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.     

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.     

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.     

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.     

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.     

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.     

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.     

Breeding for resistance to coffee berry disease caused by Colletrotrichum coffeanumNoack (Sensu Hindorf) in Coffea arabica L. I. Methods of preselection for resistance

Summary Two methods of preselection for resistance to coffee berry disease, by artificial inoculation of young coffee seedlings, have been developed recently at the Coffee Research Station in Kenya. The efficiency of these methods has been investigated in a series of experiments by comparing the results of the preselection tests with mature plant resistance, as indicated by visual field scores and artificial inoculation of berries and bud leaves of mature trees and including a large number of varieties and cultivars of Coffea arabica. The preselection test, by which the hypocotyl stems of 6-week old seedlings are inoculated with a spore suspension of the pathogen, proved to be more reliable than the second preselection test with shoot-tips of 10-month old plants. Correlation coefficients between the preselection test and mature plant resistance were resp. r=0.73–0.80 for the first test against r=0.60 for the latter.     

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.     

Interspecific hybridization between Coffea arabica L. and tetraploid C. canephora P. Ex Fr. II. Meiosis in F1 hybrids and back crosses to C. Arabica

Summary Melosis was studied in Coffea arabica, in induced tetraploid C. canephora, in their F₁ hybrid (arabusta hybrid) and in backcross generations of the hybrid with C. arabica as recurrent parent. Irregularities were observed, consisting of univalents (especially in the arabusta hybrid), multivalents (especially in tetraploid C. canephora) and uneven distribution of chromosomes at first anaphase. Chromosome distribution was improved by backcrossing. Meiotic irregularities wer negatively correlated with pollen fertility.     

AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid

S.288 an offspring of a putative spontaneous interspecific hybrid between tetraploid Coffea Arabica (2n = 4x = 44) and diploid C. liberica(2n = 2x = 22) and 17 arabica coffee introgression lines (representing F₂ and F₄) derived from the cross S.288 x Kent arabica were evaluated for introgression of C. liberica genetic material. In all, 36 AFLP primer combinations were used in the analysis. The AFLP profiles of introgressed lines were compared to five accessions each of C. arabica and C. liberica. A total of 137 polymorphic bands were scored among the 29 accessions analysed. The introgressed genotypes exhibited 102 marker bands consisting of 65 additional bands and 37missing bands associated with introgression of C. liberica genetic material. C. liberica accessions of EA group (C. liberica var liberica of Guinean origin) seemed to be the likely progenitor in the origin of natural hybrid. Analysis of genetic relationships in the introgressed lines suggested that introgression was limited to few fragments. Segregation and wide variation in number of marker fragments in the F₂ and F₄progenies were attributed to chromosome recombinations. The differences in the level of introgression between introgressed parent, F₂ and F₄ groups was not pronounced. Therefore the alien genetic material appeared to be fixed and there was no elimination or counter-selection over generations, from introgressed parent to F₄.In C. arabica accessions, only 35 polymorphic bands were seen confirming the low genetic diversity. On the contrary, although representing a small amount of alien genome introgression, the Liberica-introgressed genotypes provided notable genetic diversity. Considering the fact that the diploid species of Coffea constitute a valuable source of genetic diversity, the potential implications of variability generated by Liberica-introgressed genotypes in C. arabica breeding are discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

<Emphasis Type="BoldItalic">Coffea arabica</Emphasis> hybrid performance for yield,fertility and bean weight

