Molecular analysis of introgressive breeding in coffee (Coffea arabica L.)

Nineteen arabica coffee introgression lines (BC₁F₄) and two accessions derived from a spontaneous interspecific cross (i.e. Timor Hybrid) between Coffea arabica (2n=4x=44) and C. canephora (2n=2x=22) were analysed for the introgression of C. canephora genetic material. The Timor Hybrid-derived genotypes were evaluated by AFLP, using 42 different primer combinations, and compared to 23 accessions of C. arabica and 8 accessions of C. canephora. A total of 1062 polymorphic fragments were scored among the 52 accessions analysed. One hundred and seventy-eight markers consisting of 109 additional bands (i.e. introgressed markers) and 69 missing bands distinguished the group composed of the Timor Hybrid-derived genotypes from the accessions of C. arabica. AFLP therefore seemed to be an extremely efficient technique for DNA marker generation in coffee as well as for the detection of introgression in C. arabica. The genetic diversity observed in the Timor Hybrid-derived genotypes appeared to be approximately double that in C. arabica. Although representing only a small proportion of the genetic diversity available in C. canephora, the Timor Hybrid obviously constitutes a considerable source of genetic diversity for arabica breeding. Analysis of genetic relationships among the Timor Hybrid-derived genotypes suggested that introgression was not restricted to chromosome substitution but also involved chromosome recombinations. Furthermore, the Timor Hybrid-derived genotypes varied considerably in the number of AFLP markers attributable to introgression. In this way, the introgressed markers identified in the analysed arabica coffee introgressed genotypes were estimated to represent from 9% to 29% of the C. canephora genome. Nevertheless, the amount of alien genetic material in the introgression arabica lines remains substantial and should justify the development of adapted breeding strategies. Received: 2 February 1999 / Accepted: 12 May 1999     

Plant regeneration through somatic embryogenesis from tissues of mature oak trees: true-to-type conformity of plantlets by RAPD analysis

Somatic embryogenesis was induced in expanding leaf explants excised from epicormic shoots forced from branch segments taken at four different times of year from a mature oak (Quercus robur L.). Branch segments 2–4 cm in diameter produced most shoots when collected in March. Somatic embryos were induced on explants derived from branches of all collection dates, although collection in November seemed to afford the best results. Germination and conversion ability of embryos of embryogenic lines derived from six oak trees depended heavily on genotype, conversion rates ranging from 0 to 70%. RAPD analyses found no evidence of genetic variation either within or between the embryogenic lines established from three of these trees, or between these lines and the trees of origin, or between somatic embryo derived plantlets and the trees of origin. The embryogenic system used in this study appears to be suitable for true-to-type clonal propagation of mature oak genotypes.     

Glufosinate as an efficient inhibitor of callus proliferation in coffee tissue

Summary To improve selection of transgenic Coffea spp. tissue after transformation treatments, the effects of the selective agents chlorsulfuron, glufosinate, glyphosate, hygromycin, and kanamycin were studied on callus development from leaf explants (from greenhouse-grown plants and somaplants) and in embryogenic suspension cultures. Studied genotypes were from C. arabica, C. canephora, and the interspecific hybrids Arabusta and Congusta. A culture system based on “direct” somatic embryogenesis from C. canephora leaf explants proved to be more sensitive to selective agents than high frequency somatic embryogenesis from C. arabica or Arabusta leaf explants. With respect to the selective effect, chlorsulfuron and hygromycin provoked strong inhibition and severe necrosis, whereas glyphosate and kanamycin showed variable inhibition. Glufosinate appeared to efficiently inhibit growth of both leaf callus and callus suspensions of all genotypes tested without inducing necrosis. These properties may make the use of glufosinate advantageous in a selective growth system for detection of transformed coffee tissues.     

