to the cultivated species Piper nigrum from the wild species Piper colubrinnum.     

AFLP analysis of genetic diversity within and between populations of perennial ryegrass (Lolium perenne L.)

Amplified fragment length polymorphism (AFLP) analysis has been used to measure genetic diversity in perennial ryegrass (Lolium perenne L.) and to relate intra- and interpopulation variation to breeding history. Cluster analysis of AFLP data from contrasting populations showed features consistent with the origins of these varieties. Significant differences in intrapopulation diversity were detected and partial separation of different cultivars was observed. Restricted base cultivars, derived from small numbers of foundation clones, were suitable for this type of study, allowing near complete discrimination of closely related cultivars. Analysis of bulked samples was based on the pooling of genomic DNA from 20 individuals from 6 selected populations. Cluster analysis of AFLP data from bulked samples produced a phenogram showing relationships consistent with the results of individual analysis. AFLP profiling provides an important tool for the detection and quantification of genetic variation in perennial ryegrass. This revised version was published online in August 2006 with corrections to the Cover Date.     

Early determination of yield potential in arabica coffee by applying index selection

Summary Estimates of phenotypic and genotypic variances and covariances for a number of quantitative characters in arabica coffee, obtained from a variety trial in Kenya, were used to construct selection indices. The results indicated that the expected genetic advance in yield based on a selection index, containing the first two years yield and measurements of girth at base of stem and percentage bearing primaries, will be almost as large (relative efficiency 97%) as that obtained by straight selection based on 10-years yield totals. This would imply that a breeding cycle of 5 years will be sufficient for efficient selection for higher productivity in arabica coffee.     

Production of a new low-caffeine hybrid coffee and the biochemical mechanism of low caffeine accumulation

The GCAs are new tetraploid interspecific hybrids developed in Madagascar from Coffea eugenioides, C. canephora and C. arabica. Selected GCA having genotype UF1023 contained 0.37% DW caffeine and no detectable theobromine in green beans. Low caffeine accumulation in GCA plants is due mainly to the low biosynthetic activity of purine alkaloids, possibly the extremely weak N-methyltransferase reactions in caffeine biosynthesis. No significant catabolic activity of caffeine was found in GCA-UF1023, in common with almost all coffee plants including C. arabica.     

Interspecific hybridization between Coffea arabica L. and tetraploid C. canephora P. ex Fr. I. Fertility in F1 hybrids and backcrosses to C. Arabica

Summary The interspecific (C. arabica × tetraploid C. canephora) F₁ hybrid showed a low but highly variable fertility. An almost complete restoration to normal fertility was observed in individual trees of BC₁ and BC₂ generations with C. arabica as recurrent parent. From a comparison of various tests of fertility, it was found that pollen viability is a satisfactory measure of fertility.     

Genetic variability of Striga asiatica (L.) Kuntz based on AFLP analysis and host-parasite interaction

AFLP analysis was used to estimate genetic variability within and among 14 populations of Striga asiaticaL. Kuntze collected from different locations within the Republic of Benin. The mean within-population genetic distances ranged from 0.028 to 0.038, while the mean among-population genetic distances ranged from 0.019to 0.088, with an assumed minimum genetic distance of0.01 in each case. Intra- and inter-population variation was reflected by a highly significant R² of 0.61for the regression of geographic distance versus genetic distance. Interactions of the different Strigapopulations with susceptible host genotypes, 8338-1 (Zea mays) and CK60B (Sorghum bicolor),indicated a high degree of host-specialization, with CK60B failing to support growth of the parasite from any of the populations. The various Striga populations also exhibited different degrees of virulence on susceptible host plants. Our results support the hypothesis that different populations of this parasite may well be considered and treated as ecotypes in plant breeding programs developing resistance to S. asiatica. This revised version was published online in August 2006 with corrections to the Cover Date.