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.     

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.     

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.     

Genetic gains for yield after two back-crosses of the interspecific hybrid Libusta (Coffea canephora P. × C. liberica Bull. Ex Hiern) to C. canephora P.

The Libusta (Coffea canephora P. × C. liberica B.) programme initiated in the seventies in Côte d'Ivoire aims at improving the quality of coffee grown in low altitudes, with a yield comparable to current commercial C. canephora clones. The second generation of back‐crosses to the C. canephora (CAN) parent, BC2, are now likely to be commercially exploited as far as yield is concerned. The best BC2 progeny yielded 1386 kg of green coffee/ha/y, averaged over five harvest years. On average, the genetic gain for yield from BC1 to BC2 reached 22%. In a factorial mating design, no interaction was observed between BC1 and CAN parents, while both main effects were highly significant. This explained that observed genetic gains and further genetic gains may be achieved with appropriate strategies.     

Resistance to Coffee Berry Disease in Arabica Coffee Variety 'Ruiru 11'

General and specific combining ability effects for resistance to coffee berry disease (Colletotrichum coffeanum Noack sensu Hindorf) in Coffea arabica variety ‘Ruiru 11’ and its parents were estimated according to the North Carolina Design II. A set of nine male parents and eleven females were crossed in all possible combinations to generate ninety-nine single cross hybrids constituting the ‘Ruiru 11’ variety. The parents and their hybrid progenies were screened and the mean score data analyzed for possible genetic variation. The contributions of the parents to the total genetic variance were low hence the low narrow sense heritability (h²= 0.04). The male and female parents accounted for 9.36 % and 0.96 %, respectively, while their interaction effect accounted for 89.68 %. In the analysis of combining ability for resistance, ExB3.96 and Cat.90 exhibited significant negative general combining ability (GCA). Specific combining abilities (SCA) were negative and significant for Cat.86 × ExB3.99, Cat.127 × ExB3.116 and Cat.119 × ExB3.879 crosses. The implications of these results in selection for highly resistant ‘Ruiru 11’ progenies are discussed.     

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     

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.     

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.     

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.     

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.     

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.     

Genetic parameters of several biochemical compounds from green coffee, Coffea canephora

A factorial crossing scheme of Cofflea canephora (two parents from the Congolese group crossed to 14 parents of the Guinean group) was used to evaluate genetic parameters of several biochemical compounds, bean weight and crop outturn (ration of dry bean weight 10 fresh berry weight). For most characters studied, additive genetic effects were preponderant. Narrow-sense heritability was high for caffeine content (h²_ns= 0.80), fat matter content (h²_ns, = 0.74), bean weight (h²_ns= 0.73) and crop outturn (h²_ns= 1). It was intermediate for trigonelline (h²_ns= 0.38) and chlorogenic acid (h²_ns= 0.36) content. Only sucrose content had a low narrow-sense heritability (h²_ns=0.11). There were few genetic and enviromnental correlations, Consequences for breeding, in relation to coffee drinking quality, are discussed.     

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.     

Combining Ability of Doubled Haploids in Coffea canephora P.

Fifty-five doubled haploids (DH) of Coffea canephora were crossed with either heterozygous genotypes or DH in order to study their combining ability. Three agronomic trials were established. Marked hybrid vigour was observed for all characters analyzed including yield. Large differences were evident among top-crosses involving different DH produced from the same parental clone reflecting the high level of heterozygosity of clones. Factorial mating design analysis indicated that all genetic variance was attributable to additive effects in estimates of yield as well as plant height and leaf characteristics. The general combining ability variance component was also predominant for stem girth and susceptibility to leaf rust, although effects due to interaction were detected. Some hybrid combinations had yield comparable to standard clonal varieties. The implications of such results for breeding of Coffea canephora are discussed. Particularly, the development of F₁ hybrid varieties is envisaged.     

Resistance screening of <Emphasis Type="Italic">Coffea</Emphasis> spp. accessions for <Emphasis Type="Italic">Pratylenchus coffeae</Emphasis> and <Emphasis Type="Italic">Radopholus arabocoffeae</Emphasis> in Vietnam

Coffee varieties with resistance for the plant-parasitic nematodes Pratylenchus coffeae and Radopholus arabocoffeae are limited in Vietnam. A selection of imported varieties and high yield varieties of Arabica coffee in Vietnam were evaluated for resistance to both plant-parasitic nematode species in Northern Vietnam. The same experiments were carried out with hybrid arabica coffee, three selected clones of Coffea canephora and one clone of Coffea excelsa in the Western Highland of Vietnam. The screened coffee accessions from Ethiopia (KH1, KH13, KH20, KH21, KH29, and KH31) were susceptible and good host for P. coffeae. Also accessions 90P4 (Portugal) and Oro azteca (Mexico) had a reproduction factor Rf > 1. Pluma Hidalgo (Mexico), 90/6 (Vietnam), 90P3 (Portugal), 90P2 (Vietnam), Variedad (Mexico), 90T (Portugal), and Garnica (Mexico) were poor hosts (Rf < 1) but not tolerant to P. coffeae, expressed by a reduction of root weight compared to untreated control plants. Most of the coffee accessions tested in Northern Vietnam were intolerant to R. arabocoffeae, except 90T which showed no reduction of root weight, even at high initial nematode densities (4,000/pot). Good hosts for R. arabocoffeae were Variedad, KH1, KH21, KH29, KH20, KH31, and KH13 with Rf > 1. Pluma Hidalgo, 90/6, 90P3, 90P2, 90T, Oro azteca, and Garnica were poor hosts (Rf < 1). In the Western Highland experiment, all arabica coffee accessions were susceptible for P. coffeae with Rf ranging from 1.41 to 1.59. Tolerance to P. coffeae was found in C. liberica var. Dewevrei, Hong34 and Nhuantren. Coffea excelsa, Hong34, Nhuantren, and H1C19 were tolerant to R. arabocoffeae at the highest inoculation density (4,000 nematodes/pot). The most susceptible accessions were Nhuantren and K55. Resistance (Rf < 1) to R. arabocoffeae was found in C. liberica var. Dewevrei and Hong34. This article reports on the first screening for resistance and tolerance to P. coffeae and R. arabocoffeae in coffee accessions in Vietnam and shows promising results for enhanced coffee-breeding.     