Somatic Embryogenesis in Mature Quercus Robur Trees

Somatic embryo induction and plant regeneration have been obtained in tissues from mature Quercus robur L. trees. Epicormic shoots were forced to flush in branch segments collected from the crown of trees growing in selected stands on different collection dates. Expanding leaves from five genotypes, cultured following a multistage treatment procedure, produced somatic embryos at frequencies ranging from 0.3 to 3.6% of leaf explants, depending on genotype and collection date. After being induced, somatic embryos started a recurrent process by secondary embryogenesis which amplified the 15 embryogenic lines established. Plant recovery was achieved in 60% and 17% of matured embryos from two genotypes.     

Genotypic variation and aging effects on the embryogenic capability of <Emphasis Type="Italic">Kalopanax septemlobus</Emphasis>

In an attempt to obtain insight into the differential responsiveness of different genotypes of Kalopanax septemlobus regarding their embryogenic capacity, several parameters such as endogenous hormonal levels, DNA content, embryogenic callus proliferation and somatic embryogenesis were studied in several genotypes of this plant. Also, to understand the effect of the age of the explants on their embryogenic capacity, the same parameters were studied in two embryogenic cell lines of different ages in the selected genotype. In the present study, it was observed that the cytokinins/abscisic acid (ABA) ratio plays an important role in embryogenic capacity in the studied genotypes of K. septemlobus species. A decrease in embryogenic capacity of callus was observed with increasing age, along with a marginal decrease in the DNA content of nuclei. Further, it can be suggested from our results that young embryogenic callus is a better choice for somatic embryo formation than the long-term-maintained callus in K. septemlobus.     

In vitro selection of Coffea arabica callus for resistance to partially purified phytotoxic culture filtrates from Colletotrichum kahawae

Calli derived from hypocotyl explants of a susceptible and resistant genotype of Coffea arabica were evaluated for their response to different concentrations of partially purified culture filtrates (PPCFs) produced by Colletotrichum kahawae which are phytotoxic. The size of calli was measured non-destructively by automated image analysis. Differential responses of calli ranged from complete necrosis or reduced growth in the susceptible genotype (N39) to an absence of necrosis and rapid growth in the resistant genotype (cv. Hybrido de Timor). Subsequently, one selection cycle in the presence of PPCF was devised and applied to calli of nine C. arabica genotypes. Normal plants were regenerated through somatic embryogenesis of callus lines that survived the phytotoxin treatment and in vitro and in vivo testing of these plants against the PPCF showed that increased resistance to the toxin had been obtained. These studies suggest that in vitro selection of calli may be a feasible approach to acquiring germplasm with improved resistance to coffee berry disease.     

Biotechnological applications for the improvement of coffee (Coffea arabica L.)

Summary The important advances in coffee biotechnological techniques which have been made particularly during the last 10yr could benefit the coffee breeder in practice and open new perspectives for the development of new varieties. The molecular phylogeny of Coffea species has been established using DNA sequence data. The molecular markers have revealed an extremely reduced genetic diversity in Coffea arabica L. in comparison to C. canephora. However, wild accessions collected in the Ethiopian highlands appeared to constitute a valuable gene reservoir. A complete genetic linkage map of C. canephora was reported and additional ones are being constructed, particularly on C. arabica. The integration of Molecular Assisted Selection in coffee breeding promises to drastically increase the efficiency of breeding programs. Economically important genes of the caffeine biosynthetic pathway or genes encoding for seed storage proteins have been isolated. The high performance already achieved in the in vitro propagation process by somatic embryogenesis offers the possibility to mass propagate superior hybrids in different countries of both C. arabica (selected F₁ hybrids) and C. canephora (rootstock variety). Pilot productions by somatic embryogenesis currently permit preparation for commercial application. Somaclonal variation was observed. The percentage of the off-types can vary between 3 and 10% depending on the genotype. Seed cryopreservation enables a routine use for long-term conservation of coffee genetic resources. Transgenic plants have been obtained for the C. arabica and C. canephora cultivated species through Agrobacterium-mediated transformation which constitutes the technique now currently used to transfer directly genes in coffee plants.     

