The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and 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. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and 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.

Age-Related Rhizosphere Analysis of Coffea arabica Plants.

The analysis of large-scale sequence data has revealed that plants over time recruit certain microbes that are efficient colonizers of the rhizosphere. This enrichment phenomenon is especially seen in annual crops, but we suggest that there could have been some type of enrichment in perennial crops such as coffee plants. To verify this hypothesis, we performed a metagenomic and chemical analysis in rhizosphere with three different plant ages (young, mature, and old) and cultivated on the same farm. We verified that from mature to old plants, there was a decrease in diversity, particularly Fusarium and Plenodomus, while there was an increase in Aspergillus, Cladosporium, Metarhizium, and Pseudomonas. We also detected that the abundance of anti-microbials and ACC-deaminase grows as plants age, although denitrification and carbon fixation had reduced abundances. In summary, we detected an enrichment in the microbial community, especially in the great increase in the participation of Pseudomonas, passing from 50% of the relative abundance as the plants get older. Such enrichment can occur through the dynamics of nutrients such as magnesium and boron.

Parasitism of Meloidogyne exigua races 1 and 2 in coffee plants derived from Timor Hybrid / Parasitismo de Meloidogyne exigua raças 1 e 2 em cafeeiros derivados do Híbrido de Timor

ABSTRACT: To investigate the degree of parasitism of two populations of Meloidogyne exigua, the gall index (GI) and the reproduction factor (RF) of M. exigua races 1 (Est E2) and 2 (Est E1) were analyzed in 47 progenies on F3:4 or F4:5 generation derived from the crossing between Coffea arabica cv. Catuaí Amarelo and Timor Hybrid. C. canephora cv. Apoatã IAC 2258 and C. arabica cv. Catuaí Vermelho IAC 144 were used as resistance and susceptibility checks, respectively. The genotypes that were classified as resistant or susceptible by RF were similarly classified by GI, showing a close relationship between both methodologies. The data also indicated no differences in virulence between the nematode populations, since the progenies showed similar resistance reactions to the M. exigua races 1 and 2. According to GI from the 47 mother plants evaluated, 27 progenies (57.4%) were classified as resistant to M. exigua races 1 and 2, with GI ranging from 0.0 to 1.4 and 20 progenies (42.6%) were susceptible with GI from 2.6 to 4.4. These results showed that most of the evaluated germplasm was very promising in relation to the development of new Arabica coffee cultivars with resistance to M. exigua.

RESUMO: Com o objetivo de investigar o grau de parasitismo de duas populações de Meloidogyne exigua, o índice de galhas (IG) e o fator de reprodução (FR) de M. exigua raças 1 (Est E2) e 2 (Est E1) foram analisados em 47 progênies na geração F3:4 ou F4:5, derivadas do cruzamento entre Coffea arabica cv. Catuaí Amarelo e Híbrido de Timor. Plantas de C. canephora cv. Apoatã IAC 2258 e C. arabica cv. Catuaí Vermelho IAC 144 foram usadas como padrão de resistência e de suscetibilidade, respectivamente. Os genótipos que foram classificados como resistentes ou suscetíveis pelo FR foram similarmente classificados pelo IG, mostrando uma estreita relação entre as duas metodologias para a avaliação da resistência. Os dados também indicaram que não houve diferenças quanto à virulência entre as duas populações do nematoide, uma vez que as progênies mostraram similar reação de resistência a M. exigua raça 1 e 2. De acordo com o IG, das 47 plantas-mãe avaliadas, 27 progenies (57,4%) foram classificadas como resistentes a M. exigua raças 1 e 2, com IG variando de 0,0 a 1,4 e 20 progenies (42,6%) foram suscetíveis, com IG variando de 2,6 a 4,4. Esses resultados mostraram que a maioria dos germoplasmas avaliados foi muito promissora em relação ao desenvolvimento de novas cultivares de café Arábica com resistência a M. exigua.

Inheritance and heritability of resistance to citrus leprosis.

ABSTRACT The genetic inheritance of resistance to leprosis, the most important viral disease of citrus in Brazil, was characterized through the phenotypic assessment of 143 hybrids resulting from crosses between tangor 'Murcott' (Citrus sinensis x C. reticulata) and sweet orange 'Pêra' (C. sinensis), considered to be resistant and susceptible to the disease, respectively. All plants were grafted onto Rangpur lime (C. limonia) and inoculated with Citrus leprosis virus, cytoplasmic type through the infestation with viruliferous mites, Brevipalpus phoenicis. The experiments were arranged in a completely randomized block design with 10 replicates. Incidence and severity of the disease in leaves and stems as well as plant growth parameters (plant height and stem diameter) were recorded for 3 years after the infestation with the viruliferous mites. The average values of all variables were analyzed using principal component analysis, discriminant factorial analysis, estimation of the clonal repeatability coefficients, and frequency of the distributions of the average values for each measured variable. The principal component analysis resulted in the identification of at least two groups with resistance and susceptibility to leprosis, respectively. About 99% of all hybrids were correctly classified according to the discriminant factorial analysis. The broad-sense heritability coefficients for characteristics associated with incidence and severity of leprosis ranged from 0.88 to 0.96. The data suggest that the inheritance of resistance to leprosis may be controlled by only a few genes.