<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.     

Strategies to develop polymorphic markers for <Emphasis Type="Italic">Coffea arabica</Emphasis> L.

This study reports the implementation of three strategies for the development of genetic markers and their evaluation in both progenitors of an F2 population used for the construction of a genetic map of Coffea arabica. The strategies were Cleaved Amplified Polymorphic Sequences (CAPS), Single Strand Conformational Polymorphism (SSCP), and sequence analysis predicted Single Nucleotide Polymorphism (SNP). The methodologies were developed from different sequence sources: For CAPS, we used 25 COS sequences derived from Hedyotis spp. and 29 COSII sequences derived from Solanaceae and Rubiaceae species; for SSCP, we used 111 coffee EST sequences, 50 COSII sequences, and 10 C. arabica BAC end sequences. A low polymorphism was identified with the CAPS and SSCP methodologies. A total of 61 SNPs were identified in silico from 5,371 ESTs of coffee and from amplified, cloned, and sequenced COSII markers. Sixteen of these SNPs were validated with Luminex technology and 2 of them were polymorphic in C. arabica genotypes. This study highlights the difficulties of finding polymorphism in the species C. arabica where SNP identification seems to be the best strategy to search for polymorphic markers for this low diversity plant.     

Unraveling the origin of <Emphasis Type="Italic">Coffea arabica</Emphasis> ‘Bourbon pointu’ from La Réunion: a historical and scientific perspective

Coffee is one of the main products on the international markets, in association with oil, corn, sugar, and paper pulp. The history of coffee-tree cultivation is incompletely documented, both regarding its domestication in Africa, and its assisted dispersal throughout the world. This review focuses on the coffee mutant, Coffea arabica ‘Laurina’ (Chevalier A in Encyclopedie Biologique. Vol 28, 1947), also named ‘Bourbon pointu’. This plant is generally acknowledged to have been selected in the island of ‘Bourbon’ (La Réunion) from a field at the beginning of the 19th century. Compared with the common ‘Bourbon’ variety, ‘Bourbon pointu’ trees are dwarf, with a characteristic Christmas-tree shape and the beans have an excellent cup quality. Although cited many times in literature, the origin of this variety is ambiguous and is largely discussed even today with increasing confusion, particularly in books and local newsletters. This article provides a thorough historical and bibliographical review of coffee cultivation in La Réunion, which leads to an understanding of the bottleneck responsible for the low genetic diversity of the ‘Bourbon’-type modern varieties. Complemented by a review of the scientific studies conducted on this subject, confirmation of the veracity of the various historical accounts becomes possible, and appropriate conclusions on the origin of the ‘Bourbon pointu’ are derived. Although historical texts provide important information and represent priceless resources that give direction to scientific research, it is clear that this same research makes it possible, in turn, to clarify and to interpret historical texts.

Heterozygous genotypes are efficient testers for assessing between-population combining ability in the reciprocal recurrent selection of Coffea canephora

Coffea canephora Pierre breeding in Côte d’Ivoire is based on indirect reciprocal recurrent selection (RRSi) using the Congolese and Guinean populations. In practice, the genotypes of each population (78 Congolese genotypes and 100 Guinean genotypes) are tested with several testers from the reciprocal population: two Guinean and three Congolese testers. These testers are heterozygous as C. canephora is a strictly outcrossing species. After a first cycle of RRSi, we judged the efficiency of these testers for yield, susceptibility to coffee leaf rust (SCLR) and hundred bean weight (HBW). All the testers discriminated the tested genotypes highly significantly (P < 0.01), even though differences were found in the degrees of discrimination. For yield and SCLR, no interaction between tested genotypes and testers was observed and correlations between test values obtained from different testers were significant or highly significant. Furthermore, test values of tested genotypes could be used to predict the yield and SCLR of between-population (BP) hybrids. Prediction was always more accurate with the best tester than with the mean of several testers. As opposed to yield and SCLR, HBW showed significant interactions between tested genotypes and testers and HBW of hybrids could not be predicted from the test value of the genotypes. We conclude that only one reciprocal tester can be used in the next cycles of RRSi applied to C. canephora. This will allow either a reduced cost of selection or increased selection intensity.