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  • 1
    Electronic Resource
    Electronic Resource
    Identification of a major gene (Mex-1) from Coffea canephora conferring resistance to Meloidogyne exigua in Coffea arabica (2003)
    Oxford, UK : Blackwell Science Ltd
    Plant pathology 52 (2003), S. 0 
    Details
    ISSN: 1365-3059
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Among the most damaging root-knot nematode species, Meloidogyne exigua is especially common in Latin America and constitutes a major agronomic constraint in all major coffee-growing (Coffea arabica) areas. Growing nematode-resistant coffee represents the most promising option for control of the pest. The present study aimed to determine the mode of inheritance of the M. exigua resistance transferred into C. arabica from a related species, Coffea canephora, and to identify associated molecular markers. Segregation data analysis of F2 progeny derived from a cross between the resistant introgression line T5296 and the susceptible accession Et6 showed that the resistance to M. exigua is controlled by a simply inherited major gene (designated the Mex-1 locus). The gall index distribution exhibited by the F2 individuals suggested incomplete dominant expression. Fourteen AFLP markers were found associated with the resistance to M. exigua and a localized genetic map of the chromosome segment carrying Mex-1 was constructed. Furthermore, the association of the identified AFLP markers with Mex-1 was confirmed by analysis of a set of genotypes involving 28 introgression Arabica lines either resistant or susceptible to M. exigua in field conditions. These results represent an important starting point to enhance backcross breeding programmes and to perform an early selection of resistant seedlings.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-3059.2003.00795.x
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  • 2
    Electronic Resource
    Electronic Resource
    Molecular analysis of introgressive breeding in coffee (Coffea arabica L.) (2000)
    Springer
    Theoretical and applied genetics 100 (2000), S. 139-146 
    Details
    ISSN: 1432-2242
    Keywords: Key words Coffea arabica ; Introgression ; Genetic diversity ; Alien gene transfer ; AFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050019
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  • 3
    Electronic Resource
    Electronic Resource
    Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA (1997)
    Springer
    Theoretical and applied genetics 94 (1997), S. 947-955 
    Details
    ISSN: 1432-2242
    Keywords: Key words Coffea ; Coffee-tree ; Internal transcribed spacer region ; Nuclear ribosomal DNA ; Molecular phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Phylogenetic relationships of Coffea species were estimated from the sequences of the internal transcribed spacer (ITS 2) region of nuclear ribosomal DNA. The ITS 2 region of 37 accessions belonging to 26 Coffea taxa and to three Psilanthus species was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The level of variation was high enough to make the ITS 2 a useful tool for phylogenetic reconstruction. However, an unusual level of intraspecific variation was observed leading to some difficulty in interpreting rDNA sequence divergences. Sequences were analysed using Wagner parsimony as well as the neighbour-joining distance method. Coffea taxa were divided into several major groups which present a strong geographical correspondence (i.e. Madagascar, East Africa, Central Africa and West Africa). This organisation is well supported by cytogenetic evidence. On the other hand, the results were in contradiction with the present classification of coffee-tree taxa into two genera, namely Coffea and Psilanthus. Furthermore, additivity of parental rDNA types was not observed in the allotetraploid species C. arabica.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050500
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  • 4
    Electronic Resource
    Electronic Resource
    Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L. (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 626-632 
    Details
    ISSN: 1432-2242
    Keywords: Chloroplast DNA ; Coffea ; Inheritance ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract CpDNA variation among 52 tree samples belonging to 25 different taxa of Coffea and two species of Psilanthus was assessed by RFLP analysis on both the total chloroplast genome and the atpB-rbcL intergenic region. Twelve variable characters were distinguished allowing the identification of 12 different plastomes. The low sequence divergence observed might suggest that Coffea is a young genus. The results were in contradiction with the present classification into two genera. Additionally, cpDNA inheritance was studied in interspecific hybrids between C. arabica and C. canephora, and in an intraspecific progeny of C. canephora, using PCR-based markers. Both studies showed exclusively maternal inheritance of cpDNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00417958
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  • 5
    Electronic Resource
    Electronic Resource
    Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L. (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 626-632 
    Details
    ISSN: 1432-2242
    Keywords: Key words Chloroplast DNA ; Coffea ; Inheritance ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract CpDNA variation among 52 tree samples belonging to 25 different taxa of Coffea and two species of Psilanthus was assessed by RFLP analysis on both the total chloroplast genome and the atpB-rbcL intergenic region. Twelve variable characters were distinguished allowing the identification of 12 different plastomes. The low sequence divergence observed might suggest that Coffea is a young genus. The results were in contradiction with the present classification into two genera. Additionally, cpDNA inheritance was studied in interspecific hybrids between C. arabica and C. canephora, and in an intraspecific progeny of C. canephora, using PCR-based markers. Both studies showed exclusively maternal inheritance of cpDNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050325