Transgenic coffee fruits from <Emphasis Type="Italic">Coffea arabica</Emphasis> genetically modified by bombardment

The genetic modification of Coffea arabica fruits is an important tool for the investigation of physiological characteristics and functional validation of genes related to coffee bean quality traits. In this work, plants of C. arabica cultivar Catuaí Vermelho were successfully genetically modified by bombardment of embryogenic calli. Calli were obtained from 90% of the leaf explants cultivated in a callogenesis-inducing medium modified with 20 μM 2,4-dichlorophenoxyacetic acid (2,4-D). The resulting calli were bombarded with the pBI426 vector containing a uidA and nptII gene fusion that was driven by the double CaMV35s promoter. Kanamycin-selected embryos were positive for β-glucuronidase (GUS) activity in histochemical assays and for target gene amplification by polymerase chain reaction. Integration of the nptII gene was confirmed by Southern blot and showed a low copy number (one to three) of insertions. Transformed plants showed normal development and settled fruits. GUS expression was assessed in the flower and fruit organs demonstrating the capacity of the double CaMV35s promoter to drive long-term stable expression of uidA in C. arabica fruit tissues. Moreover, we obtained a T₁ progeny presenting 3:1 Mendelian segregation of the uidA gene. This investigation is the first to report exogenous gene expression in coffee fruits and transgenic inheritance in C. arabica plants.     

Responses of cells and protoplasts of Coffea arabica genotypes to partially purified culture filtrates produced by Colletotrichum kahawae

Hypocotyl-derived calli of genotypes and segregating populations of Coffea arabica, differing in susceptibility to Colletotrichum kahawae, were used to produce cell suspensions and protoplasts which were exposed to partially purified culture filtrates (PPCFs) prepared from the pathogen. The growth and viability of PPCF-treated cells and protoplasts were measured using packed cell volume, fluorescein diacetate staining and a colorimetric assay involving the tetrazolium salt MTT. Differential responses of cells and protoplasts were influenced by genotype, time of exposure and PPCF concentration. Protoplasts of resistant genotypes responded differentially from more susceptible genotypes as early as 4 h after challenge with the phytotoxin, suggesting that they were more sensitive than cell suspensions to the treatments. Protoplasts exposed to PPCFs from C. kahawae may therefore be used to screen and select genotypes resistant to, or tolerant of, coffee berry disease. Received: 10 April 1996 / Revision received: 25 August 1996 / Accepted: 15 September 1996     

Detection of genetic diversity and selective gene introgression in coffee using RAPD markers

RAPD (randomly amplified polymorphic DNA) markers generated by arbitary decamers have been successfully employed to detect genetic polymorphisms between coffee species and between Coffea arabica genotypes. The RAPD profiles were used to construct dendrograms and these were consistent with the known history and evolution of Coffea arabica. Material originating from Ethiopia and the arabica sub-groups — C. arabica var. typica and C. arabica var. bourbon — were clearly distinguished. RAPD analysis therefore reflects morphological differences between the sub-groups and the geographical origin of the coffee material. Species-specific amplification products were also identified, but, more importantly, amplification products specific to C. canephora were identified in two C. arabica genotypes, Rume Sudan and Catimor 5175. This diagnostic product is therefore indicative of interspecific gene flow in coffee and has biological implications for selective introgressive hybridisation in coffee. Our study demonstrates the power of the polymerase chain reaction technology for the generation of genetic markers for long-lived perennial tree and bush crops.On study leave from: Universidad de San Carlos de Guatemala, Facultad de Agronomia, Ciudad Universitaria, Zona 12, Apartado Postal No. 1545, Guatemala, Central America     

Population structure and genetic diversity of coffee progenies derived from Catuaí and Híbrido de Timor revealed by genome-wide SNP marker