The performance of F1 hybrid plants derived from crosses between traditional varieties of Coffea arabica of Latin America with a wild collection of Sudan–Ethiopian origin were studied for yield, fertility and bean weight. Sudan–Ethiopian material possesses resistance to certain diseases, and possibly, better beverage quality. The objective of this breeding programme is to widen the very narrow genetic base of Central American coffee, even while increasing quality and productivity. The hybrid plants were obtained from two factorial crosses made and evaluated in two locations. They were compared in the two field trials using the six maternal lines as controls. Observations were taken on vegetative characters, annual and cumulated yield, dry weight of 100 beans, extent of early abortion as measured by the fraction of peaberries and post-zygotic ovule fertility as measured by the fraction of mature no-floating berries in water (FF). The F1 hybrid population were compared to the populations of maternal lines for the aforementioned variables. An index-based selection was done in the hybrid populations employing three traits, yield, 100-bean weight and the post-zygotic fertility (FF). The performance of the selected hybrids was then compared to those of the best parental control lines in each trial. The hybrid populations yielded 22–47% more than the maternal lines, but hybrids showed significantly more sterility than the parental control lines. Selection in the hybrid populations using the three selected traits led to significant genetic gain for yield and dry weight of 100 beans, and insignificant gain for fertility (FF). When selected on the basis of fertility alone, increase in yield and 100-bean weight were not obtained within the hybrid populations. By applying selection on yield and 100-bean weight, the selected hybrids produced 11–47% higher yields than the best line along with significantly higher or identical 100-bean weight and performed identically for fertility. The yield performance of hybrids between the Latin American material and the wild Sudan–Ethiopian material calls for further selection effort for improving beverage quality.     

Doubled haploids of Coffea canephora: development,fertility and agronomic characteristics

Summary Doubled haploids (DH) of Coffea canephora Pierre were developed using haploid embryos which occur spontaneously in association with polyembryony. The frequencies of polyembryonic seeds and haploid embryos varied according to the parental genotypes. However, production of a large number of DH seemed possible from all genotypes. More than 750 DHs produced from various genotypes were grown under field conditions and evaluated for different characters of agronomic importance. Approximately half of DH genotypes did not survive, suggesting a strong, negative effect of homozygosity. Inbreeding depression is particularly severe on general vigor and reproductive aspects. For several characters studied such as leaf shape, leaf rust resistance and hundred bean weight, considerable genetic variations were observed within and between groups of DHs constituted by the DHs produced from the same clone. Despite their low vigor and reduced fertility, the DHs of C. canephora offer new possibilities in genetic research and coffee breeding.     

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.     

Selection for bean and liquor qualities within related hybrids of Arabica coffee in multilocal field trials

The success of a new variety of Arabica coffee (Coffea arabica L.) depends to an important extent on its liquor and bean qualities. Selection for these traits is however constrained by the prevalence of large genotype-by-environment (G×E)interactions in conjunction with the low genetic variability characteristic of this species. The aim of this study was to assess the extent to which key bean and liquor traits are affected by the environments and could be combined in order to improve the efficiency of selection for coffee quality in a narrow genetic basis set of hybrids obtained from a set of related lines and collectively representing the Ruiru 11 cultivar. Twenty-one full-sib families representative of this hybrid cultivar grown in Kenya in five sites exhibiting strong edaphic and climatic differences were used for the study. Rainfall amounts during various phases of berry development were used to explain the differences observed in the discriminating abilities of the locations for bean and liquor traits. The results showed that these families were best differentiated for bean sizes in the site where moisture supply was optimal throughout berry expansion and filling stages, whereas discrimination on the basis of liquor traits were best observed in the site where moderate moisture stress occurred during bean filling stage. The overall precision in prediction of family values was low for liquor qualities; but a much more efficient selection for large bold beans, optimally based on the AA grade was shown to be possible. Selection indices for family selection were computed to realize a trade-off between genetic gains in bean size and liquor flavour. This revised version was published online in August 2006 with corrections to the Cover Date.     

