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Coffea arabica, an allotetraploid hybrid of Coffea eugenioidesand Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabicaaccession and modern representatives of its diploid progenitors, C. eugenioidesand C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Bacterial halo blight caused by Pseudomonas syringaepv. garcaeis a limiting disease to the coffee crop due to difficulty and low efficiency of the chemical control on field conditions. The simultaneous use of windbreaks and resistant cultivars seem to be the most appropriate measure of disease management. Although the bacterial halo blight resistance has been extensively studied in Coffea arabica, information about the reaction of C. canephoragermplasm is not available. Thus, the objective of this study was to identify resistance sources to the bacterial halo blight in C. canephoragermplasm, for use in breeding programs. Several commercial cultivars, botanical varieties, clones and hybrids of C. canephorawere tested against a highly virulent P. syringaepv. garcaestrain through artificial inoculations in greenhouse conditions. Only 1.4% of 2.421 evaluated plants were considered resistant to the disease. Our results showed the alarming vulnerability of Coffea canephoracrop and germplasm to the bacterial halo blight from Brazil and the need to select resistant cultivars.

Bacterial halo blight, caused by Pseudomonas syringae pv. garcae, is an important disease of coffee crop occurring in Brazil and other countries. In recent years, outbreaks of this disease have damaged several coffee crops in Brazil. Aggressiveness and genetic diversity of 25 strains of P. s. pv. garcae, obtained between the years 1958 and 2011, in 23 cities of São Paulo and Minas Gerais states, as well as three strains from Kenya were evaluated in this study. The strains were inoculated on coffee seedlings cultivar Mundo Novo, and their genetic diversity was evaluated by ERIC-PCR, REP-PCR, and their combination. All the strains were pathogenic to the coffee seedlings; the results of pathogenicity tests, in both experiments, could be divided in four aggressiviness classes (highly aggressive; aggressive; moderately aggressive and less aggressive). The Kenyan strains grouped separately from the Brazilian strains with ERIC-PCR and the combination of ERIC- and REP-PCR. The Brazilian strains could be grouped in two sub-clusters, the first including the older strains, obtained from 1958 to 1978, and the other comprising the remaining strains. With a few exceptions, strains isolated from 1997 to 2011, grouped mainly by their region of origin, were predominantly isolated from higher altitude regions, above 800 m. This probably occurred because the climatic conditions that prevail in these regions, characterized by milder temperatures and regular rainfall, are favorable for the coffee crop and for the production of high quality coffee beverage, but can be also favorable to bacterial halo blight. [ABSTRACT FROM AUTHOR]

Coffee resistance to Pseudomonas syringae pv. garcae has been associated to pleiotropic effect of SH1 allele, present in coffee plants resistant to certain races of Hemileia vastatrix, the causal agent of leaf rust, or genetic linkage between resistance alleles to both pathogens. To validate this hypothesis, 63 coffee plants in F2 generation were evaluated for resistance to 2 isolates of H. vastatrix carriers of alleles, respectively, v2, v5 (isolate I/2015) and v1; v2; v5 (isolate II/2015) with the objective to confirm presence of SH1 allele in resistant plants to isolate I/2015. The same coffee plants were evaluated for resistance to a mixture of P. syringae pv. garcae strains highly pathogenic to coffee. Results showed that, among F2 coffee allele SH1 carriers, resistant to isolate I/2015, resistant and susceptible plants to bacterial halo blight were found; the same segregation occurs between F2 homozygous for SH1 allele, susceptible to the same isolate (I/2015) of H. vastatrix. Results also indicate that there is no pleiotropic effect of gene or allele SH1 connection between genes conferring resistance to leaf rust caused by H. vastatrix and bacterial halo blight caused by P. syringae pv. garcae. [ABSTRACT FROM AUTHOR]

Abstract.: Binding of several Bacillus thuringiensisδ-endotoxins was studied on histological midgut sections of larvae of coffee leaf miner Perileucoptera coffeella from Brazil and Perileucoptera sp from Madagascar. CryIA(a), CryIA(b), CryIA(c), CryIB, CryIE, and CryIIA were tested for binding, and only CryIA(c), CryIB, and CryIE yielded a positive response. The toxins bound to the whole midgut, and the result was identical on both insect populations. The same toxins, to the number of which CryIC was added, were tested on larvae of P. coffeella. CryIA(c) and CryIB were toxic with an LC50 of 1.47 μg/ml and 21.93 μg/ml, respectively. CryIE was not toxic to P. coffeella. CryIA(c) and CryIB were tested for synergistic activity and were shown to act by cumulative effect when delivered to the insect larvae as a mixture.