The use of single nucleotide polymorphism (SNP) molecular markers has provided advances in selection methodologies used in breeding programs of different crops, reducing cost and time of cultivar release. Despite the great economic and social importance of Coffea arabica, studies with SNP markers are scarce and a small number of SNP are available for this species, when compared with other crops of agronomic importance. Thus, the objective of this study was to identify and validate SNP molecular markers for the species Coffea arabica and to introduce these markers to genetic breeding by means of an accurate analysis of the diversity and genetic structure of breeding populations of this species. After quality filtering, 11,187 SNP markers were selected from the coffee population obtained from crosses between the genotypes Catuaí and Híbrido de Timor. A great number of markers were distributed in the 11 chromosomes, within transcribed regions, and were used to estimate the genetic dissimilarity among the individuals of the breeding population. Dendrogram analysis and a Bayesian approach demonstrated the formation of two groups and the discrimination of all genotypes evaluated. The expressive number of SNP molecular markers distributed throughout C. arabica genome was efficient to discriminate all the accessions evaluated in the experiment, clustering them according to their genealogies. This work identified mixtures within the progenies. The genotyping data also provided detailed information about the parental genotypes and led to the identification of new candidate parents to be introduced to the breeding program. The study discussed population structure and its consequence in obtaining improved varieties of C. arabica.     

Effects of Leaf Wetness Duration and Inoculum Level on Resistance of Wheat Genotypes to Pyrenophora tritici-repentis

Percent leaf necrosis and lesion length on wheat genotypes increased markedly with increasing duration of leaf wetness (up to 24h or 48 h) following inoculation with Pyrenophora tritici-repentis. A long wetting duration favoured less disease development on resistant (Fink's'), and moderately resistant (Bon/YR/3/F3570//KAL/BB) genotypes than on susceptible Glenlea. No significant difference in per cent necrosis was detected among the upper three leaf positions within a genotype. A long wetness duration had a varying effect on the resistance of wheat genotypes, depending upon the inoculum level. Increasing the inoculum level along with the leaf wetness period increased the per cent leaf necrosis on all three wheat genotypes tested. However, the ranking of the genotype for resistance did not alter even after prolonged duration of leaf wetness (up to 96 h) and/or high inoculum level (12000 conidia/ml water). Various post-inoculation wet-periods in combination with high conidia concentrations in inoculum should be used in identifying highly resistant germplasm in breeding populations at the seedling stage of the wheats.     

Effects of Leaf Wetness Duration and Inoculum Level on Resistance of Wheat Genotypes to Pyrenophora tritici-repentis

Percent leaf necrosis and lesion length on wheat genotypes increased markedly with increasing duration of leaf wetness (up to 24h or 48 h) following inoculation with Pyrenophora tritici-repentis. A long wetting duration favoured less disease development on resistant (Fink's'), and moderately resistant (Bon/YR/3/F3570/KAL/BB) genotypes than on susceptible Glenlea. No significant difference in percent necrosis was detected among the upper three leaf positions within a genotype. A long wetnessduration had a varying effect on the resistance of wheat genotypes, depending upon the inoculum level. Increasing the inoculum level along with the leaf wetness period increased the per cent leaf necrosis on all three wheat genotypes tested. However, the, ranking of the genotype for resistance did not alter even after prolonged duration of leaf wetness (up to 96 h) and/or high inoculum level (12000 conidia/ml water). Various post-inoculation wet-periods in combination with high conidia concentrations in inoculum should be used in identifying highly resistant germplasm in breeding populations at the seedling stage of the wheats.     

Effect of different cryoprotectant procedures on the recovery and maturation ability of cryopreserved <Emphasis Type="Italic">Pinus pinea</Emphasis> embryogenic lines of different ages

Strategies for genetic improvement programs of Pinus pinea L, an important tree species of the Mediterranean ecosystem, are focused on increasing pine nut yield. Somatic embryogenesis and cryopreservation of elite genotypes are emerging as key components of advanced forest breeding programs. This study was carried out with embryogenic lines of different ages obtained from selected half-sib families of the species. The effect of three cryoprotectant procedures on the recovery and maturation ability was tested in embryogenic lines that showed different growth rate, two of them at different ages. In general, cryopreservation drastically reduced growth rates of frozen and rewarmed tissues; however, the use of 5% PEG–sucrose–DMSO dramatically increased growth rates of rewarmed embryogenic cultures. Overall, embryogenic lines of stone pine were suitable for cryopreservation. Seven out of eight lines were recovered, although the initial growth rates were variable. Five of six lines including the three oldest ones were recovered using 5% PEG–sucrose–DMSO. No relation was observed between age and growth rate of embryogenic lines and their response to cryopreservation. The line 2F47 showed the most stable response after long-term subculture and recovery after cryopreservation, at different ages. On the contrary, younger embryogenic lines either recovered after cryopreservation or did not, depending on the applied procedure. Maturation of some of the older lines was restored or enhanced after cryopreservation. Somatic embryos were obtained in three out of five tested embryogenic lines recovered from cryopreservation. However, only a few plantlets from cryopreserved lines were regenerated indicating the process must be optimized further before it is a practical adjunct to breeding.     