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  • 6
    Electronic Resource
    Electronic Resource
    Molecular characterisation and origin of the Coffea arabica L. genome (1999)
    Springer
    Molecular genetics and genomics 261 (1999), S. 259-266 
    Details
    ISSN: 1617-4623
    Keywords: Key words Africa ; Amphidiploidy ; Coffee tree ; Molecular cytogenetics ; Restriction fragment length polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Restriction fragment length polymorphism (RFLP) markers were used in combination with genomic in situ hybridisation (GISH) to investigate the origin of the allotetraploid species Coffea arabica (2n = 44). By comparing the RFLP patterns of potential diploid progenitor species with those of C. arabica, the sources of the two sets of chromosomes, or genomes, combined in C. arabica were identified. The genome organisation of C. arabica was confirmed by GISH using simultaneously labelled total genomic DNA from the two putative genome donor species as probes. These results clearly suggest that C. arabica is an amphidiploid formed by hybridisation between C. eugenioides and C. canephora, or ecotypes related to these diploid species. Our results also indicate low divergence between the two constituent genomes of C. arabica and those of its progenitor species, suggesting that the speciation of C. arabica took place relatively recently. Precise localisation in Central Africa of the site of the speciation of C. arabica, based on the present distribution of the coffee species, appears difficult, since the constitution and extent of tropical forest has varied considerably during the late Quaternary period.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004380050965
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  • 7
    Electronic Resource
    Electronic Resource
    Genetic diversity for RAPD markers between cultivated and wild accessions of Coffea arabica (1996)
    Springer
    Euphytica 87 (1996), S. 59-64 
    Details
    ISSN: 1573-5060
    Keywords: Coffea arabica ; coffee ; diversity ; genetic resources ; heterosis ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00022965
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  • 8
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    Regulatory Divergence between Parental Alleles Determines Gene Expression Patterns in Hybrids (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-18
    Description: Both hybridization and allopolyploidization generate novel phenotypes by conciliating divergent genomes and regulatory networks in the same cellular context. To understand the rewiring of gene expression in hybrids, the total expression of 21,025 genes and the allele-specific expression of over 11,000 genes were quantified in interspecific hybrids and their parental species, Coffea canephora and Coffea eugenioides using RNA-seq technology. Between parental species, cis - and trans -regulatory divergences affected around 32% and 35% of analyzed genes, respectively, with nearly 17% of them showing both. The relative importance of trans -regulatory divergences between both species could be related to their low genetic divergence and perennial habit. In hybrids, among divergently expressed genes between parental species and hybrids, 77% was expressed like one parent (expression level dominance), including 65% like C. eugenioides . Gene expression was shown to result from the expression of both alleles affected by intertwined parental trans- regulatory factors. A strong impact of C. eugenioides trans -regulatory factors on the upregulation of C. canephora alleles was revealed. The gene expression patterns appeared determined by complex combinations of cis - and trans -regulatory divergences. In particular, the observed biased expression level dominance seemed to be derived from the asymmetric effects of trans -regulatory parental factors on regulation of alleles. More generally, this study illustrates the effects of divergent trans -regulatory parental factors on the gene expression pattern in hybrids. The characteristics of the transcriptional response to hybridization appear to be determined by the compatibility of gene regulatory networks and therefore depend on genetic divergences between the parental species and their evolutionary history.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.) (2016)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2016-09-09
    Description: Allopolyploidization is a biological process that has played a major role in plant speciation and evolution. Genomic changes are common consequences of polyploidization, but their dynamics over time are still poorly understood. Coffea arabica , a recently formed allotetraploid, was chosen to study genetic changes that accompany allopolyploid formation. Both RNA-seq and DNA-seq data were generated from two genetically distant C. arabica accessions. Genomic structural variation was investigated using C. canephora , one of its diploid progenitors, as reference genome. The fate of 9047 duplicate homeologous genes was inferred and compared between the accessions. The pattern of SNP density along the reference genome was consistent with the allopolyploid structure. Large genomic duplications or deletions were not detected. Two homeologous copies were retained and expressed in 96% of the genes analyzed. Nevertheless, duplicated genes were found to be affected by various genomic changes leading to homeolog loss or silencing. Genetic and epigenetic changes were evidenced that could have played a major role in the stabilization of the unique ancestral allotetraploid and its subsequent diversification. While the early evolution of C. arabica mainly involved homeologous crossover exchanges, the later stage appears to have relied on more gradual evolution involving gene conversion and homeolog silencing.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 10
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    Gene introgression into Coffea arabica by way of triploid hybrids (C. arabica × C. canephora) (2002)
    Springer Nature
    Details
    Publication Date: 2002-12-01
    Print ISSN: 0018-067X
    Electronic ISSN: 1365-2540
    Topics: Biology
    Published by Springer Nature
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