Reciprocal recurrent selection applied to Coffea canephora Pierre. I. Characterization and evaluation of breeding populations and value of intergroup hybrids

Summary Two breeding populations have been identified with Coffea canephora, based on geographical and genetic differences: the Guinean group from West Africa and the Congolese group from central Africa. A reciprocal recurrent selection programme based on these groups was initiated in Côte d'Ivoire in 1984. Genotypes of both groups available in field collections are either of cultivated or wild origin.Genotypic and phenotypic variability was evaluated within and between the groups for the following characteristics: isozyme patterns, architecture, drought tolerance and vigour, technological and organoleptic traits, pest and disease resistance. Variation between and within groups was found to be large. Based on isozyme analysis and phenotypic observations, two subgroups were identified within the Congolese group. Phenotypic values of parents and testers used in the first cycle of reciprocal recurrent selection are presented.Results of two intergroup hybrid trials indicate high yield and vigour for these hybrids compared to intragroup hybrids, justifying the reciprocal selection approach. Furthermore, the variation observed indicates that recurrent selection would allow progress for selection traits for both populations and intergroup hybrids.     

Race-specificity and inheritance of incomplete resistance to coffee leaf rust in some Icatu coffee progenies and derivatives of Hibrido de Timor

Summary Selfed and cross-pollinated progenies of Icatu coffee plants and derivatives of Híbrido de Timor, with susceptibility or moderate resistance to coffee rust in the field, were tested with Hemileia vastatrix race II and isolate 2 (Is. 2) in the greenhouse or laboratory. Progenies from plants with a susceptible reaction type in the field (scores 8 and 9) all showed homogeneous levels of susceptibility similar to that of the control cultivars Mundo Novo and Catuaí of Coffea arabica. Variation for incomplete resistance was mainly expressed by low or heterogeneous reaction types and also by longer latency periods. Incomplete resistance to race II of some Icatu and Catimor plants, which is overcome by Is. 2, appeared to depend on a partially dominant gene. The expression of this gene may vary also according to the genetic background and some residual resistance to Is. 2 was observed. A few derivatives of Híbrido de Timor were more resistant to Is. 2 than to race II, suggesting the presence of a resistant factor to Is. 2 in this germplasm. Segregation in progenies from other plants with incomplete resistance to race II suggested presence of one or a few genes only, which in homozygous condition or in combination seem to confer near-complete or complete resistance. The results suggest that selection for incomplete resistance, expressed by intermediate reaction types, in Icatu and derivatives of Híbrido de Timor may not provide durable resistance to coffee rust. On the other hand, due to apparent additive gene action, phenotypic selection of plants with a highly resistant reaction type could facilitate the accumulation of several resistance alleles in one genotype, which could provide an efficient barrier against new race formation of the pathogen.     

Comparison of the sensitivity of the mean and the mode in screening coffee seedlings for resistance to coffee berry disease Colletotrichum coffeanum Noack sensu Hindorf (A short communication)

Summary The utility of the modal grade as an alternative to the mean grade in the pre-selection test for screening seedlings of Coffea arabica L. for resistance to coffee berry disease (CBD) caused by Colletotrichum coffeanum NOACK sensu HINDORF was examined. Three criteria were used to compare the sensitivity of the modal grade with that of the mean grade when partitioning 6 weeks old seedlings into different resistance classes. The criteria were: the sensitivity of the two statistics as estimators of central tendency, the sensitivity of the modal grade and the mean grade as selection criteria and the correlation between the two statistics.The modal grade was neither more sensitive in detecting genotypes that fell in diffent resistance classes nor more severe than the mean grade in screening for genotypes susceptible to CBD. In the cases studied, the modal grad was highly correlated with the mean grade (r_s ranged from 0.55^**–0.82^**). Hence, it is concluded that there are practically no gains in adopting the modal grade as a pre-selection criterion in preference to the mean grade.     

Pollen storage in cocoyam (Xanthosoma sagittifolium (L.) Schott)

Summary The effect of different storage conditions on cocoyam pollen viability was investigated. Two levels of temperature (0° and 5°C) and four levels of relative humidity (0, 10, 20 and 30 percent) represented the storage environments.Viable cocoyam pollen could be obtained after 28 days in storage. The best storage condition was 5°C and 30% relative humidity.