A comparison of shoot regeneration from protoplasts and leaf discs of different genotypes of the cultivated tomato

Summary Shoot regeneration from leaf discs and leaf mesophyll protoplasts of 11 genotypes of Lycopersicon esculentum (the cultivated tomato), were compared. In both regeneration procedures genotypic differences were observed between inbred lines, and also between F1 hybrids and their parental lines. In the tested hybrid genotypes no heterosis effect with respect to shoot regeneration capacity was observed. A correlation between shoot regeneration from leaf discs and from leaf mesophyll protoplasts was apparent in the tested genotypes. This suggests that using the described procedure, shoot regeneration from leaf discs can be usef for rapid pre-screening for regeneration capacity from protoplasts of tomato genotypes.     

Genetic transformation of commercial breeding lines of alfalfa (Medicago sativa)

Bio-engineering technologies are now routinely used for the genetic improvement of many agricultural crops. However, breeding lines of Medicago sativa are not easily amenable to genetic transformation and therefore cannot benefit from the molecular tools that have been developed for genetic manipulations. This paper describes a strategy that has been developed to transfer DNA into commercially important breeding lines of winter-hardy alfalfa via Agrobacterium infection. Three highly regenerative genotypes have been selected from ca 1000 genotypes within 11 breeding lines. They have been used as basic material for an extensive genetic transformation trial. Combinations of genotypes (11.9, 8.8, 1.5) expression vectors (pGA482, pGA643, pBibKan) and bacterial strains (C58, A281, LBA4404) were tested for their ability to produce stable transgenic material. Putative transgenic plantlets were further screened by nptII-specific PCR amplification, Southern hybridization and recallusing assays. One genotype (1.5) gave only one transformant out of 432 individual trials. With the two other genotypes, efficiency of transformation (kanamycin-resistant calluses obtained/explant tested) ranged from 0 to 0.92 depending on the strain/vector combination used. Statistical interactions underline the possibility of obtaining good genotype-strain-vector combinations for alfalfa transformation. Predicted transformation probability indicates that with strain LBA4404 containing the vector pGA482 and genotype 11.9, transformation efficiency is above 60% and 10% or more of the calluses retain embryogenic potential. PCR amplification and Southern hybridization of randomly chosen regenerated plantlets demonstrated that all embryos developing on 50 g ml^-1 kanamycin had a stable genomic insertion of nptII. Sexual crosses with untransformed genotypes showed that segregation of the transgenic trait followed Mendelian heredity.     

Isolation and characterization of nine microsatellite markers from Coffea arabica L., showing wide cross‐species amplifications

Genetic improvement of coffee (Coffea arabica L.) is constrained by low genetic diversity and lack of genetic markers, suitable screening tools, information on the genetic make‐up of available gene pool and long generation time. In this context, use of DNA markers such as microsatellites that provide high genetic‐resolution becomes highly desirable. Here, we report the development of nine new microsatellite markers from partial genomic library of an elite variety of Coffea arabica. The developed microsatellites revealed robust cross‐species amplifications in 17 related species of coffee, and their Polymorphic Information Content varied from 0 to 0.6, 0 to 0.78 and 0.67 to 0.90 for the arabica, robusta genotypes and species representatives, respectively. The data thus suggest their potential use as genetic markers for assessment of germplasm diversity and linkage analysis of coffee.     

Differential gene expression in embryogenic and non-embryogenic clusters from cell suspension cultures ofCoffea arabica

Somatic embryogenesis (SE) is a very useful system for studying the differentiation process in plants and involves gene regulation at several levels. During SE induction in Coffea arabica cv. Catura Rojo two types of cell clusters, embryogenic (EC) and non-embryogenic (NEC), were observed. The goal of this work was to compare the most relevant characteristics between EC and NEC for a better understanding of the mechanism driving SE. Morphohistological observations indicated a correlation between the morphological features of clusters and their embryogenic competence. On the other hand, no variation at the DNA level, studied by AFLP, were found to explain the disparity in embryogenic competence of clusters, but gene expression, observed by RNA differential display, and SDS-PAGE showed differences that can explain that disparity. Our results lead us to propose that differential gene expression can modulate the embryogenic capacity of coffee cells and that the number of genes turned off in somatic cells to allow for the change from a somatic to an embryogenic state, is higher than those genes that are turned on.     

Somatic embryogenesis and organogenesis in apomictic and sexual Brachiaria brizantha

Brachiaria brizantha (syn. Urochloa brizantha) is an important tropical forage grass widely cultivated in Brazil. In order to optimize tissue culture conditions for B. brizantha, in vitro culture of mature seeds, basal segments and leaf segments from in vitro plants of an apomictic and a sexual genotype of B. brizantha was performed. When cultured on different media, leaf segments yielded non-embryogenic calluses which formed several roots. Friable calluses from mature seeds and basal segments explants incubated on Murashige and Skoog medium supplemented with 2,4-dichlorophenoxyacetic acid and 6-benzyladenine yielded 80% compact and nodular embryogenic structures. Calluses with such compact embryogenic structures were highly regenerable upon transfer to medium supplemented with kinetin and naphthalene acetic acid. They produced isolated somatic embryos, multiple fused scutelli or isolated scutellum with polyembryos that germinated into isolated or multiple shoots. Green and morphologically normal plants were obtained for the two genotypes. Changing the media from pH 5.8 to pH 4.0 increased the number of explants that formed calluses as well as the number of shoots per explant. When embryogenic calluses from mature seeds were successively sub-cultured for 4 months, aiming at repetitive somatic embryogenesis, all the regenerated plants were albinos. The embryogenic nature of the compact structure was confirmed by scanning electron microscopy.     

Marker-assisted selection provides arabica coffee with genes from other <Emphasis Type="Italic">Coffea</Emphasis> species targeting on multiple resistance to rust and coffee berry disease

Selecting superior genotypes is facilitated by marker-assisted selection (MAS), which is particularly suitable for transferring disease resistance alleles because it nullifies environmental effects and allows selection of resistant individuals in the absence of the pathogen or race, enabling preventive breeding. Molecular markers linked to two major genes (S_H3 and S_H?), conferring resistance to coffee rust, and those linked to the Ck-1 gene, conferring resistance to coffee berry disease (CBD), have previously been identified. These markers were validated and used in a progeny of crosses between Indian selections with Coffea arabica cultivars. Eleven resistant individuals homozygous for S_H3 were identified by MAS. Of these, seven carry S_H? from Híbrido de Timor and the gene introduced from Coffea liberica (S_H3). S_H? was characterized as derived from Coffea canephora. Thus, it was possible to identify C. arabica genotypes carrying important genes for rust resistance introgressed from other coffee species. MAS also allowed identification of sources of CBD resistance for use in preventive breeding for resistance to this serious disease. Using two validated molecular markers, two coffee plants carrying Ck-1 were identified: the UFV 328-60 genotype (F₂) was resistant and homozygous based on both molecular markers but exhibited no markers related to S_H3 and S_H?, and the UFV 317-12 genotype (F₁) was resistant and homozygous but resistant and heterozygous based on CBD-Sat207 and CBD-Sat235, respectively. Along with possessing Ck-1, the latter carries S_H?. Overall, plants carrying different genes for resistance to rust and CBD were identified. These plants are important sources for gene pyramiding in breeding programs aimed at multiple and durable resistance.